aja School of Engineering and Applied Sciences 2006 Chemical and Biological Engineering

Graduate Research Symposium

Presenting research on Bioengineering

Cell and Tissue Bioengineering Gene Therapy Cell Adhesion Transport Processes in Biological Systems

Nanoscale Materials Science and Engineering Heterogeneous Catalysis olymer Self-Assembly Surfactant and Block Cop Nanoparticle Synthesis and Characterization

Molecular and Multiscale Modeling Statistical Thermodynamics Molecular Simulation Applied Computational Quantum Chemistry

Graduate Student Poster Presentations 2nd floor Furnas Hall UB North Campus

Wednesday October 18 2006 330 - 430 pm

Symposium Organizing Committee Dr Mattheos Koffas 716-645-2911 x2221 mkoffasengbuffaloedu Dr Sheldon Park 716-645-2911 x2212 sjpark6buffaloedu Dr Manolis Tzanakakis 716-645-2911 x2206 emtzanengbuffaloedu

Department of Chemical and Biological Engineering

University at Buffalo (SUNY) Buffalo NY 14260-4200

Integrative Research at the

Frontiers of Chemical and

Biological Engineering

Chemical and Biological Engineering

Faculty Paschalis Alexandridis (MIT) bull amphiphilic polymers self-assembly complex fluids nanomaterials interfacial phenomena Stelios T Andreadis (Michigan) bull bioengineering gene therapy tissue engineering of genetically modified skin Jeffrey R Errington (Cornell) bull molecular simulation statistical thermodynamics biopreservation Vladimir Hlavacek (ICT -Prague) bull reaction engineering nanopowders explosives and detonations analysis of chemical plants Mattheos Koffas (MIT) bull metabolic engineering bioinformatics David A Kofke (Pennsylvania) bull molecular modeling and simulation solid phase equilibria Carl R F Lund (Wisconsin) bull heterogeneous catalysis chemical kinetics reaction engineering Sriram Neelamegham (Rice) bull biomedical engineering cell biomechanics vascular engineering Johannes M Nitsche (MIT) bull fluid mechanics transport phenomena bioactive surfaces biological pores transdermal transport Sheldon J Park (Harvard) bull protein engineering protein carbohydrate interaction molecular dynamics Eli Ruckenstein (Bucharest) bull catalysis surface phenomena colloids and emulsions biocompatible surfaces and materials Michael E Ryan (McGill) bull polymer and ceramics processing rheology non-Newtonian fluid mechanics Mark T Swihart (Minnesota) bull chemical kinetics modeling of reactive flows computational chemistry nanoparticle formation E (Manolis) S Tzanakakis (Minnesota) bull cell and tissue engineering stem cell biotechnology Adjunct FacultyT J (Lakis) Mountziaris (Princeton) bull electronic and photonic materials nanoparticles biosensors multiphase flows Athos Petrou (Purdue) bull spectroscopy semiconductor nanostructures Carel Jan van Oss (Sorbonne) bull colloid and interface science Frederick Sachs (Upstate Med Center Syracuse) bull single molecule biophysics

Emeritus Faculty in Residence Robert J Good (Michigan) bull adhesion and

interface science philosophy of science Thomas W Weber (Cornell) bull process control Sol W Weller (Chicago) bull catalysis coal

liquefaction history of chemical engineering

Chemical and Biological Engineering faculty participate in many interdisciplinary centers and initiatives including The Center for Advanced Molecular Biology and Immunology The Center for Computational Research The Center for Advanced Photonic and Electronic Materials The Institute for Lasers Photonics and Biophotonics The Center of Excellence in Bioinformatics and The Center for Advanced Technology for Biomedical Devices

httpwwwcbebuffaloedu

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TABLE OF CONTENTS BIOLOGICAL ENGINEERING

1 IN SILICO SIMULATION OF GENOME-SCALE INTRACELLULAR FLUX MODELS FOR ENGINEERING PHENYLPROPANOID BIOSYNTHESIS IN ESCHERICHIA COLI 6

2 ENGINEERING ESCHERICHIA COLI FOR PLANT PHARMACEUTICS PRODUCTION 7

3 MUTASYNTHESIS OF NOVEL UNNATURAL FLAVONOIDS 8

4 ENGINEERING THE E COLI UDP-GLUCOSE SYNTHESIS PATHWAY FOR ANTHOCYANIN BIOSYNTHESIS 9

5 ENGINEERING PLANT PIGMENT BIOSYNTHESIS IN ESCHERICHIA COLI 10

6 EXPLORING METABOLONS FOR IMPROVEMENT IN PLANT-SPECIFIC FLAVANONE PRODUCTION FROM ESCHERICHIA COLI 11

7 RECYCLING ACETATE FOR IMPROVEMENT OF FLAVONOID PRODUCTIONS FROM ESCHERICHIA COLI 12

8 CHARACTERIZATION OF BONE MARROW DERIVED SMOOTH MUSCLE CELLS AND ITS APPLICATION IN VASCULAR ENGINEERING 13

9 PURIFICATION OF RECOMBINANT RETROVIRUS FOR GENE THERAPY14

10 INVOLVEMENT OF THE CCAATENHANCER-BINDING PROTEINS IN THE INTERACTIONS OF KGF AND INTEGRIN Α5 CONTROLLING CELL PROLIFERATION AND MIGRATION15

11 DISTINCT CCAATENHANCER BINDING PROTEIN ISOFORMS MEDIATE KERATINOCYTE GROWTH FACTOR-INDUCED MIGRATION AND PROLIFERATION OF EPITHELIAL CELLS 16

12 EGFR SIGNALING PATHWAYS AFFECT RETROVIRAL GENE TRANSFER TO EPITHELIAL CELLS17

13 THE ROLE OF THE JNK PATHWAY IN LENTIVIRAL TRANSDUCTION PROCESSES 18

14 A SYNTHETIC SUGAR AS A POTENTIAL ANTI-INFLAMMATORY DRUG19

15 SOLUTION STRUCTURE OF HUMAN VON WILLEBRAND FACTOR STUDIED USING SMALL ANGLE NEUTRON SCATTERING20

16 FROM LIGAND BINDING TO TRANSCRIPTION AN INTEGRATED MODEL FOR TUMOR NECROSIS FACTOR INDUCED NF-κB ACTIVATION 21

17 ANTI-PF4 ANTIBODIES RECOGNIZE NEUTROPHIL SURFACE BOUND PLATELET FACTOR 4 (PF-4) AND INDUCE NEUTROPHIL ACTIVATION AND ADHESION22

18 EXPLORING INTERCELLULAR CHANNELS WITH A HINDERED DIFFUSION MODEL OF ION TRANSPORT23

p 3 of 44

19 A COMPUTATIONAL MODEL OF TRANSIENT DRUGCHEMICAL DIFFUSION THROUGH HUMAN SKIN IN THE VICINITY OF A HAIR FOLLICLE 24

20 PROPAGATION OF PLURIPOTENT EMBRYONIC STEM CELLS UNDER SERUM-FREE CONDITIONS IN A SCALABLE BIOREACTOR25

21 EFFECTS OF FLAVONOIDS ON PANCREATIC β-CELL INSULIN REGULATION26

22 CROSSTALK BETWEEN WNT SIGNALING AND INSULIN REGULATORY NETWORK IN PANCREATIC β-CELLS27

NANOSCALE MATERIALS SCIENCE AND ENGINEERING

23 SYNTHESIS OF ZINC SULFIDE NANAPARTICLES BY SPRAY PYROLYSIS28

24 SYNTHESIS OF TELLURIUM DIOXIDE NANOPARTICLES BY SPRAY PYROLYSIS29

25 CONTROL MECHANISMS FOR THE MOLECULAR ASSEMBLY OF AMPHIPHILES30

26 WATER GAS SHIFT OVER IRON OXIDE CATALYSTS 31

27 ADSORPTION OF ETHANOL AND WATER VAPORS ON 3Aring AND 4Aring ZEOLITES 32

28 POLYMER CONFORMATION IN WATER AND POLAR ORGANIC SOLVENTS33

MOLECULAR AND MULTISCALE MODELING

29 WATER GAS SHIFT OVER IRON OXIDE CATALYSTS MICROKINETIC MODELING 34

30 EXPLORING THE PHASE BEHAVIOUR OF A SIMPLE MODEL PROTEIN USING MOLECULAR SIMULATION35

31 ORTHOGONAL POLYNOMIAL METHOD TO COMPUTE THE DENSITY OF STATES 36

32 COMPUTER SIMULATIONS IN COMPLEX FLUIDS 37

33 MODELING OF INDUSTRIAL PRESSURE SWING ADSORPTION PROCESS FOR FUEL ETHANOL PRODUCTION38

34 ATOMISTIC MODELING OF GRAIN BOUNDARY DIFFUSION IN SN-AG-CU SOLDER USING TRANSITION PATH SAMPLING 39

35 A COMPUTATIONAL STUDY OF THE PROPERTIES OF WATER NEAR A PROTEIN SURFACE WITH ADDED SOLUTE40

36 RELATIONSHIP BETWEEN THE THERMODYNAMICS AND DYNAMICS OF A MOLECULAR FLUID41

37 DETERMINING CONTACT ANGLES FROM MOLECULAR SIMULATION 42

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38 ASSESSING CRYSTAL FREE ENERGY43

39 GRAND CANONICAL MONTE CARLO SIMULATIONS OF WATER ADSORPTION ON GRAPHITE SURFACE 44

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BIOLOGICAL ENGINEERING

1 In Silico Simulation Of Genome-Scale Intracellular Flux Models For Engineering Phenylpropanoid Biosynthesis In Escherichia Coli

Zachary L Fowler William Gikandi and Mattheos AG KoffasDepartment of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

The molecular components of any organism can be readily found from the genome sequence where by application of reductionist methods generates a genomic lsquoparts listrsquo incorporating all cellular functions Using this information elucidation of all enzymatic reactions within the organism is achieved to develop the organismrsquos metabolic topology A subsequent construction and simulation of steady state flux models can describe production limitations of the organism on a genomic level By applying Quadratic Programming in the framework of a Genetic Algorithm we can predict genetic perturbations specifically gene deletions which cause an increased metabolic flux to pathways of interest By comparing wild-type network profiles to those of perturbed networks gene over expressions can also be identified Additionally a minimal level of cellular growth can be enforced to ensure the prediction of viable cell phenotypes

Flavonoids are currently used as dietary supplements and along with several of their substituted unnatural analogues have potential therapeutic value in cancer treatments While readily found in plants the extraction of substantial amounts is difficult resulting in an increased interest in biochemical production of these compounds We can create production platforms to increase the biosynthetic yield of these valuable compounds through the incorporation and co-expression of genes controlling the enzymatic production of flavonoids as well as the targeted deletion of native genes controlling competing enzymatic processes within the host organism This work details the use of intracellular flux models to engineering the biosynthesis of apigenin a flavone in Escherichia coli Key Words flavonoids optimization genetic algorithm flux balance analysis

p 6 of 44

2 Engineering Escherichia Coli For Plant Pharmaceutics Production

Effendi Leonard and Mattheos Koffas Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

Flavonoids are plant-derived secondary metabolites with various health promoting properties and are being evaluated in preliminary trials for treatment of various diseases from cancer to diabetes Since microbial fermentation is a cost-saving alternative to chemical synthesis or plant extraction we aim to develop recombinant platforms that can efficiently produce plant flavonoid pharmaceutics

We present the metabolic engineering of bacterium Escherichia coli for flavonoid biosynthesis Implantation of artificial flavonoid biosynthetic pathways through simultaneous expression of plant-derived genes resulted in the biosynthesis of a library of flavonoid molecules which includes flavanones flavones flavonols flavanols and anthocyanins The minute amount of endogeneous malonyl-CoAs required for flavonoid building blocks limits the high-level production of flavonoids from E coli To overcome this limitation frontiers of cellular engineering the flavonoid producer strains by manipulations of the intracellular fatty acid metabolism were pursued The metabolic manipulation to increase malonyl-CoA contents through the introduction of a novel malonate operon elevated flavonoid production up to 4-folds In conjunction with cessation of the recycling of malonyl-CoA into acetyl-CoA by inhibition of β-ketoacyl acyl carrier proteins flavonoids were produced at high levels up to hundreds of milligram per liter quantity

Lastly to allow plant estrogen isoflavone synthesis in E coli we present the design of a series of soybean membrane-bound P450 IFS chimeras to search for progenies that simultaneously exhibit functionality and high turnover catalysis in E coli Isoflavone productions from E coli harboring the most effective IFS variant were superior when compared to that from the natural plant resources and the recombinant S cerevisiae The protein engineering achievements complete the endeavor to synthesize all six main flavonoid classes from E coli

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3 Mutasynthesis Of Novel Unnatural Flavonoids

Joseph A Chemler Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas Email jchemlerbuffaloedu Flavonoids are a large class of plant secondary metabolites that are involved in the beneficial effects diets rich in fruits and vegetables have in human health The overall goal of our work is the biosynthesis of novel flavonoid molecules using genetically tractable microbial species such as Escherichia coli and Saccharomyces cerevisiae (yeast) This is achieved through episomal introduction of the flavonoid metabolic circuits from various plant species in these organisms Using the constructed recombinant strains mutasynthesis allows the production of novel unnatural flavonoid analogues with different substitutions on the flavonoid core structure consisting of hydroxyl fluoro and amino groups By expressing different combinations of flavonoid enzymes in the recombinant strains a number of flavonoid subclasses have been synthesized including flavanones 5-deoxyflavonones flavones dihydroflavonols leucoanthocyanidins and anthocyanidins A library of over 25 novel unnatural flavonoids has been made and continues to expand by extending the flavonoid pathway We are currently investigating the use of some of the synthesized compounds for diabetes and obesity treatments Key Words Flavonoid mutasythesis Escherichia coli Saccharomyces cerevisiae

p 8 of 44

4 Engineering The E Coli UDP-Glucose Synthesis Pathway For Anthocyanin Biosynthesis

Zhen Li Yajun Yan and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are water soluble vacuolar flavonoid pigments that appear red to blue according to pH In the pathway of anthocyanin synthesis the last step that performs the glycosylation of unstable anthocyanidin to the relatively stable anthocyanin is catalyzed by the enzyme UDP-glucose flavonoid 3-oxoglycosyltransferase (UF3GT) Glycosyltransferases belong to group-transfer enzymes that catalyze the transfer of a sugar molecule from its activated form to an acceptor The most commonly used activated substrates are sugar nucleotides such as UDP-glucose and UDP-galactose But enzyme substrate the sugar nucleotide is much expensive to use in a stoichiometric ratio Therefore we plan to use whole cells as catalysts where sugar nucleotide cofactors are regenerated UDP-glucose is the starting point of the synthesis of other UDP-sugars Its yield directly influences the rate synthesis of any oligosaccharides containing these sugars Two enzymes directly involved in the synthesis of UDP-glucose from glucose-6-phosphate phosphoglucomutase (PGM catalyzing the conversion of glucose-6-phosphate to glucose-1-phosphate) and UDP-glucose pyrophosphorylase (GalU catalyzing the formation of UDP-glucose from glucose-1-phosphate and uridine triphosphate) were overexpressed The impact of overexpression of PGM and GalU will be investigated through the synthesis of UDP-glucose The overexpression of PGM and GalU can also increase the yield of anthocyanin This work will have an extended impact in the biosynthesis of various glycosylated natural products in addition to anthocyanins such as antibiotics

p 9 of 44

5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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Integrative Research at the

Frontiers of Chemical and

Biological Engineering

Chemical and Biological Engineering

Faculty Paschalis Alexandridis (MIT) bull amphiphilic polymers self-assembly complex fluids nanomaterials interfacial phenomena Stelios T Andreadis (Michigan) bull bioengineering gene therapy tissue engineering of genetically modified skin Jeffrey R Errington (Cornell) bull molecular simulation statistical thermodynamics biopreservation Vladimir Hlavacek (ICT -Prague) bull reaction engineering nanopowders explosives and detonations analysis of chemical plants Mattheos Koffas (MIT) bull metabolic engineering bioinformatics David A Kofke (Pennsylvania) bull molecular modeling and simulation solid phase equilibria Carl R F Lund (Wisconsin) bull heterogeneous catalysis chemical kinetics reaction engineering Sriram Neelamegham (Rice) bull biomedical engineering cell biomechanics vascular engineering Johannes M Nitsche (MIT) bull fluid mechanics transport phenomena bioactive surfaces biological pores transdermal transport Sheldon J Park (Harvard) bull protein engineering protein carbohydrate interaction molecular dynamics Eli Ruckenstein (Bucharest) bull catalysis surface phenomena colloids and emulsions biocompatible surfaces and materials Michael E Ryan (McGill) bull polymer and ceramics processing rheology non-Newtonian fluid mechanics Mark T Swihart (Minnesota) bull chemical kinetics modeling of reactive flows computational chemistry nanoparticle formation E (Manolis) S Tzanakakis (Minnesota) bull cell and tissue engineering stem cell biotechnology Adjunct FacultyT J (Lakis) Mountziaris (Princeton) bull electronic and photonic materials nanoparticles biosensors multiphase flows Athos Petrou (Purdue) bull spectroscopy semiconductor nanostructures Carel Jan van Oss (Sorbonne) bull colloid and interface science Frederick Sachs (Upstate Med Center Syracuse) bull single molecule biophysics

Emeritus Faculty in Residence Robert J Good (Michigan) bull adhesion and

interface science philosophy of science Thomas W Weber (Cornell) bull process control Sol W Weller (Chicago) bull catalysis coal

liquefaction history of chemical engineering

Chemical and Biological Engineering faculty participate in many interdisciplinary centers and initiatives including The Center for Advanced Molecular Biology and Immunology The Center for Computational Research The Center for Advanced Photonic and Electronic Materials The Institute for Lasers Photonics and Biophotonics The Center of Excellence in Bioinformatics and The Center for Advanced Technology for Biomedical Devices

httpwwwcbebuffaloedu

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TABLE OF CONTENTS BIOLOGICAL ENGINEERING

1 IN SILICO SIMULATION OF GENOME-SCALE INTRACELLULAR FLUX MODELS FOR ENGINEERING PHENYLPROPANOID BIOSYNTHESIS IN ESCHERICHIA COLI 6

2 ENGINEERING ESCHERICHIA COLI FOR PLANT PHARMACEUTICS PRODUCTION 7

3 MUTASYNTHESIS OF NOVEL UNNATURAL FLAVONOIDS 8

4 ENGINEERING THE E COLI UDP-GLUCOSE SYNTHESIS PATHWAY FOR ANTHOCYANIN BIOSYNTHESIS 9

5 ENGINEERING PLANT PIGMENT BIOSYNTHESIS IN ESCHERICHIA COLI 10

6 EXPLORING METABOLONS FOR IMPROVEMENT IN PLANT-SPECIFIC FLAVANONE PRODUCTION FROM ESCHERICHIA COLI 11

7 RECYCLING ACETATE FOR IMPROVEMENT OF FLAVONOID PRODUCTIONS FROM ESCHERICHIA COLI 12

8 CHARACTERIZATION OF BONE MARROW DERIVED SMOOTH MUSCLE CELLS AND ITS APPLICATION IN VASCULAR ENGINEERING 13

9 PURIFICATION OF RECOMBINANT RETROVIRUS FOR GENE THERAPY14

10 INVOLVEMENT OF THE CCAATENHANCER-BINDING PROTEINS IN THE INTERACTIONS OF KGF AND INTEGRIN Α5 CONTROLLING CELL PROLIFERATION AND MIGRATION15

11 DISTINCT CCAATENHANCER BINDING PROTEIN ISOFORMS MEDIATE KERATINOCYTE GROWTH FACTOR-INDUCED MIGRATION AND PROLIFERATION OF EPITHELIAL CELLS 16

12 EGFR SIGNALING PATHWAYS AFFECT RETROVIRAL GENE TRANSFER TO EPITHELIAL CELLS17

13 THE ROLE OF THE JNK PATHWAY IN LENTIVIRAL TRANSDUCTION PROCESSES 18

14 A SYNTHETIC SUGAR AS A POTENTIAL ANTI-INFLAMMATORY DRUG19

15 SOLUTION STRUCTURE OF HUMAN VON WILLEBRAND FACTOR STUDIED USING SMALL ANGLE NEUTRON SCATTERING20

16 FROM LIGAND BINDING TO TRANSCRIPTION AN INTEGRATED MODEL FOR TUMOR NECROSIS FACTOR INDUCED NF-κB ACTIVATION 21

17 ANTI-PF4 ANTIBODIES RECOGNIZE NEUTROPHIL SURFACE BOUND PLATELET FACTOR 4 (PF-4) AND INDUCE NEUTROPHIL ACTIVATION AND ADHESION22

18 EXPLORING INTERCELLULAR CHANNELS WITH A HINDERED DIFFUSION MODEL OF ION TRANSPORT23

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19 A COMPUTATIONAL MODEL OF TRANSIENT DRUGCHEMICAL DIFFUSION THROUGH HUMAN SKIN IN THE VICINITY OF A HAIR FOLLICLE 24

20 PROPAGATION OF PLURIPOTENT EMBRYONIC STEM CELLS UNDER SERUM-FREE CONDITIONS IN A SCALABLE BIOREACTOR25

21 EFFECTS OF FLAVONOIDS ON PANCREATIC β-CELL INSULIN REGULATION26

22 CROSSTALK BETWEEN WNT SIGNALING AND INSULIN REGULATORY NETWORK IN PANCREATIC β-CELLS27

NANOSCALE MATERIALS SCIENCE AND ENGINEERING

23 SYNTHESIS OF ZINC SULFIDE NANAPARTICLES BY SPRAY PYROLYSIS28

24 SYNTHESIS OF TELLURIUM DIOXIDE NANOPARTICLES BY SPRAY PYROLYSIS29

25 CONTROL MECHANISMS FOR THE MOLECULAR ASSEMBLY OF AMPHIPHILES30

26 WATER GAS SHIFT OVER IRON OXIDE CATALYSTS 31

27 ADSORPTION OF ETHANOL AND WATER VAPORS ON 3Aring AND 4Aring ZEOLITES 32

28 POLYMER CONFORMATION IN WATER AND POLAR ORGANIC SOLVENTS33

MOLECULAR AND MULTISCALE MODELING

29 WATER GAS SHIFT OVER IRON OXIDE CATALYSTS MICROKINETIC MODELING 34

30 EXPLORING THE PHASE BEHAVIOUR OF A SIMPLE MODEL PROTEIN USING MOLECULAR SIMULATION35

31 ORTHOGONAL POLYNOMIAL METHOD TO COMPUTE THE DENSITY OF STATES 36

32 COMPUTER SIMULATIONS IN COMPLEX FLUIDS 37

33 MODELING OF INDUSTRIAL PRESSURE SWING ADSORPTION PROCESS FOR FUEL ETHANOL PRODUCTION38

34 ATOMISTIC MODELING OF GRAIN BOUNDARY DIFFUSION IN SN-AG-CU SOLDER USING TRANSITION PATH SAMPLING 39

35 A COMPUTATIONAL STUDY OF THE PROPERTIES OF WATER NEAR A PROTEIN SURFACE WITH ADDED SOLUTE40

36 RELATIONSHIP BETWEEN THE THERMODYNAMICS AND DYNAMICS OF A MOLECULAR FLUID41

37 DETERMINING CONTACT ANGLES FROM MOLECULAR SIMULATION 42

p 4 of 44

38 ASSESSING CRYSTAL FREE ENERGY43

39 GRAND CANONICAL MONTE CARLO SIMULATIONS OF WATER ADSORPTION ON GRAPHITE SURFACE 44

p 5 of 44

BIOLOGICAL ENGINEERING

1 In Silico Simulation Of Genome-Scale Intracellular Flux Models For Engineering Phenylpropanoid Biosynthesis In Escherichia Coli

Zachary L Fowler William Gikandi and Mattheos AG KoffasDepartment of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

The molecular components of any organism can be readily found from the genome sequence where by application of reductionist methods generates a genomic lsquoparts listrsquo incorporating all cellular functions Using this information elucidation of all enzymatic reactions within the organism is achieved to develop the organismrsquos metabolic topology A subsequent construction and simulation of steady state flux models can describe production limitations of the organism on a genomic level By applying Quadratic Programming in the framework of a Genetic Algorithm we can predict genetic perturbations specifically gene deletions which cause an increased metabolic flux to pathways of interest By comparing wild-type network profiles to those of perturbed networks gene over expressions can also be identified Additionally a minimal level of cellular growth can be enforced to ensure the prediction of viable cell phenotypes

Flavonoids are currently used as dietary supplements and along with several of their substituted unnatural analogues have potential therapeutic value in cancer treatments While readily found in plants the extraction of substantial amounts is difficult resulting in an increased interest in biochemical production of these compounds We can create production platforms to increase the biosynthetic yield of these valuable compounds through the incorporation and co-expression of genes controlling the enzymatic production of flavonoids as well as the targeted deletion of native genes controlling competing enzymatic processes within the host organism This work details the use of intracellular flux models to engineering the biosynthesis of apigenin a flavone in Escherichia coli Key Words flavonoids optimization genetic algorithm flux balance analysis

p 6 of 44

2 Engineering Escherichia Coli For Plant Pharmaceutics Production

Effendi Leonard and Mattheos Koffas Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

Flavonoids are plant-derived secondary metabolites with various health promoting properties and are being evaluated in preliminary trials for treatment of various diseases from cancer to diabetes Since microbial fermentation is a cost-saving alternative to chemical synthesis or plant extraction we aim to develop recombinant platforms that can efficiently produce plant flavonoid pharmaceutics

We present the metabolic engineering of bacterium Escherichia coli for flavonoid biosynthesis Implantation of artificial flavonoid biosynthetic pathways through simultaneous expression of plant-derived genes resulted in the biosynthesis of a library of flavonoid molecules which includes flavanones flavones flavonols flavanols and anthocyanins The minute amount of endogeneous malonyl-CoAs required for flavonoid building blocks limits the high-level production of flavonoids from E coli To overcome this limitation frontiers of cellular engineering the flavonoid producer strains by manipulations of the intracellular fatty acid metabolism were pursued The metabolic manipulation to increase malonyl-CoA contents through the introduction of a novel malonate operon elevated flavonoid production up to 4-folds In conjunction with cessation of the recycling of malonyl-CoA into acetyl-CoA by inhibition of β-ketoacyl acyl carrier proteins flavonoids were produced at high levels up to hundreds of milligram per liter quantity

Lastly to allow plant estrogen isoflavone synthesis in E coli we present the design of a series of soybean membrane-bound P450 IFS chimeras to search for progenies that simultaneously exhibit functionality and high turnover catalysis in E coli Isoflavone productions from E coli harboring the most effective IFS variant were superior when compared to that from the natural plant resources and the recombinant S cerevisiae The protein engineering achievements complete the endeavor to synthesize all six main flavonoid classes from E coli

p 7 of 44

3 Mutasynthesis Of Novel Unnatural Flavonoids

Joseph A Chemler Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas Email jchemlerbuffaloedu Flavonoids are a large class of plant secondary metabolites that are involved in the beneficial effects diets rich in fruits and vegetables have in human health The overall goal of our work is the biosynthesis of novel flavonoid molecules using genetically tractable microbial species such as Escherichia coli and Saccharomyces cerevisiae (yeast) This is achieved through episomal introduction of the flavonoid metabolic circuits from various plant species in these organisms Using the constructed recombinant strains mutasynthesis allows the production of novel unnatural flavonoid analogues with different substitutions on the flavonoid core structure consisting of hydroxyl fluoro and amino groups By expressing different combinations of flavonoid enzymes in the recombinant strains a number of flavonoid subclasses have been synthesized including flavanones 5-deoxyflavonones flavones dihydroflavonols leucoanthocyanidins and anthocyanidins A library of over 25 novel unnatural flavonoids has been made and continues to expand by extending the flavonoid pathway We are currently investigating the use of some of the synthesized compounds for diabetes and obesity treatments Key Words Flavonoid mutasythesis Escherichia coli Saccharomyces cerevisiae

p 8 of 44

4 Engineering The E Coli UDP-Glucose Synthesis Pathway For Anthocyanin Biosynthesis

Zhen Li Yajun Yan and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are water soluble vacuolar flavonoid pigments that appear red to blue according to pH In the pathway of anthocyanin synthesis the last step that performs the glycosylation of unstable anthocyanidin to the relatively stable anthocyanin is catalyzed by the enzyme UDP-glucose flavonoid 3-oxoglycosyltransferase (UF3GT) Glycosyltransferases belong to group-transfer enzymes that catalyze the transfer of a sugar molecule from its activated form to an acceptor The most commonly used activated substrates are sugar nucleotides such as UDP-glucose and UDP-galactose But enzyme substrate the sugar nucleotide is much expensive to use in a stoichiometric ratio Therefore we plan to use whole cells as catalysts where sugar nucleotide cofactors are regenerated UDP-glucose is the starting point of the synthesis of other UDP-sugars Its yield directly influences the rate synthesis of any oligosaccharides containing these sugars Two enzymes directly involved in the synthesis of UDP-glucose from glucose-6-phosphate phosphoglucomutase (PGM catalyzing the conversion of glucose-6-phosphate to glucose-1-phosphate) and UDP-glucose pyrophosphorylase (GalU catalyzing the formation of UDP-glucose from glucose-1-phosphate and uridine triphosphate) were overexpressed The impact of overexpression of PGM and GalU will be investigated through the synthesis of UDP-glucose The overexpression of PGM and GalU can also increase the yield of anthocyanin This work will have an extended impact in the biosynthesis of various glycosylated natural products in addition to anthocyanins such as antibiotics

p 9 of 44

5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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TABLE OF CONTENTS BIOLOGICAL ENGINEERING

1 IN SILICO SIMULATION OF GENOME-SCALE INTRACELLULAR FLUX MODELS FOR ENGINEERING PHENYLPROPANOID BIOSYNTHESIS IN ESCHERICHIA COLI 6

2 ENGINEERING ESCHERICHIA COLI FOR PLANT PHARMACEUTICS PRODUCTION 7

3 MUTASYNTHESIS OF NOVEL UNNATURAL FLAVONOIDS 8

4 ENGINEERING THE E COLI UDP-GLUCOSE SYNTHESIS PATHWAY FOR ANTHOCYANIN BIOSYNTHESIS 9

5 ENGINEERING PLANT PIGMENT BIOSYNTHESIS IN ESCHERICHIA COLI 10

6 EXPLORING METABOLONS FOR IMPROVEMENT IN PLANT-SPECIFIC FLAVANONE PRODUCTION FROM ESCHERICHIA COLI 11

7 RECYCLING ACETATE FOR IMPROVEMENT OF FLAVONOID PRODUCTIONS FROM ESCHERICHIA COLI 12

8 CHARACTERIZATION OF BONE MARROW DERIVED SMOOTH MUSCLE CELLS AND ITS APPLICATION IN VASCULAR ENGINEERING 13

9 PURIFICATION OF RECOMBINANT RETROVIRUS FOR GENE THERAPY14

10 INVOLVEMENT OF THE CCAATENHANCER-BINDING PROTEINS IN THE INTERACTIONS OF KGF AND INTEGRIN Α5 CONTROLLING CELL PROLIFERATION AND MIGRATION15

11 DISTINCT CCAATENHANCER BINDING PROTEIN ISOFORMS MEDIATE KERATINOCYTE GROWTH FACTOR-INDUCED MIGRATION AND PROLIFERATION OF EPITHELIAL CELLS 16

12 EGFR SIGNALING PATHWAYS AFFECT RETROVIRAL GENE TRANSFER TO EPITHELIAL CELLS17

13 THE ROLE OF THE JNK PATHWAY IN LENTIVIRAL TRANSDUCTION PROCESSES 18

14 A SYNTHETIC SUGAR AS A POTENTIAL ANTI-INFLAMMATORY DRUG19

15 SOLUTION STRUCTURE OF HUMAN VON WILLEBRAND FACTOR STUDIED USING SMALL ANGLE NEUTRON SCATTERING20

16 FROM LIGAND BINDING TO TRANSCRIPTION AN INTEGRATED MODEL FOR TUMOR NECROSIS FACTOR INDUCED NF-κB ACTIVATION 21

17 ANTI-PF4 ANTIBODIES RECOGNIZE NEUTROPHIL SURFACE BOUND PLATELET FACTOR 4 (PF-4) AND INDUCE NEUTROPHIL ACTIVATION AND ADHESION22

18 EXPLORING INTERCELLULAR CHANNELS WITH A HINDERED DIFFUSION MODEL OF ION TRANSPORT23

p 3 of 44

19 A COMPUTATIONAL MODEL OF TRANSIENT DRUGCHEMICAL DIFFUSION THROUGH HUMAN SKIN IN THE VICINITY OF A HAIR FOLLICLE 24

20 PROPAGATION OF PLURIPOTENT EMBRYONIC STEM CELLS UNDER SERUM-FREE CONDITIONS IN A SCALABLE BIOREACTOR25

21 EFFECTS OF FLAVONOIDS ON PANCREATIC β-CELL INSULIN REGULATION26

22 CROSSTALK BETWEEN WNT SIGNALING AND INSULIN REGULATORY NETWORK IN PANCREATIC β-CELLS27

NANOSCALE MATERIALS SCIENCE AND ENGINEERING

23 SYNTHESIS OF ZINC SULFIDE NANAPARTICLES BY SPRAY PYROLYSIS28

24 SYNTHESIS OF TELLURIUM DIOXIDE NANOPARTICLES BY SPRAY PYROLYSIS29

25 CONTROL MECHANISMS FOR THE MOLECULAR ASSEMBLY OF AMPHIPHILES30

26 WATER GAS SHIFT OVER IRON OXIDE CATALYSTS 31

27 ADSORPTION OF ETHANOL AND WATER VAPORS ON 3Aring AND 4Aring ZEOLITES 32

28 POLYMER CONFORMATION IN WATER AND POLAR ORGANIC SOLVENTS33

MOLECULAR AND MULTISCALE MODELING

29 WATER GAS SHIFT OVER IRON OXIDE CATALYSTS MICROKINETIC MODELING 34

30 EXPLORING THE PHASE BEHAVIOUR OF A SIMPLE MODEL PROTEIN USING MOLECULAR SIMULATION35

31 ORTHOGONAL POLYNOMIAL METHOD TO COMPUTE THE DENSITY OF STATES 36

32 COMPUTER SIMULATIONS IN COMPLEX FLUIDS 37

33 MODELING OF INDUSTRIAL PRESSURE SWING ADSORPTION PROCESS FOR FUEL ETHANOL PRODUCTION38

34 ATOMISTIC MODELING OF GRAIN BOUNDARY DIFFUSION IN SN-AG-CU SOLDER USING TRANSITION PATH SAMPLING 39

35 A COMPUTATIONAL STUDY OF THE PROPERTIES OF WATER NEAR A PROTEIN SURFACE WITH ADDED SOLUTE40

36 RELATIONSHIP BETWEEN THE THERMODYNAMICS AND DYNAMICS OF A MOLECULAR FLUID41

37 DETERMINING CONTACT ANGLES FROM MOLECULAR SIMULATION 42

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38 ASSESSING CRYSTAL FREE ENERGY43

39 GRAND CANONICAL MONTE CARLO SIMULATIONS OF WATER ADSORPTION ON GRAPHITE SURFACE 44

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BIOLOGICAL ENGINEERING

1 In Silico Simulation Of Genome-Scale Intracellular Flux Models For Engineering Phenylpropanoid Biosynthesis In Escherichia Coli

Zachary L Fowler William Gikandi and Mattheos AG KoffasDepartment of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

The molecular components of any organism can be readily found from the genome sequence where by application of reductionist methods generates a genomic lsquoparts listrsquo incorporating all cellular functions Using this information elucidation of all enzymatic reactions within the organism is achieved to develop the organismrsquos metabolic topology A subsequent construction and simulation of steady state flux models can describe production limitations of the organism on a genomic level By applying Quadratic Programming in the framework of a Genetic Algorithm we can predict genetic perturbations specifically gene deletions which cause an increased metabolic flux to pathways of interest By comparing wild-type network profiles to those of perturbed networks gene over expressions can also be identified Additionally a minimal level of cellular growth can be enforced to ensure the prediction of viable cell phenotypes

Flavonoids are currently used as dietary supplements and along with several of their substituted unnatural analogues have potential therapeutic value in cancer treatments While readily found in plants the extraction of substantial amounts is difficult resulting in an increased interest in biochemical production of these compounds We can create production platforms to increase the biosynthetic yield of these valuable compounds through the incorporation and co-expression of genes controlling the enzymatic production of flavonoids as well as the targeted deletion of native genes controlling competing enzymatic processes within the host organism This work details the use of intracellular flux models to engineering the biosynthesis of apigenin a flavone in Escherichia coli Key Words flavonoids optimization genetic algorithm flux balance analysis

p 6 of 44

2 Engineering Escherichia Coli For Plant Pharmaceutics Production

Effendi Leonard and Mattheos Koffas Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

Flavonoids are plant-derived secondary metabolites with various health promoting properties and are being evaluated in preliminary trials for treatment of various diseases from cancer to diabetes Since microbial fermentation is a cost-saving alternative to chemical synthesis or plant extraction we aim to develop recombinant platforms that can efficiently produce plant flavonoid pharmaceutics

We present the metabolic engineering of bacterium Escherichia coli for flavonoid biosynthesis Implantation of artificial flavonoid biosynthetic pathways through simultaneous expression of plant-derived genes resulted in the biosynthesis of a library of flavonoid molecules which includes flavanones flavones flavonols flavanols and anthocyanins The minute amount of endogeneous malonyl-CoAs required for flavonoid building blocks limits the high-level production of flavonoids from E coli To overcome this limitation frontiers of cellular engineering the flavonoid producer strains by manipulations of the intracellular fatty acid metabolism were pursued The metabolic manipulation to increase malonyl-CoA contents through the introduction of a novel malonate operon elevated flavonoid production up to 4-folds In conjunction with cessation of the recycling of malonyl-CoA into acetyl-CoA by inhibition of β-ketoacyl acyl carrier proteins flavonoids were produced at high levels up to hundreds of milligram per liter quantity

Lastly to allow plant estrogen isoflavone synthesis in E coli we present the design of a series of soybean membrane-bound P450 IFS chimeras to search for progenies that simultaneously exhibit functionality and high turnover catalysis in E coli Isoflavone productions from E coli harboring the most effective IFS variant were superior when compared to that from the natural plant resources and the recombinant S cerevisiae The protein engineering achievements complete the endeavor to synthesize all six main flavonoid classes from E coli

p 7 of 44

3 Mutasynthesis Of Novel Unnatural Flavonoids

Joseph A Chemler Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas Email jchemlerbuffaloedu Flavonoids are a large class of plant secondary metabolites that are involved in the beneficial effects diets rich in fruits and vegetables have in human health The overall goal of our work is the biosynthesis of novel flavonoid molecules using genetically tractable microbial species such as Escherichia coli and Saccharomyces cerevisiae (yeast) This is achieved through episomal introduction of the flavonoid metabolic circuits from various plant species in these organisms Using the constructed recombinant strains mutasynthesis allows the production of novel unnatural flavonoid analogues with different substitutions on the flavonoid core structure consisting of hydroxyl fluoro and amino groups By expressing different combinations of flavonoid enzymes in the recombinant strains a number of flavonoid subclasses have been synthesized including flavanones 5-deoxyflavonones flavones dihydroflavonols leucoanthocyanidins and anthocyanidins A library of over 25 novel unnatural flavonoids has been made and continues to expand by extending the flavonoid pathway We are currently investigating the use of some of the synthesized compounds for diabetes and obesity treatments Key Words Flavonoid mutasythesis Escherichia coli Saccharomyces cerevisiae

p 8 of 44

4 Engineering The E Coli UDP-Glucose Synthesis Pathway For Anthocyanin Biosynthesis

Zhen Li Yajun Yan and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are water soluble vacuolar flavonoid pigments that appear red to blue according to pH In the pathway of anthocyanin synthesis the last step that performs the glycosylation of unstable anthocyanidin to the relatively stable anthocyanin is catalyzed by the enzyme UDP-glucose flavonoid 3-oxoglycosyltransferase (UF3GT) Glycosyltransferases belong to group-transfer enzymes that catalyze the transfer of a sugar molecule from its activated form to an acceptor The most commonly used activated substrates are sugar nucleotides such as UDP-glucose and UDP-galactose But enzyme substrate the sugar nucleotide is much expensive to use in a stoichiometric ratio Therefore we plan to use whole cells as catalysts where sugar nucleotide cofactors are regenerated UDP-glucose is the starting point of the synthesis of other UDP-sugars Its yield directly influences the rate synthesis of any oligosaccharides containing these sugars Two enzymes directly involved in the synthesis of UDP-glucose from glucose-6-phosphate phosphoglucomutase (PGM catalyzing the conversion of glucose-6-phosphate to glucose-1-phosphate) and UDP-glucose pyrophosphorylase (GalU catalyzing the formation of UDP-glucose from glucose-1-phosphate and uridine triphosphate) were overexpressed The impact of overexpression of PGM and GalU will be investigated through the synthesis of UDP-glucose The overexpression of PGM and GalU can also increase the yield of anthocyanin This work will have an extended impact in the biosynthesis of various glycosylated natural products in addition to anthocyanins such as antibiotics

p 9 of 44

5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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 DAN 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 NLD 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 ESP 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 SUO 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 ITA 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 NOR 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 SVE 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 gtgtgtgt setdistillerparamsltlt HWResolution [2400 2400] PageSize [612000 792000]gtgt setpagedevice

19 A COMPUTATIONAL MODEL OF TRANSIENT DRUGCHEMICAL DIFFUSION THROUGH HUMAN SKIN IN THE VICINITY OF A HAIR FOLLICLE 24

20 PROPAGATION OF PLURIPOTENT EMBRYONIC STEM CELLS UNDER SERUM-FREE CONDITIONS IN A SCALABLE BIOREACTOR25

21 EFFECTS OF FLAVONOIDS ON PANCREATIC β-CELL INSULIN REGULATION26

22 CROSSTALK BETWEEN WNT SIGNALING AND INSULIN REGULATORY NETWORK IN PANCREATIC β-CELLS27

NANOSCALE MATERIALS SCIENCE AND ENGINEERING

23 SYNTHESIS OF ZINC SULFIDE NANAPARTICLES BY SPRAY PYROLYSIS28

24 SYNTHESIS OF TELLURIUM DIOXIDE NANOPARTICLES BY SPRAY PYROLYSIS29

25 CONTROL MECHANISMS FOR THE MOLECULAR ASSEMBLY OF AMPHIPHILES30

26 WATER GAS SHIFT OVER IRON OXIDE CATALYSTS 31

27 ADSORPTION OF ETHANOL AND WATER VAPORS ON 3Aring AND 4Aring ZEOLITES 32

28 POLYMER CONFORMATION IN WATER AND POLAR ORGANIC SOLVENTS33

MOLECULAR AND MULTISCALE MODELING

29 WATER GAS SHIFT OVER IRON OXIDE CATALYSTS MICROKINETIC MODELING 34

30 EXPLORING THE PHASE BEHAVIOUR OF A SIMPLE MODEL PROTEIN USING MOLECULAR SIMULATION35

31 ORTHOGONAL POLYNOMIAL METHOD TO COMPUTE THE DENSITY OF STATES 36

32 COMPUTER SIMULATIONS IN COMPLEX FLUIDS 37

33 MODELING OF INDUSTRIAL PRESSURE SWING ADSORPTION PROCESS FOR FUEL ETHANOL PRODUCTION38

34 ATOMISTIC MODELING OF GRAIN BOUNDARY DIFFUSION IN SN-AG-CU SOLDER USING TRANSITION PATH SAMPLING 39

35 A COMPUTATIONAL STUDY OF THE PROPERTIES OF WATER NEAR A PROTEIN SURFACE WITH ADDED SOLUTE40

36 RELATIONSHIP BETWEEN THE THERMODYNAMICS AND DYNAMICS OF A MOLECULAR FLUID41

37 DETERMINING CONTACT ANGLES FROM MOLECULAR SIMULATION 42

p 4 of 44

38 ASSESSING CRYSTAL FREE ENERGY43

39 GRAND CANONICAL MONTE CARLO SIMULATIONS OF WATER ADSORPTION ON GRAPHITE SURFACE 44

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BIOLOGICAL ENGINEERING

1 In Silico Simulation Of Genome-Scale Intracellular Flux Models For Engineering Phenylpropanoid Biosynthesis In Escherichia Coli

Zachary L Fowler William Gikandi and Mattheos AG KoffasDepartment of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

The molecular components of any organism can be readily found from the genome sequence where by application of reductionist methods generates a genomic lsquoparts listrsquo incorporating all cellular functions Using this information elucidation of all enzymatic reactions within the organism is achieved to develop the organismrsquos metabolic topology A subsequent construction and simulation of steady state flux models can describe production limitations of the organism on a genomic level By applying Quadratic Programming in the framework of a Genetic Algorithm we can predict genetic perturbations specifically gene deletions which cause an increased metabolic flux to pathways of interest By comparing wild-type network profiles to those of perturbed networks gene over expressions can also be identified Additionally a minimal level of cellular growth can be enforced to ensure the prediction of viable cell phenotypes

Flavonoids are currently used as dietary supplements and along with several of their substituted unnatural analogues have potential therapeutic value in cancer treatments While readily found in plants the extraction of substantial amounts is difficult resulting in an increased interest in biochemical production of these compounds We can create production platforms to increase the biosynthetic yield of these valuable compounds through the incorporation and co-expression of genes controlling the enzymatic production of flavonoids as well as the targeted deletion of native genes controlling competing enzymatic processes within the host organism This work details the use of intracellular flux models to engineering the biosynthesis of apigenin a flavone in Escherichia coli Key Words flavonoids optimization genetic algorithm flux balance analysis

p 6 of 44

2 Engineering Escherichia Coli For Plant Pharmaceutics Production

Effendi Leonard and Mattheos Koffas Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

Flavonoids are plant-derived secondary metabolites with various health promoting properties and are being evaluated in preliminary trials for treatment of various diseases from cancer to diabetes Since microbial fermentation is a cost-saving alternative to chemical synthesis or plant extraction we aim to develop recombinant platforms that can efficiently produce plant flavonoid pharmaceutics

We present the metabolic engineering of bacterium Escherichia coli for flavonoid biosynthesis Implantation of artificial flavonoid biosynthetic pathways through simultaneous expression of plant-derived genes resulted in the biosynthesis of a library of flavonoid molecules which includes flavanones flavones flavonols flavanols and anthocyanins The minute amount of endogeneous malonyl-CoAs required for flavonoid building blocks limits the high-level production of flavonoids from E coli To overcome this limitation frontiers of cellular engineering the flavonoid producer strains by manipulations of the intracellular fatty acid metabolism were pursued The metabolic manipulation to increase malonyl-CoA contents through the introduction of a novel malonate operon elevated flavonoid production up to 4-folds In conjunction with cessation of the recycling of malonyl-CoA into acetyl-CoA by inhibition of β-ketoacyl acyl carrier proteins flavonoids were produced at high levels up to hundreds of milligram per liter quantity

Lastly to allow plant estrogen isoflavone synthesis in E coli we present the design of a series of soybean membrane-bound P450 IFS chimeras to search for progenies that simultaneously exhibit functionality and high turnover catalysis in E coli Isoflavone productions from E coli harboring the most effective IFS variant were superior when compared to that from the natural plant resources and the recombinant S cerevisiae The protein engineering achievements complete the endeavor to synthesize all six main flavonoid classes from E coli

p 7 of 44

3 Mutasynthesis Of Novel Unnatural Flavonoids

Joseph A Chemler Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas Email jchemlerbuffaloedu Flavonoids are a large class of plant secondary metabolites that are involved in the beneficial effects diets rich in fruits and vegetables have in human health The overall goal of our work is the biosynthesis of novel flavonoid molecules using genetically tractable microbial species such as Escherichia coli and Saccharomyces cerevisiae (yeast) This is achieved through episomal introduction of the flavonoid metabolic circuits from various plant species in these organisms Using the constructed recombinant strains mutasynthesis allows the production of novel unnatural flavonoid analogues with different substitutions on the flavonoid core structure consisting of hydroxyl fluoro and amino groups By expressing different combinations of flavonoid enzymes in the recombinant strains a number of flavonoid subclasses have been synthesized including flavanones 5-deoxyflavonones flavones dihydroflavonols leucoanthocyanidins and anthocyanidins A library of over 25 novel unnatural flavonoids has been made and continues to expand by extending the flavonoid pathway We are currently investigating the use of some of the synthesized compounds for diabetes and obesity treatments Key Words Flavonoid mutasythesis Escherichia coli Saccharomyces cerevisiae

p 8 of 44

4 Engineering The E Coli UDP-Glucose Synthesis Pathway For Anthocyanin Biosynthesis

Zhen Li Yajun Yan and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are water soluble vacuolar flavonoid pigments that appear red to blue according to pH In the pathway of anthocyanin synthesis the last step that performs the glycosylation of unstable anthocyanidin to the relatively stable anthocyanin is catalyzed by the enzyme UDP-glucose flavonoid 3-oxoglycosyltransferase (UF3GT) Glycosyltransferases belong to group-transfer enzymes that catalyze the transfer of a sugar molecule from its activated form to an acceptor The most commonly used activated substrates are sugar nucleotides such as UDP-glucose and UDP-galactose But enzyme substrate the sugar nucleotide is much expensive to use in a stoichiometric ratio Therefore we plan to use whole cells as catalysts where sugar nucleotide cofactors are regenerated UDP-glucose is the starting point of the synthesis of other UDP-sugars Its yield directly influences the rate synthesis of any oligosaccharides containing these sugars Two enzymes directly involved in the synthesis of UDP-glucose from glucose-6-phosphate phosphoglucomutase (PGM catalyzing the conversion of glucose-6-phosphate to glucose-1-phosphate) and UDP-glucose pyrophosphorylase (GalU catalyzing the formation of UDP-glucose from glucose-1-phosphate and uridine triphosphate) were overexpressed The impact of overexpression of PGM and GalU will be investigated through the synthesis of UDP-glucose The overexpression of PGM and GalU can also increase the yield of anthocyanin This work will have an extended impact in the biosynthesis of various glycosylated natural products in addition to anthocyanins such as antibiotics

p 9 of 44

5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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38 ASSESSING CRYSTAL FREE ENERGY43

39 GRAND CANONICAL MONTE CARLO SIMULATIONS OF WATER ADSORPTION ON GRAPHITE SURFACE 44

p 5 of 44

BIOLOGICAL ENGINEERING

1 In Silico Simulation Of Genome-Scale Intracellular Flux Models For Engineering Phenylpropanoid Biosynthesis In Escherichia Coli

Zachary L Fowler William Gikandi and Mattheos AG KoffasDepartment of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

The molecular components of any organism can be readily found from the genome sequence where by application of reductionist methods generates a genomic lsquoparts listrsquo incorporating all cellular functions Using this information elucidation of all enzymatic reactions within the organism is achieved to develop the organismrsquos metabolic topology A subsequent construction and simulation of steady state flux models can describe production limitations of the organism on a genomic level By applying Quadratic Programming in the framework of a Genetic Algorithm we can predict genetic perturbations specifically gene deletions which cause an increased metabolic flux to pathways of interest By comparing wild-type network profiles to those of perturbed networks gene over expressions can also be identified Additionally a minimal level of cellular growth can be enforced to ensure the prediction of viable cell phenotypes

Flavonoids are currently used as dietary supplements and along with several of their substituted unnatural analogues have potential therapeutic value in cancer treatments While readily found in plants the extraction of substantial amounts is difficult resulting in an increased interest in biochemical production of these compounds We can create production platforms to increase the biosynthetic yield of these valuable compounds through the incorporation and co-expression of genes controlling the enzymatic production of flavonoids as well as the targeted deletion of native genes controlling competing enzymatic processes within the host organism This work details the use of intracellular flux models to engineering the biosynthesis of apigenin a flavone in Escherichia coli Key Words flavonoids optimization genetic algorithm flux balance analysis

p 6 of 44

2 Engineering Escherichia Coli For Plant Pharmaceutics Production

Effendi Leonard and Mattheos Koffas Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

Flavonoids are plant-derived secondary metabolites with various health promoting properties and are being evaluated in preliminary trials for treatment of various diseases from cancer to diabetes Since microbial fermentation is a cost-saving alternative to chemical synthesis or plant extraction we aim to develop recombinant platforms that can efficiently produce plant flavonoid pharmaceutics

We present the metabolic engineering of bacterium Escherichia coli for flavonoid biosynthesis Implantation of artificial flavonoid biosynthetic pathways through simultaneous expression of plant-derived genes resulted in the biosynthesis of a library of flavonoid molecules which includes flavanones flavones flavonols flavanols and anthocyanins The minute amount of endogeneous malonyl-CoAs required for flavonoid building blocks limits the high-level production of flavonoids from E coli To overcome this limitation frontiers of cellular engineering the flavonoid producer strains by manipulations of the intracellular fatty acid metabolism were pursued The metabolic manipulation to increase malonyl-CoA contents through the introduction of a novel malonate operon elevated flavonoid production up to 4-folds In conjunction with cessation of the recycling of malonyl-CoA into acetyl-CoA by inhibition of β-ketoacyl acyl carrier proteins flavonoids were produced at high levels up to hundreds of milligram per liter quantity

Lastly to allow plant estrogen isoflavone synthesis in E coli we present the design of a series of soybean membrane-bound P450 IFS chimeras to search for progenies that simultaneously exhibit functionality and high turnover catalysis in E coli Isoflavone productions from E coli harboring the most effective IFS variant were superior when compared to that from the natural plant resources and the recombinant S cerevisiae The protein engineering achievements complete the endeavor to synthesize all six main flavonoid classes from E coli

p 7 of 44

3 Mutasynthesis Of Novel Unnatural Flavonoids

Joseph A Chemler Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas Email jchemlerbuffaloedu Flavonoids are a large class of plant secondary metabolites that are involved in the beneficial effects diets rich in fruits and vegetables have in human health The overall goal of our work is the biosynthesis of novel flavonoid molecules using genetically tractable microbial species such as Escherichia coli and Saccharomyces cerevisiae (yeast) This is achieved through episomal introduction of the flavonoid metabolic circuits from various plant species in these organisms Using the constructed recombinant strains mutasynthesis allows the production of novel unnatural flavonoid analogues with different substitutions on the flavonoid core structure consisting of hydroxyl fluoro and amino groups By expressing different combinations of flavonoid enzymes in the recombinant strains a number of flavonoid subclasses have been synthesized including flavanones 5-deoxyflavonones flavones dihydroflavonols leucoanthocyanidins and anthocyanidins A library of over 25 novel unnatural flavonoids has been made and continues to expand by extending the flavonoid pathway We are currently investigating the use of some of the synthesized compounds for diabetes and obesity treatments Key Words Flavonoid mutasythesis Escherichia coli Saccharomyces cerevisiae

p 8 of 44

4 Engineering The E Coli UDP-Glucose Synthesis Pathway For Anthocyanin Biosynthesis

Zhen Li Yajun Yan and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are water soluble vacuolar flavonoid pigments that appear red to blue according to pH In the pathway of anthocyanin synthesis the last step that performs the glycosylation of unstable anthocyanidin to the relatively stable anthocyanin is catalyzed by the enzyme UDP-glucose flavonoid 3-oxoglycosyltransferase (UF3GT) Glycosyltransferases belong to group-transfer enzymes that catalyze the transfer of a sugar molecule from its activated form to an acceptor The most commonly used activated substrates are sugar nucleotides such as UDP-glucose and UDP-galactose But enzyme substrate the sugar nucleotide is much expensive to use in a stoichiometric ratio Therefore we plan to use whole cells as catalysts where sugar nucleotide cofactors are regenerated UDP-glucose is the starting point of the synthesis of other UDP-sugars Its yield directly influences the rate synthesis of any oligosaccharides containing these sugars Two enzymes directly involved in the synthesis of UDP-glucose from glucose-6-phosphate phosphoglucomutase (PGM catalyzing the conversion of glucose-6-phosphate to glucose-1-phosphate) and UDP-glucose pyrophosphorylase (GalU catalyzing the formation of UDP-glucose from glucose-1-phosphate and uridine triphosphate) were overexpressed The impact of overexpression of PGM and GalU will be investigated through the synthesis of UDP-glucose The overexpression of PGM and GalU can also increase the yield of anthocyanin This work will have an extended impact in the biosynthesis of various glycosylated natural products in addition to anthocyanins such as antibiotics

p 9 of 44

5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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BIOLOGICAL ENGINEERING

1 In Silico Simulation Of Genome-Scale Intracellular Flux Models For Engineering Phenylpropanoid Biosynthesis In Escherichia Coli

Zachary L Fowler William Gikandi and Mattheos AG KoffasDepartment of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

The molecular components of any organism can be readily found from the genome sequence where by application of reductionist methods generates a genomic lsquoparts listrsquo incorporating all cellular functions Using this information elucidation of all enzymatic reactions within the organism is achieved to develop the organismrsquos metabolic topology A subsequent construction and simulation of steady state flux models can describe production limitations of the organism on a genomic level By applying Quadratic Programming in the framework of a Genetic Algorithm we can predict genetic perturbations specifically gene deletions which cause an increased metabolic flux to pathways of interest By comparing wild-type network profiles to those of perturbed networks gene over expressions can also be identified Additionally a minimal level of cellular growth can be enforced to ensure the prediction of viable cell phenotypes

Flavonoids are currently used as dietary supplements and along with several of their substituted unnatural analogues have potential therapeutic value in cancer treatments While readily found in plants the extraction of substantial amounts is difficult resulting in an increased interest in biochemical production of these compounds We can create production platforms to increase the biosynthetic yield of these valuable compounds through the incorporation and co-expression of genes controlling the enzymatic production of flavonoids as well as the targeted deletion of native genes controlling competing enzymatic processes within the host organism This work details the use of intracellular flux models to engineering the biosynthesis of apigenin a flavone in Escherichia coli Key Words flavonoids optimization genetic algorithm flux balance analysis

p 6 of 44

2 Engineering Escherichia Coli For Plant Pharmaceutics Production

Effendi Leonard and Mattheos Koffas Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

Flavonoids are plant-derived secondary metabolites with various health promoting properties and are being evaluated in preliminary trials for treatment of various diseases from cancer to diabetes Since microbial fermentation is a cost-saving alternative to chemical synthesis or plant extraction we aim to develop recombinant platforms that can efficiently produce plant flavonoid pharmaceutics

We present the metabolic engineering of bacterium Escherichia coli for flavonoid biosynthesis Implantation of artificial flavonoid biosynthetic pathways through simultaneous expression of plant-derived genes resulted in the biosynthesis of a library of flavonoid molecules which includes flavanones flavones flavonols flavanols and anthocyanins The minute amount of endogeneous malonyl-CoAs required for flavonoid building blocks limits the high-level production of flavonoids from E coli To overcome this limitation frontiers of cellular engineering the flavonoid producer strains by manipulations of the intracellular fatty acid metabolism were pursued The metabolic manipulation to increase malonyl-CoA contents through the introduction of a novel malonate operon elevated flavonoid production up to 4-folds In conjunction with cessation of the recycling of malonyl-CoA into acetyl-CoA by inhibition of β-ketoacyl acyl carrier proteins flavonoids were produced at high levels up to hundreds of milligram per liter quantity

Lastly to allow plant estrogen isoflavone synthesis in E coli we present the design of a series of soybean membrane-bound P450 IFS chimeras to search for progenies that simultaneously exhibit functionality and high turnover catalysis in E coli Isoflavone productions from E coli harboring the most effective IFS variant were superior when compared to that from the natural plant resources and the recombinant S cerevisiae The protein engineering achievements complete the endeavor to synthesize all six main flavonoid classes from E coli

p 7 of 44

3 Mutasynthesis Of Novel Unnatural Flavonoids

Joseph A Chemler Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas Email jchemlerbuffaloedu Flavonoids are a large class of plant secondary metabolites that are involved in the beneficial effects diets rich in fruits and vegetables have in human health The overall goal of our work is the biosynthesis of novel flavonoid molecules using genetically tractable microbial species such as Escherichia coli and Saccharomyces cerevisiae (yeast) This is achieved through episomal introduction of the flavonoid metabolic circuits from various plant species in these organisms Using the constructed recombinant strains mutasynthesis allows the production of novel unnatural flavonoid analogues with different substitutions on the flavonoid core structure consisting of hydroxyl fluoro and amino groups By expressing different combinations of flavonoid enzymes in the recombinant strains a number of flavonoid subclasses have been synthesized including flavanones 5-deoxyflavonones flavones dihydroflavonols leucoanthocyanidins and anthocyanidins A library of over 25 novel unnatural flavonoids has been made and continues to expand by extending the flavonoid pathway We are currently investigating the use of some of the synthesized compounds for diabetes and obesity treatments Key Words Flavonoid mutasythesis Escherichia coli Saccharomyces cerevisiae

p 8 of 44

4 Engineering The E Coli UDP-Glucose Synthesis Pathway For Anthocyanin Biosynthesis

Zhen Li Yajun Yan and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are water soluble vacuolar flavonoid pigments that appear red to blue according to pH In the pathway of anthocyanin synthesis the last step that performs the glycosylation of unstable anthocyanidin to the relatively stable anthocyanin is catalyzed by the enzyme UDP-glucose flavonoid 3-oxoglycosyltransferase (UF3GT) Glycosyltransferases belong to group-transfer enzymes that catalyze the transfer of a sugar molecule from its activated form to an acceptor The most commonly used activated substrates are sugar nucleotides such as UDP-glucose and UDP-galactose But enzyme substrate the sugar nucleotide is much expensive to use in a stoichiometric ratio Therefore we plan to use whole cells as catalysts where sugar nucleotide cofactors are regenerated UDP-glucose is the starting point of the synthesis of other UDP-sugars Its yield directly influences the rate synthesis of any oligosaccharides containing these sugars Two enzymes directly involved in the synthesis of UDP-glucose from glucose-6-phosphate phosphoglucomutase (PGM catalyzing the conversion of glucose-6-phosphate to glucose-1-phosphate) and UDP-glucose pyrophosphorylase (GalU catalyzing the formation of UDP-glucose from glucose-1-phosphate and uridine triphosphate) were overexpressed The impact of overexpression of PGM and GalU will be investigated through the synthesis of UDP-glucose The overexpression of PGM and GalU can also increase the yield of anthocyanin This work will have an extended impact in the biosynthesis of various glycosylated natural products in addition to anthocyanins such as antibiotics

p 9 of 44

5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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2 Engineering Escherichia Coli For Plant Pharmaceutics Production

Effendi Leonard and Mattheos Koffas Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260

Flavonoids are plant-derived secondary metabolites with various health promoting properties and are being evaluated in preliminary trials for treatment of various diseases from cancer to diabetes Since microbial fermentation is a cost-saving alternative to chemical synthesis or plant extraction we aim to develop recombinant platforms that can efficiently produce plant flavonoid pharmaceutics

We present the metabolic engineering of bacterium Escherichia coli for flavonoid biosynthesis Implantation of artificial flavonoid biosynthetic pathways through simultaneous expression of plant-derived genes resulted in the biosynthesis of a library of flavonoid molecules which includes flavanones flavones flavonols flavanols and anthocyanins The minute amount of endogeneous malonyl-CoAs required for flavonoid building blocks limits the high-level production of flavonoids from E coli To overcome this limitation frontiers of cellular engineering the flavonoid producer strains by manipulations of the intracellular fatty acid metabolism were pursued The metabolic manipulation to increase malonyl-CoA contents through the introduction of a novel malonate operon elevated flavonoid production up to 4-folds In conjunction with cessation of the recycling of malonyl-CoA into acetyl-CoA by inhibition of β-ketoacyl acyl carrier proteins flavonoids were produced at high levels up to hundreds of milligram per liter quantity

Lastly to allow plant estrogen isoflavone synthesis in E coli we present the design of a series of soybean membrane-bound P450 IFS chimeras to search for progenies that simultaneously exhibit functionality and high turnover catalysis in E coli Isoflavone productions from E coli harboring the most effective IFS variant were superior when compared to that from the natural plant resources and the recombinant S cerevisiae The protein engineering achievements complete the endeavor to synthesize all six main flavonoid classes from E coli

p 7 of 44

3 Mutasynthesis Of Novel Unnatural Flavonoids

Joseph A Chemler Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas Email jchemlerbuffaloedu Flavonoids are a large class of plant secondary metabolites that are involved in the beneficial effects diets rich in fruits and vegetables have in human health The overall goal of our work is the biosynthesis of novel flavonoid molecules using genetically tractable microbial species such as Escherichia coli and Saccharomyces cerevisiae (yeast) This is achieved through episomal introduction of the flavonoid metabolic circuits from various plant species in these organisms Using the constructed recombinant strains mutasynthesis allows the production of novel unnatural flavonoid analogues with different substitutions on the flavonoid core structure consisting of hydroxyl fluoro and amino groups By expressing different combinations of flavonoid enzymes in the recombinant strains a number of flavonoid subclasses have been synthesized including flavanones 5-deoxyflavonones flavones dihydroflavonols leucoanthocyanidins and anthocyanidins A library of over 25 novel unnatural flavonoids has been made and continues to expand by extending the flavonoid pathway We are currently investigating the use of some of the synthesized compounds for diabetes and obesity treatments Key Words Flavonoid mutasythesis Escherichia coli Saccharomyces cerevisiae

p 8 of 44

4 Engineering The E Coli UDP-Glucose Synthesis Pathway For Anthocyanin Biosynthesis

Zhen Li Yajun Yan and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are water soluble vacuolar flavonoid pigments that appear red to blue according to pH In the pathway of anthocyanin synthesis the last step that performs the glycosylation of unstable anthocyanidin to the relatively stable anthocyanin is catalyzed by the enzyme UDP-glucose flavonoid 3-oxoglycosyltransferase (UF3GT) Glycosyltransferases belong to group-transfer enzymes that catalyze the transfer of a sugar molecule from its activated form to an acceptor The most commonly used activated substrates are sugar nucleotides such as UDP-glucose and UDP-galactose But enzyme substrate the sugar nucleotide is much expensive to use in a stoichiometric ratio Therefore we plan to use whole cells as catalysts where sugar nucleotide cofactors are regenerated UDP-glucose is the starting point of the synthesis of other UDP-sugars Its yield directly influences the rate synthesis of any oligosaccharides containing these sugars Two enzymes directly involved in the synthesis of UDP-glucose from glucose-6-phosphate phosphoglucomutase (PGM catalyzing the conversion of glucose-6-phosphate to glucose-1-phosphate) and UDP-glucose pyrophosphorylase (GalU catalyzing the formation of UDP-glucose from glucose-1-phosphate and uridine triphosphate) were overexpressed The impact of overexpression of PGM and GalU will be investigated through the synthesis of UDP-glucose The overexpression of PGM and GalU can also increase the yield of anthocyanin This work will have an extended impact in the biosynthesis of various glycosylated natural products in addition to anthocyanins such as antibiotics

p 9 of 44

5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

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p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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3 Mutasynthesis Of Novel Unnatural Flavonoids

Joseph A Chemler Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas Email jchemlerbuffaloedu Flavonoids are a large class of plant secondary metabolites that are involved in the beneficial effects diets rich in fruits and vegetables have in human health The overall goal of our work is the biosynthesis of novel flavonoid molecules using genetically tractable microbial species such as Escherichia coli and Saccharomyces cerevisiae (yeast) This is achieved through episomal introduction of the flavonoid metabolic circuits from various plant species in these organisms Using the constructed recombinant strains mutasynthesis allows the production of novel unnatural flavonoid analogues with different substitutions on the flavonoid core structure consisting of hydroxyl fluoro and amino groups By expressing different combinations of flavonoid enzymes in the recombinant strains a number of flavonoid subclasses have been synthesized including flavanones 5-deoxyflavonones flavones dihydroflavonols leucoanthocyanidins and anthocyanidins A library of over 25 novel unnatural flavonoids has been made and continues to expand by extending the flavonoid pathway We are currently investigating the use of some of the synthesized compounds for diabetes and obesity treatments Key Words Flavonoid mutasythesis Escherichia coli Saccharomyces cerevisiae

p 8 of 44

4 Engineering The E Coli UDP-Glucose Synthesis Pathway For Anthocyanin Biosynthesis

Zhen Li Yajun Yan and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are water soluble vacuolar flavonoid pigments that appear red to blue according to pH In the pathway of anthocyanin synthesis the last step that performs the glycosylation of unstable anthocyanidin to the relatively stable anthocyanin is catalyzed by the enzyme UDP-glucose flavonoid 3-oxoglycosyltransferase (UF3GT) Glycosyltransferases belong to group-transfer enzymes that catalyze the transfer of a sugar molecule from its activated form to an acceptor The most commonly used activated substrates are sugar nucleotides such as UDP-glucose and UDP-galactose But enzyme substrate the sugar nucleotide is much expensive to use in a stoichiometric ratio Therefore we plan to use whole cells as catalysts where sugar nucleotide cofactors are regenerated UDP-glucose is the starting point of the synthesis of other UDP-sugars Its yield directly influences the rate synthesis of any oligosaccharides containing these sugars Two enzymes directly involved in the synthesis of UDP-glucose from glucose-6-phosphate phosphoglucomutase (PGM catalyzing the conversion of glucose-6-phosphate to glucose-1-phosphate) and UDP-glucose pyrophosphorylase (GalU catalyzing the formation of UDP-glucose from glucose-1-phosphate and uridine triphosphate) were overexpressed The impact of overexpression of PGM and GalU will be investigated through the synthesis of UDP-glucose The overexpression of PGM and GalU can also increase the yield of anthocyanin This work will have an extended impact in the biosynthesis of various glycosylated natural products in addition to anthocyanins such as antibiotics

p 9 of 44

5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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 ITA 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 NOR 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 SVE ltFEFF0041006e007600e4006e00640020006400650020006800e4007200200069006e0073007400e4006c006c006e0069006e006700610072006e00610020006e00e40072002000640075002000760069006c006c00200073006b0061007000610020005000440046002d0064006f006b0075006d0065006e00740020006d006500640020006800f6006700720065002000620069006c0064007500700070006c00f60073006e0069006e00670020006f006300680020006400e40072006d006500640020006600e50020006200e400740074007200650020007500740073006b00720069006600740073006b00760061006c0069007400650074002e0020005000440046002d0064006f006b0075006d0065006e00740065006e0020006b0061006e002000f600700070006e006100730020006d006500640020004100630072006f0062006100740020006f00630068002000520065006100640065007200200035002e003000200065006c006c00650072002000730065006e006100720065002egt gtgtgtgt setdistillerparamsltlt HWResolution [2400 2400] PageSize [612000 792000]gtgt setpagedevice

4 Engineering The E Coli UDP-Glucose Synthesis Pathway For Anthocyanin Biosynthesis

Zhen Li Yajun Yan and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are water soluble vacuolar flavonoid pigments that appear red to blue according to pH In the pathway of anthocyanin synthesis the last step that performs the glycosylation of unstable anthocyanidin to the relatively stable anthocyanin is catalyzed by the enzyme UDP-glucose flavonoid 3-oxoglycosyltransferase (UF3GT) Glycosyltransferases belong to group-transfer enzymes that catalyze the transfer of a sugar molecule from its activated form to an acceptor The most commonly used activated substrates are sugar nucleotides such as UDP-glucose and UDP-galactose But enzyme substrate the sugar nucleotide is much expensive to use in a stoichiometric ratio Therefore we plan to use whole cells as catalysts where sugar nucleotide cofactors are regenerated UDP-glucose is the starting point of the synthesis of other UDP-sugars Its yield directly influences the rate synthesis of any oligosaccharides containing these sugars Two enzymes directly involved in the synthesis of UDP-glucose from glucose-6-phosphate phosphoglucomutase (PGM catalyzing the conversion of glucose-6-phosphate to glucose-1-phosphate) and UDP-glucose pyrophosphorylase (GalU catalyzing the formation of UDP-glucose from glucose-1-phosphate and uridine triphosphate) were overexpressed The impact of overexpression of PGM and GalU will be investigated through the synthesis of UDP-glucose The overexpression of PGM and GalU can also increase the yield of anthocyanin This work will have an extended impact in the biosynthesis of various glycosylated natural products in addition to anthocyanins such as antibiotics

p 9 of 44

5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

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p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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5 Engineering Plant Pigment Biosynthesis In Escherichia Coli

Yajun Yan Zhen Li and Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Anthocyanins are red purple or blue plant pigments responsible for the flower and fruit colors together with betalains and carotenoids In the past two decades anthocyanins received extensive studies for their anti-oxidative anti-inflammatory anti-cancer anti-obesity and cardioprotective properties Their core metabolic biosynthetic pathway consists of flavanone 3-hydroxylase (FHT) dihydroflavonol 4-reductase (DFR) leucoanthocyanidin reductase (LAR) anthocyanidin synthase (ANS) and UDP-glucose flavonoid 3-O-glucosyltransferase (3GT) This pathway leads to the biosynthesis of the first stable glycosylated anthocyanins

In this study several anthocyanin biosynthetic enzymes have been characterized from different plant species and employed for the pathway construction leading from cheap precursors such as flavanones to anthocyanins in Escherichia coli More specifically the recombinant E coli cells successfully achieved milligram level production of two anthocyanins pelargonidin 3-O-glucoside (098mgL) and cyanidin 3-O-gluside (207mgL) from their respective flavanone precursors naringenin and eriodictyol Cyanidin 3-O-glucoside was produced at even higher yields (161 mglt) from green tea catechin Cofactor effect studies showed that the glucosyl donor UDP-glucose contributed the most to production optimization of anthocyanins in the recombinant strains Therefore various metabolic engineering strategies are currently employed for enhancing the homogenous synthesis of UDP-glucose in the host cells In addition the biosynthesis of several other anthocyanin molecules with unique colorations and medicinal properties is currently explored

p 10 of 44

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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 gtgtgtgt setdistillerparamsltlt HWResolution [2400 2400] PageSize [612000 792000]gtgt setpagedevice

6 Exploring Metabolons For Improvement In Plant-Specific Flavanone Production From Escherichia Coli

Kok Hong Lim Effendi Leonard and Mattheos AG Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Biotinylation performed by the enzyme biotin ligase (BirA) is among the rarest post-translational modifications that occur in a limited number of metabolic enzymes and is essential for cell survival and proliferation The biotinylation of the enzyme acetyl-CoA carboxylase (ACCase) in particular is essential as it is the first step in fatty acid biosynthesis In addition a number of high-value metabolites such as antibiotics and plant polyphenols derive from malonyl-CoA the product of ACCase In the present study we explored the role of the protein complex of ACCase and BirA in increasing the synthesis of malonyl-CoA which is the direct precursor of flavonoid molecules such as naringenin pinocembrin and eriodictyol E coli carrying flavonoid biosynthesis gene clusters together with different variants of ACCase and BirA increase the production of naringenin pinocembrin and eriodictyol by 32 88 and 71 respectively from phenylpropanic acid The successful engineering of an optimized carbon flux from acetyl-CoA a native E coli cellular metabolite to flavonoid xenobiotics opens the possibility of further production improvement by further redirecting native cellular carbon fluxes to acetyl-CoA

p 11 of 44

7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

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p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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7 Recycling Acetate For Improvement Of Flavonoid Productions From Escherichia Coli

Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas Department of Chemical and Biological Engineering 303 Furnas Hall State University of New York at Buffalo Buffalo NY 14260-4200 httpwwwengbuffaloedu~mkoffas

Acetate is a toxic by-product of glucose metabolism in Escherichia coli In the present work endogeneous metabolic networks of E coli were re-designed to improve the autonomous recycling of acetate into acetyl-CoA In conjunction with the elevation of acetyl-CoA carboxylase level the metabolic engineering strategy was implemented to improve the recombinant productions of high-value plant-derived flavonoids When the high affinity acetate assimilation enzyme acetyl-CoA synthetase (ACS) was over-expressed the production of three flavonoids naringenin eriodictyol and pinocembrin increased up-to 2 5 and 2 folds respectively The elevation of the low affinity acetate pathway comprising phosphotransacetylase (PTA) and acetate kinase (ACK) resulted in a similar improvement of flavonoid productions It is evident that metabolic engineering methods to recycle waste products can be use to improve the production of high-value heterologous metabolites

p 12 of 44

8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

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TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

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TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

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4

5

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78v4

v3

v2

v7

v15

v20

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NF-κBv16v14

v13

v31IKK_IκB

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19

15 18 25

v12v11

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IκB v28

16

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IKKi

IKK_IκB_NF-κB

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Transcriptionv27

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p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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8 Characterization Of Bone Marrow Derived Smooth Muscle Cells And Its Application In Vascular Engineering

Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis Department Chemical and Biological Engineering State University at Buffalo NY 14220 hpeng3buffaloedu

Cardiovascular disease (CVD) is a leading cause of death in developed countries Autologous blood vessel surgery is the most promising treatment to CVD However up to 40 of patients do not have ideal blood vessel for autologous vessel transplantation Therefore to construct an artificial blood vessel has become extremely important The cell source of vessel and low mechanical strength are two major problems for blood vessel engineering We have successfully isolated smooth muscle cells from bone marrow stem cells We manipulated retrovirus with smooth muscle cell specific promoter and EGFP genes and isolated the cells transfected by retrovirus With EGFP expression cells are sorted by flow cytometry Second we characterize the Bone Marrow derived Smooth Muscle Cells (BMSMC) by Reverse transcription PCR western blot and immunocytochemistry The BMSMCs showed many smooth muscle cells specific markers We further cultured BMSMCs to construct blood vessel The fibrin-based blood vessel showed high mechanical strength and comparable reactivity to natural vessel Above all Bone Marrow derived Smooth Muscle Cells not only provide an alternative cell source but also have ideal properties for blood vessel engineering Key Words Bone marrow derived smooth muscle cells reverse transcription PCR

p 13 of 44

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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 gtgtgtgt setdistillerparamsltlt HWResolution [2400 2400] PageSize [612000 792000]gtgt setpagedevice

9 Purification Of Recombinant Retrovirus For Gene Therapy

Deepa Makkar Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 Retroviral vectors are vehicles of choice for delivery of genes for both therapeutic and research purposes Despite their inherent efficiency in delivering genes to cells that they interact with efficiency of retroviral gene delivery remains low This is due to the low titer of the vector stocks and the presence of transduction inhibitors Purification of vector preparations is mandatory to prevent toxicity inflammation or immune response due to vector components and cellular and medium contaminants such as serum The purification of retroviral vectors still remains a challenge due to their large particle sizes low diffusion rates and rapid inactivation In the past our laboratory has obtained high efficiencies of gene transfer by immobilizing retrovirus particles on extracellular matrix molecule fibronectin (FN) Now we propose the use of FN coated polystyrene beads to purify and concentrate virus This method allows maintenance of viral infectivity high recoveries of infectious particles removal of transduction inhibitors and concentrating the viral supernatants Our method includes capture of the retrovirus on FN coated polystyrene beads elution with sodium chloride dialysis and ultrafiltration Retroviruses bind to the heparin-binding domain of FN and use of polystyrene beads helps in overcoming the diffusion limitations Our work aims to produce injectable-grade virus preparations to achieve final implementation of these vectors as therapeutics Next we intend to use a micro-fabrication based technique that concentrates this purified virus by limiting the surface that the virus can bind to on a scale that is relevant to the distances the virus particle can traverse Key Words Retroviruses gene transfer fibronectin polystyrene beads micro-fabrication

p 14 of 44

10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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10 Involvement Of The CCAATEnhancer-Binding Proteins In The Interactions Of KGF And Integrin Α5 Controlling Cell Proliferation And Migration

Juhee Han Piyush Koria and Stelios T Andreadis Department of Chemical and Biological Engineering State University of New York at Buffalo Amherst NY 14260 The CCAATenhancer-binding proteins (cebp) are a family of basic region leucine zipper (bZIP) transcription factors that includes six members cebpα β γ δ ε and ζ Cebps plays an important role in controlling cell proliferation and differentiation Recently our lab discovered that cebps are involved in the molecular interactions of keratinocyte growth factor (KGF) with integrins KGF promotes proliferation and migration of human keratinocytes which bind to fibronectin through integrin α5β1 KGF and this integrin are highly expressed in migrating keratinocytes during wound healing Expression of cebpα was decreased by KGF which increased cell growth because cebpα might block cell-cycle progression In the same context growth of A431 transfected with α5 overexpression plasmid was severely inhibited Cebpβ knockout mutant of A431 became highly proliferative indicating antiproliferative function of cebpβ Immunocytochemistry assay indicated that KGF stimulated phosphorylation and nuclear localization of cebpβ in engineered skin equivalent We also found that KGF increased the mRNA of integrin subunit α5 in primary keratinocytes A431 cells and engineered skin equivalent Moreover promoter activity of α5 was dependent on cebp binding site and cebpβ knockout mutant blocked increase in α5 promoter activity mediated by KGF These observations led to conclude that activated cebpβ binds to promoter site of integrin α5 encoding gene and initiates α5 expression An understanding on the role of cebp family in the interaction between KGF with integrins controlling cell proliferation and migration provides an important key for designing therapeutic target for treatment of incurable wounds Key Words cebp KGF integrin α5 proliferation migration

p 15 of 44

11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

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p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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11 Distinct CCAATEnhancer Binding Protein Isoforms Mediate Keratinocyte

Growth Factor-Induced Migration And Proliferation Of Epithelial Cells

Piyush Koria amp Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA

Keratinocyte growth factor (KGF) and integrin alpha5-beta1 are not expressed in normal skin but they are both highly upregulated in the migrating epidermis during wound healing Here we report that KGF increased alpha-5 mRNA and protein levels in cultured keratinocytes and stratified skin equivalents Promoter studies indicated that KGF-induced integrin alpha-5 promoter activation was dependent on the CEBP transcription factor binding site Accordingly KGF decreased expression of CEBP-alpha in the basal and suprabasal layers of the epidermis and CEBP-alpha overexpressing cells failed to increase proliferation in response to KGF On the other hand KGF induced sustained phosphorylation and nuclear localization of CEBP-beta In addition a dominant negative form of CEBP-beta inhibited alpha-5 promoter activity while blocking CEBP-beta with siRNA diminished integrin alpha-5 expression and increased cell proliferation Taken together our data indicate that KGF increased keratinocyte proliferation by decreasing CEBP-alpha in the basal and suprabasal epidermal layers and at the same time upregulated integrin alpha-5 expression by phosphorylating CEBP-beta

p 16 of 44

12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

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IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

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TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

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IκB v28

16

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[IκB]n23 26

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Transcriptionv27

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p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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12 EGFR Signaling Pathways Affect Retroviral Gene Transfer To Epithelial Cells

Raghvendra Singh Stelios T Andreadis Department of Chemical amp Biological Engineering University at Buffalo The State University of New York Amherst NY14260 USA Although a lot of progress has been made in molecular design of retrovirus vectors the interactions of recombinant retrovirus with host cells remain largely elusive The inability of recombinant retrovirus to transduce non-dividing cells prompted several studies to determine optimal cocktails of growth factors andor extracellular matrix molecules to promote gene transfer to slowly diving cells and in particular stem cells In contrast to previous reports that growth factors increased gene transfer we found that treatment of human epidermal cells with EGFR ligands ie EGF TGF-alpha or HB-EGF decreased gene transfer Conversely treatment with an EGFR function blocking antibody or inhibition of EGFR tyrosine phosphorylation enhanced gene transfer in a dose dependent manner In addition abolishing PKC-delta but not PKC-zeta with chemical inhibitors or siRNA reversed the effects of EGF and restored gene transfer indicating that the effect of EGFR activation is mediated through PKC-delta Our results implicate EGFR and PKC-delta in retroviral infection of epidermal keratinocytes and may have wide implications for retrovirus gene transfer or design of antiretroviral therapies Currently we are looking at the role of other effectors of growth factor mediated pathways like Ras Raf and src and their interaction with PKC-delta Also we examine the step(s) of viral life cycle that might be affected by PKC-delta Our results shed light into virus-cell interactions and may suggest novel strategies to improve gene transfer and reduce the unwanted effects of virus infection

p 17 of 44

13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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13 The Role Of The JNK Pathway In Lentiviral Transduction Processes

Meng Horng Lee and Stelios T Andreadis Department of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260

Lentiviral vectors are currently the most widely used gene transfer system in biomedical fields

including gene therapy and tissue engineering because lentiviral mediated gene transfer offers the advantages over other gene transfer vehicles primarily as an ability of the stability to integrate DNA in successfully transduced target cells However the application of lentiviral vectors has its limitation because the average number of genes delivered to the target cells is often too low to achieve the desired effect To overcome this drawback we focus on exploring the signaling pathways inside the cell which affect the transduction of lentivirus

Here we demonstrat that activated c-jun-N-terminal protein kinases (JNK) pathway is necessary for lentiviral transduction processes The chemical inhibitor of the JNK SP600125 abolishes JNK phosphorylation and diminishes the retroviral transduction efficiency Besides we prove that the JNK pathway influence lentiviral transduction is independent of affecting cell cycle Furthermore we use SP600125 to block the JNK pathway in different time points during lentiviral transduction processes The results indicates that the JNK pathway does not directly influence viral particles and the JNK pathway only involves in early steps of lentiviral transduction processes It suggests that the JNK pathway affects the processes of virus entry or trafficking inside the cell Consequently we are currently constructing JNK dominant cells and JNK negative cells by siRNA technology to clarify the role of the JNK pathway in viral entry and movement

p 18 of 44

14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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14 A Synthetic Sugar As A Potential Anti-Inflammatory Drug

Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khushi L Matta2 and Sriram Neelamegham1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu 2 Department of Cancer Biology Roswell Park Cancer Institute Buffalo NY 14263 Web httpwwwroswellparkorgdocument_3441_631html email khushimattaroswellparkorg OBJECTIVE Novel strategies to control the binding of adhesion molecules belonging to the selectin family are required for the treatment of inflammatory diseases This study tested the possibility that synthetic sugar analogs can compete with naturally occurring sugars to metabolically modify the pattern of glycosylation on cellular glycoproteins and inhibit the selectin mediated inflammatory process METHODS Modified sugar analogs were added to the growth media of leukocytic cell lines and changes in glycan structure as well as selectin binding function of these leukocytes were monitored Novel quantitative flow cytometry studies were employed where the selectin ligand PSGL-1 (P-selectin Glycoprotein Ligand-1) from cell lysates was immunoprecipitated onto polystyrene beads and subsequently probed with antibodies to glycan epitopes Western blot studies were done to verify and substantiate the glycosylation changes in PSGL-1 as observed by flow cytometry studies RESULTS Treatment with a modified analog of sugar was able to alter the carbohydrate structure on glycoproteins and reduce the selectin binding function of leukocytes Flow Cytometry studies with immunoprecipitated PSGL-1 ligand from treated cells confirmed the glycan changes in this glycoprotein The PSGL-1 isolated from these cells migrated faster than those from untreated cells in western blots CONCLUSION Alteration in glycosylation associated with PSGL-1 ligand resulted in reduced leukocyte binding consistent with the hypothesis of metabolic modification by sugar analogs Key Words Glycosyltransferases Selectin Leukocytes Sugars

p 19 of 44

15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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15 Solution Structure Of Human Von Willebrand Factor Studied Using Small Angle Neutron Scattering

Indrajeet Singh Sriram Neelamegham Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 Web httpwwwengbuffaloedu~neel email neelengbuffaloedu Von Willebrand factor (VWF) binding to platelets under high fluid shear is an important step regulating atherothrombosis We applied light and small-angle neutron scattering to study the solution structure of human VWF multimers and protomer Results suggest that these proteins resemble prolate ellipsoids with radius of gyration (Rg) of ~75nm and ~30nm for multimer and protomer respectively The ellipsoid dimensionsradii are 175times28nm for multimers and 70times91nm for protomers Substructural repeat domains are evident within multimeric-VWF that are indicative of elements of the protomer quarternary structure (16nm) and individual functional domains (45nm) Amino acids occupy only ~2 of the multimer and protomer volume compared to 98 for serum albumin and 35 for fibrinogen VWF treatment with GuanidineHCl which increases VWF susceptibility to proteolysis by ADAMTS-13 causes local structural changes at length scaleslt10nm without altering protein Rg Treatment of multimer but not protomer-VWF with random homobifunctional linker BS3 prior to reduction of inter-monomer disulfide linkages and western blotting reveals a pattern of dimer and trimer units that indicate the presence of stable inter-monomer non-covalent interactions within the multimer Overall multimeric VWF appears to be a loosely packed ellipsoidal protein with non-covalent interactions between different monomer units stabilizing its solution structure Local changes in multimer conformation are sufficient for ADAMTS-13 mediated proteolysis

p 20 of 44

16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

[A20mRNA]n21

[A20mRNA_deg]n

A20_deg

v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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16 From Ligand Binding To Transcription An Integrated Model For Tumor Necrosis Factor Induced NF-κB Activation

Gang Liu and Sriram Neelamegham Department of Chemical and Biological Engineering State University of New York Buffalo NY 14260 USA Email neelengbuffaloedu Tumor necrosis factor (TNF)-induced Nuclear Factor kappa B (NF-κB) signaling plays an important role in regulating cell function and human inflammatory ailments Blockers of TNF activity including antibodies and soluble TNF receptor have found clinical application We constructed a computational model for TNF induced signaling that couples TNF receptor activation complex formation with the IκB Kinase (IKK)-NF-κB module The model incorporates the effects of A20 which triggers Receptor Interacting Protein (RIP) degradation This computational model considers both the negative-feedbacks imposed by IκB and A20 Parameters in the model are shown to fit several recent data sets in published literature Also published experimental data over a range of TNF dose fit the model SensitivityPerturbation analysis predicts key reactions the variation of which may alter the magnitude and nature of nuclear NF-κB oscillations In particular the simulations suggest that the time-dependent change in phosphorylated IKK levels is a key parameter that regulates the period of NF-κB oscillation Key Words Systems Biology Tumor Necrosis Factor NF-κB Computational Biology Biochemical Feedback Sensitivity Analysis

14A20

[IκBmRNA_deg]n

IKK

IKK

TNFα_TNFR1_TRADD_RIP_TRAF2_MEKK3_IKK13

12v6

v5

11

9

10

TNFα_TNFR1_TRADD_TRAF2_RIP

TNFα_TNFR1_TRADD_RIP_TRAF2-MEKK3

MEKK3

TNFα TNFα_TNFR1TNFR1+TRADD

TNFα_TNFR1_TRADDTRAF2

TNFα_TNFR1_TRADD_TRAF2RIP

v11 2 3

4

5

6

78v4

v3

v2

v7

v15

v20

v19

v22

v21

IκB_NF-κB

+

NF-κBv16v14

v13

v31IKK_IκB

22

19

15 18 25

v12v11

v9

v10

v17

v8

17

IκB v28

16

IKK(i)_deg

IKKi

IKK_IκB_NF-κB

IκB_deg

Cytoplasm

[IκB_NF-κB]nNucleus

[IκB]n23 26

24

16

Transcriptionv27

v29

v25[NF-κB]n

[IκBmRNA]nv30

v23

v24

v18

20

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v26

p 21 of 44

17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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17 Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Platelet Factor 4 (PF-

4) And Induce Neutrophil Activation And Adhesion

Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1 1 Department of Chemical and Biological Engineering State University of New York at Buffalo 913 Furnas Hall Buffalo NY 14260 2 Department of Pediatrics State University of New York at Buffalo Buffalo NY 14214 Heparin-induced thrombocytopenia (HIT) is a common complication of heparin therapy HIT pathogenesis studies revealed that antibodies recognizing PF4-heparin complex activated platelets through its Fc receptor binding to platelet In this project we investigated neutrophil activation induced by recombinant PF4 (rPF4) or PF4 purified from human platelets (hPF4) in the presence of antibodies to PF4 Our results showed neutrophil activation marked by Mac-1 upregulation and neutrophil shape change was induced by costimulation of PF4 and monoclonal anti-PF4 antibodies (clone 1972 and 1973) but not by PF4 or antibodies alone nor by costimulation of PF4 and isotype control antibody Mac-1 upregulation was mediated through Fc receptor (FcγRIIa or CD32a) since anti-CD32a monoclonal antibody IV3 abrogated this activation Confocal microscopy revealed clustering and colocalization of PF4 and FcγRIIa upon neutrophil activation Inhibition studies showed heparin and Chondroitinase ABC abolished PF4 binding and neutrophil activation To study activation domain(s) point mutation was introduced by changing specific amino acid(s) of hPF4 to those of rat PF4 since rat PF4 failed to induce neutrophil activation Arginine49 was important for PF4 binding to neutrophil Mutation of PTA37-39 domain increased PF4 binding to neutrophil but reduced antibody binding and Mac-1 upregulation Another important neutrophil activation domain is Leucine55 Mac-1 upregulation was proved to be functional in mediating homotypic aggregation under shear 30 aggregation was formed after shearing rPF4 and 1972 primed neutrophil for 25min Inhibition studies proved aggregation was partially mediated by Mac-1 and PF4 was able to bridge neutrophil homotypic aggregation with the help of Mac-1 Key Words Platelet factor 4 Mac-1 upregulation FcγRIIa adhesion Heparin-Induced Thrombocytopenia

p 22 of 44

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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 DAN 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 NLD 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 ESP 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 SUO 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 ITA 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 NOR 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 SVE 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 gtgtgtgt setdistillerparamsltlt HWResolution [2400 2400] PageSize [612000 792000]gtgt setpagedevice

18 Exploring Intercellular Channels With A Hindered Diffusion Model Of Ion Transport

Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1 1 Department of Chemical amp Biological Engineering SUNY at Buffalo NY 14260 2 Department of Biochemistry UTHSCSA San Antonio TX Web httpwwwbiochemuthscsaedu~bjn email nicholsonbuthscsaedu Objective Gap junctions are intercellular channels that connect and transfer ionssignaling molecules and metabolites between the cytoplasm of two neighboring cells Their role in mediating intercellular signaling is crucial to homeostasis and electrical synchronization of heart beat Loss of their constituent protein connexin (Cx) produces disease states related to impeded ion transfer like partial cardiac conductance block (Cx40) and ventricular arrhythmias (Cx43) in the heart This study involved development of a pore-scale hindered diffusion model to understand the underlying mechanism of ion transport through gap junctions and to assess the influence of charged amino acids in the channel wall on conductance Methods A realistic axisymmetric channel geometry of a Cx43 channel is constructed (source Protein Data Bank) The governing ionic flux equations consisted of concentration as well as electrical gradient across the channel and are coupled with the Poisson equation of charge distribution Hydrodynamic calculations are done to estimate the diffusivity of ions in these channels Finite difference technique is used to solve the equations numerically Results The current-voltage characteristic of a neutral pore is found to be linear from these simulations as expected in such channels The conductance obtained from our model correlates well with the values obtained using the Goldman-Hodgkin-Katz formulation used widely in literature The conductance is 3-fold higher than the experimentally observed values indicative of the influence of structural features like the distribution of charges on the channel wall on conductance Conclusion The hindered diffusion model developed in this study can be used as an effective tool to investigate the effect of features like size shape and charge distribution of the gap junction Key Words Connexin ion conductance hindered diffusion

p 23 of 44

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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 ITA ltFEFF00550073006100720065002000710075006500730074006500200069006d0070006f007300740061007a0069006f006e00690020007000650072002000630072006500610072006500200064006f00630075006d0065006e00740069002000500044004600200063006f006e00200075006e00610020007200690073006f006c0075007a0069006f006e00650020006d0061006700670069006f00720065002000700065007200200075006e00610020007100750061006c0069007400e00020006400690020007300740061006d007000610020006d00690067006c0069006f00720065002e0020004900200064006f00630075006d0065006e00740069002000500044004600200070006f00730073006f006e006f0020006500730073006500720065002000610070006500720074006900200063006f006e0020004100630072006f00620061007400200065002000520065006100640065007200200035002e003000200065002000760065007200730069006f006e006900200073007500630063006500730073006900760065002egt NOR 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 SVE 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 gtgtgtgt setdistillerparamsltlt HWResolution [2400 2400] PageSize [612000 792000]gtgt setpagedevice

19 A Computational Model Of Transient DrugChemical Diffusion Through Human Skin In The Vicinity Of A Hair Follicle

Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1

1Department of Chemical and Biological Engineering State University of New York University at Buffalo Furnas Hall Buffalo New York 14260-4200 httpwwwcbebuffaloedunitschehtm yhdancikbuffaloedu 2College of Pharmacy University of Cincinnati Medical Center OH 45267-0004 httpwww pharmacyucedu kastingbucmailucedu This paper addresses the manner in which chemicals applied to skin penetrate into dermal tissue around hair follicles Aside from follicular drug delivery per se quantitative modeling of this process is important to topical and transdermal drug delivery generally as well as risk assessment of chemical exposure because hair follicles and other appendages can contribute significantly to skin permeability by providing shunt pathways through the epidermal barrier A comprehensive finite difference model has been developed to solve the transient diffusion equation describing transport of an unionized chemical species through skin in a large cylindrical volume surrounding a realistic geometrical representation of the hair follicle The numerical technique introduces a novel non-orthogonal coordinate system fitted to the follicles outer boundary Inputs to the calculation are the partition and diffusion coefficients of the applied drug in each skin layer the permeability of the outer root sheath (ORS) taken as the hair folliclersquos outer boundary and volumetric rate coefficients describing clearance into the systemic circulation Concentration profiles for a model permeant representing the lipophilic dye Bodipy FLreg C5 (BFL) were obtained for upper and lower bound estimates on the permeability of the ORS and compared to experimentally obtained published in vitro (no clearance via the vasculature) dye distributions around hair follicles The results show the infundibulum to be the structure via which the hair follicle increases permeation into dermal tissue A simulation of the in vivo permeation of BFL shows that typical levels of clearance by the vasculature decrease average dermal concentrations by 80 to 90 Key words hair follicle percutaneous penetration mathematical model diffusion

p 24 of 44

20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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20 Propagation Of Pluripotent Embryonic Stem Cells Under Serum-Free

Conditions In A Scalable Bioreactor

Daniel E Kehoe and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Because embryonic stem cells (ESCs) are capable of becoming any cell type in the body they are an ideal starting material for many clinical applications Such ESC-based therapies will require production of undifferentiated stem cells in large quantities Currently undifferentiated stem cells are cultured as a monolayer (2-D) Our research explores the possibility of generating ESCs in a stirred tank reactor which is amendable to scale up and provides better control of process variables than typical 2-D culture systems

Initially mouse ESCs (mESCs) were expanded as pluripotent aggregates in a suspension bioreactor with culture volumes of 50 ml An average of 40-fold expansion was achieved in a 4-day period while cell viability was above 85 Cultured mESC expressed comparable levels of Oct-4 SSEA-1 Nanog and Rex-1 with mESCs cultured in static cultures Cell pluripotency did not diminish even after multiple passages in a suspension bioreactor In addition mESCs propagated in this culture system were successfully employed in differentiation assays Furthermore control of the average size of the pluripotent aggregates was achieved by modulating the agitation rate By lowering the impeller speed from 100 rpm to 60 rpm the average aggregate size almost doubled after four days of culture

Subsequently the bioreactor cultures were scaled-up to larger working volumes The increase in culture volume substantially boosted the total number of viable cells over the culture period Compared to smaller scale cultures cell number increased as the volume increased with a similar overall fold increase Maintenance of cultured mESC pluripotency was confirmed by the presence of corresponding markers and differentiation assays similar to smaller volume bioreactor experiments

Fetal Bovine Serum (FBS) which is currently used for the culture of ESCs increases substantially the cost of the culture medium limiting efforts for the development of systems with larger volumes compared to laboratory scale bioreactors In addition the use of FBS for the culture of ESCs introduces undesirable animal products For clinical applications removal of animal products is important so the ESCs do not carry over pathogens from the media to engineered products We have successfully used a defined medium replacing FBS-supplemented medium for the culture of ESCs This defined medium does not have the lot-to-lot variability associated with FBS containing medium After three successive passages in a serum-free bioreactor we were able to sustain a 15-fold increase of viable cells

This study bolsters the implementation of stirred-tank bioreactors for the expansion of uncommitted stem cells for use in a clinical setting and eases the transition to a large scale 3-D culture Although mESCs were used in this study as a model the findings will contribute to the development of culture systems for the expansion of human embryonic stem cells in clinically relevant scales for utilization as therapeutics

Keywords Stem cells serum-free bioreactor scale-up

p 25 of 44

21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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21 Effects Of Flavonoids On Pancreatic β-Cell Insulin Regulation

Lye T Lock M Koffas and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Flavonoids are natural phenolic compounds found in plants Over 4000 structurally unique flavonoids had been discovered in plant sources so far Various studies have shown that flavonoids have antioxidant properties and may be used as anticancer agents In addition flavonoids are known to affect metabolic and signaling moieties which act as intracellular mediators of insulin function in response to glucose in pancreatic β-cells

Our study focused on the effect of flavonoids on pancreatic β-cell insulin regulation Type 2 diabetes patients are characterized by insulin resistance due to increasing obesity aging or illness To that end pancreatic insulin release must be augmented to compensate for insulin resistance Evidently molecules with insulinotropic properties are ideal candidates as pharmacological agents for the treatment of diabetic patients

We examined the insulinotropic properties for various natural and unnatural compounds isolated from plants or produced by recombinant microorganisms Catechin apigenin and naringenin were shown to modulate the secretory characteristics of pancreatic β-cells at various concentrations Upon glucose stimulation the amount of secreted insulin was enhanced in β-cells treated with 1-100 microM of each of the above compounds compared to untreated cells Similarly eriodictyol and afzelechin enhanced insulin secretion under stimulatory glucose concentrations However no significant changes were observed in the insulin content under the conditions we investigated Insulin secretion is mediated by cyclic AMP (cAMP) To that end increases in glucose-stimulated insulin secretion due to incubation of β-cells with a flavonoid were concomitant with increases in the levels of cAMP The transcription of preproinsulin gene was also examined in flavonoid-treated cells Eriodictyol-treated cells showed higher levels of preproinsulin mRNA compared to controls These results suggest that the compounds studied here exhibit insulinotropic properties and warrant further investigation into the mechanisms by which flavonoids alter pancreatic β-cell insulin function The outcome of this work may help in the development of novel therapeutics for diabetes as well as shed light on Type 2 diabetes etiology

Keywords Pancreatic β-cells diabetes flavonoids insulin cyclic AMP

p 26 of 44

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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 ITA 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 NOR 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 SVE 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 gtgtgtgt setdistillerparamsltlt HWResolution [2400 2400] PageSize [612000 792000]gtgt setpagedevice

22 Crosstalk Between Wnt Signaling And Insulin Regulatory Network In Pancreatic β-Cells

Dong Hui Jing and E S Tzanakakis Department of Chemical and Biological Engineering State University of New York at Buffalo Furnas Hall Buffalo New York 14260-4200

Wnts are a family of secreted glycoproteins that play essential roles in directing cell patterning growth and differentiation both during development and in adult tissues Wnt signaling through the so-called canonical pathway is mediated by a family of receptor proteins Frizzled (Fz) which prevent the glycogen synthase kinase-3β (GSK-3β) from phosphorylating β-catenin This enables β-catenin stabilization and translocation to the nucleus where it binds transcription factors of the T-cell factor (TCF)lymphoid enhancer factor (LEF) family

Although the Wnt pathway has been investigated in the contexts of development and cancer recent reports have pointed to other roles that this pathway may play in various functions including insulin regulation Cells cultured with Wnt3a markedly stimulate glucose-induced insulin secretion Deletion of the β-catenin gene in the epithelium of the pancreas and duodenum in transgenic mouse embryos leads to a reduction in endocrine islet numbers indicating the importance of Wnt signaling in pancreatic development Aberrant Wnt signal transduction may also be involved in pancreas pathologies such as diabetes and pancreatic adenocarcinoma These findings intimately link Wnt signaling and pancreatic β-cells and warrant further investigation

We set out to gain a better understanding of the role of Wnt signaling in insulin function of pancreatic β-cells As a first step towards this goal we have developed experimental methods necessary for subsequent studies Initially a method was established for activating the canonical Wnt signaling in human (HEK293) and mouse (NIH3T3) cells which are known to have an intact Wnt pathway Signaling activation by Wnt ligands was probed via monitoring of the translocation and accumulation of β-catenin in the nucleus Wnt activation was also tested by employing a reporter assay involving promoter sequences targeted by Wnt Preliminary results suggest that the canonical pathway in β-cell lines cannot be directly activated by Wnt ligands or inhibitors of GSK-3β This may be linked to the elevated glucose levels that β-cell lines experience in culture akin to the environment of islet cells of Type 2 diabetes patients This possible link warrants further investigation especially considering that Wnt activation in islets was shown to result in increased insulin secretion in response to glucose Keywords Wnt diabetes insulin pancreatic β-cells β-catenin

p 27 of 44

NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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NANOSCALE MATERIALS SCIENCE AND ENGINEERING 23 Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis

Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3

1 Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 E-mail hzhang5buffaloedu 2 Department of Chemistry University at Buffalo Natural Science Complex Buffalo NY 14260-4200 3 Chemical and Biological Engineering University at Buffalo 506 Furnas Hall Buffalo NY 14260-4200 httpwwwchemebuffaloeduswihart E-mail swihartengbuffaloedu Zinc sulfide is a II-VI semiconductor with a direct band gap in the near-UV region Here we demonstrate the preparation of ZnS nanoparticles (NPs) by spray pyrolysis using zinc diethyldithiocarbamate as a single-source precursor Solutions of this precursor in toluene are dispersed into fine droplets by an atomizer and then carried into a tube furnace where they evaporate fully and ZnS NPs nucleate from the vapor phase The NPs were characterized by transmission electron microscopy (TEM) high-resolution TEM (HRTEM) and optical spectroscopies The NPs are about 3 ndash 20 nm in diameter and are crystalline as indicated by the presence of lattice fringes in HRTEM and by selective-area electron diffraction Their XRD pattern shows a single peak indexed to the (111) plane of the cubic zinc blende lattice The UV absorption spectrum shows peaks in the range of 330-380 nm and the NPrsquos exhibit bright blue photoluminescent emission under UV illumination The presence of heterogeneous ZnS ldquonanorodsrdquo was also observed in ZnS NPs dispersions These nanorods were probably formed by ldquooriented attachmentrdquo from ZnS NPs HRTEM imaging shows that the lattice spacing is 263 Aring corresponding to the (200) plane of the cubic zinc blende structure of ZnS Small nanorods (10 nm 50 nm) appear to have formed directly from gas phase in some cases The formation mechanism in this case has not been identified Key Words Zinc sulfide spray pyrolysis nanoparticle aerosol and semiconductor

p 28 of 44

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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 ITA 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 NOR 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 SVE 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 gtgtgtgt setdistillerparamsltlt HWResolution [2400 2400] PageSize [612000 792000]gtgt setpagedevice

24 Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyrolysis

Hongwang Zhang and Mark T Swihart Chemical and Biological Engineering University at Buffalo 404 Furnas Hall Buffalo NY 14260-4200 httpwwwbuffaloedu~hzhang5 Tellurite glasses have two useful optical properties high refractive index and high optical nonlinearity that make them attractive for a range of applications Unlike other metal oxide nanoparticles that are prepared in large quantities by vapor phase processes TeO2 nanoparticles have not been prepared by such methods We describe the vapor-phase synthesis of TeO2 nanoparticles from an aqueous solution of Te(OH)6 that is dispersed into fine droplets by an atomizer These droplets are carried through a furnace where they evaporate and decompose resulting in nucleation of TeO2 nanoparticles The nanoparticles were characterized by TEM XPS FTIR and XRD Particle size distributions measured online using a scanning mobility particle spectrometer demonstrated that a furnace temperature above 700 ordmC was required for full evaporation of the precursor droplets Thermogravimetric analysis shows that the Te(OH)6 converts to TeO2 without evaporating when heated at 5 to 100 ordmCmin This contrasts sharply with the complete evaporation observed in the spray pyrolysis reactor where heating rates exceed 50000 ordmCmin The effects of operating parameters on nanoparticle composition production rate and size were also studied This laboratory-scale process is producing up to 80 mghr of TeO2 nanoparticles with particle diameters from 10 to 40 nm Particles this small exhibit negligible scattering of visible light and have potential applications in the linear and nonlinear refractive index engineering of polymer nanocomposites and as host matrices for rare-earth ions acting as IR to visible upconverters The method allows their synthesis in macroscopic quantities from an inexpensive and environmentally friendly precursor Key Words Tellurium dioxides telluria spray pyrolysis nanoparticle aerosol

p 29 of 44

25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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25 Control Mechanisms For The Molecular Assembly Of Amphiphiles

Christopher L Wirth Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY 14260-4200 Recent technological advances have allowed scientists and engineers to make significant progress in the field of nano- to micro- scale structured materials Targeted drug delivery systems and inorganic nanomaterials have huge potential in the health and energy industries while nanowires synthesized by a polymer template have the potential to make our wildest computing dreams a reality These are just a few examples of an extremely robust research area However at the heart of all the grandiose nano-structured dreams are a few straightforward yet mind-bendingly difficult questions centered on the production and control of such materials Motivated by this we considered the formation and structure of surfactant micelles in aqueous solutions in the presence of molecules that can interact with the surfactant or with the solvent water In particular we considered the solution properties of the ldquomodelrdquo surfactant sodium dodecyl sulfate (SDS) in the presence of cyclodextrins (CDs) and alkanols by means of conductivity measurements The cavity afforded by α-CD or (2-Hydroxypropyl)-β-CD molecules can accommodate the water-insoluble alkyl part of SDS forming a supramolecular complex and thus modulating the critical micellization concentration (CMC) at which SDS molecules start to self-assemble Currently we are investigating this control mechanism as a functional component in a non-toxic aqueous phase ldquobottom-uprdquo synthesis of gold (Au) particles Our group has recently demonstrated that an ionic surfactant SDS enhances particle synthesis kinetics

p 30 of 44

26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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26 Water Gas Shift Over Iron Oxide Catalysts

Rainee VanNatter Carl RL Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 E-mail lundengbuffaloedu Quantum chemical calculations and microkinetic modeling are being carried out to study the water gas shift reaction over iron oxide catalysts Different model surfaces have been generated from the Fe3O4 single crystal structure The mechanistic thermochemistry of water-gas shift is being studied by computational chemistry using these model surfaces while kinetic modelling is used to compare the computed thermochemistry and energetics to experiment The objective of these comparisons is to determine (1) the oft-disputed mechanism of the water-gas shift reaction over the high-temperature iron-oxide shift catalysts and (2) determine the structure of the catalyst surface The same model surfaces are being used to study the effect of substitutional promoters upon the thermochemistry of water-gas shift For example a model surface corresponding to copper-promoted magnetite was created by replacing an octahedrally coordinated iron cation with a copper cation The thermochemistry has then been calculated using the substituted copper cation as the active site and also using an iron cation adjacent to the copper cation as the active site The objective of these studies is to determine whether Polanyi-type relations exist between various steps in the mechanism and to determine how substitutional promotion affects such relationships A further goal of both these studies is to begin to understand the relationship between catalyst structure and activity Key Words water gas shift iron oxide catalyst quantum chemical calculations

p 31 of 44

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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ltFEFF005500740069006c0069007a006500200065007300740061007300200063006f006e00660069006700750072006100e700f5006500730020007000610072006100200063007200690061007200200064006f00630075006d0065006e0074006f0073002000500044004600200063006f006d00200075006d00610020007200650073006f006c007500e700e3006f00200064006500200069006d006100670065006d0020007300750070006500720069006f0072002000700061007200610020006f006200740065007200200075006d00610020007100750061006c0069006400610064006500200064006500200069006d0070007200650073007300e3006f0020006d0065006c0068006f0072002e0020004f007300200064006f00630075006d0065006e0074006f0073002000500044004600200070006f00640065006d0020007300650072002000610062006500720074006f007300200063006f006d0020006f0020004100630072006f006200610074002c002000520065006100640065007200200035002e0030002000650020007300750070006500720069006f0072002egt DAN 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 ESP 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 SUO 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 ITA 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 NOR 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 SVE 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 gtgtgtgt setdistillerparamsltlt HWResolution [2400 2400] PageSize [612000 792000]gtgt setpagedevice

27 Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites

Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 Molecular sieves or zeolites are crystalline aluminosilicate materials which are comprised of passages containing very specific pore sizes that exclude certain molecules and selectively adsorb others based on differences in molecular diameters Accurate adsorption equilibrium data is information essential to efficiently design and optimize adsorption columns Little is know about how zeolite manufacturers measure their equilibrium data Adsorption isotherms reveal thermodynamic information about the equilibrium relationship between how much water (or ethanol) can be adsorbed onto zeolite structure at different partial pressures and temperatures Technical publications addressing the subject of equilibrium data for water are available but for the waterethanol binary mixture (or ethanol alone) practical literature is almost nonexistent The goal of this study was to conduct gravimetric tests to acquire adsorption equilibrium data across a wide range of partial pressures and temperatures for single components of water and ethanol on 18rdquo and 116rdquo Grace 3Aring and 4Aring molecular sieves Water isotherms were measured with air as a carrier gas resulting in equilibrium data that reasonably matched manufacturer provided data at lower temperatures Ethanol equilibrium was obtained by using helium as a carrier gas Acquired data will be used to design commercial scale adsorber for ethanol-water separation Key Words adsorption equilibria 3A and 4A zeolites water ethanol gravimetry

p 32 of 44

28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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28 Polymer Conformation In Water And Polar Organic Solvents

Eleftheria Antoniou Carlos Buitrago Marina Tsianou Paschalis Alexandridis Department of Chemical and Biological Engineering University at Buffalo The State University of New York 303 Furnas Hall Buffalo NY 14260-4200 E-mail antoniouengbuffaloedu Polymers are widely used in aqueous media to provide structure solubilization domains andor colloidal stability Underlying these functions are inter- and intra-molecular interactions which depend on (i) the nature of the polymers (ii) solution conditions (eg salinity pH) and (iii) external stimuli (eg temperature shear) The solution behavior and interactions of associating polymers can be profoundly affected by the presence in water of polar organic solvents andor solutes which are ubiquitous in pharmaceutical and coating formulations This presentation will highlight our ongoing phase behavior and rheological investigation of solvent and solute effects on polysaccharide polymers The observed effects on the polymer conformation are correlated with the solubility parameters of the solventsolute Key Words rheology Dextran organic solvents solubility parameters polymers

p 33 of 44

MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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MOLECULAR AND MULTISCALE MODELING

29 Water Gas Shift Over Iron Oxide Catalysts Microkinetic Modeling

John S Coleman Carl RF Lund University at Buffalo The State University of New York 303 Furnas Hall (North Campus) Amherst NY 14260 Microkinetic modeling is a powerful tool in heterogeneous catalysis research In our current research this method is being applied to iron-chrome oxide catalysts for the water gas shift reaction A five step mechanism serves as the starting point for detailed kinetics of the reaction on the catalyst surface Comparison with experimental data allows for a detailed model of the reaction to be formed Using this model the effects of activation energies and surface bond strengths can be seen allowing for model predictions to direct new catalyst design Using sensitivity analysis of the model parameters surface oxygen bond strength plays an important role in shaping the overall rate on traditional water gas shift catalysts Decreasing surface oxygen bond strength has shown to increase the overall rate of reaction Using this as a predictive basis copper was added as a promoter to iron-chrome catalysts as it has shown in literature to reduce the peak temperature for the reduction of iron-chrome catalysts Experimental results show an increase in overall conversion of copper promoted iron-chrome compared to traditional iron-chrome catalysts Microkinetic analysis of the experimental results of a copper promoted iron oxide catalyst is included to show the correlations of predictive results from the initial model to catalyst composition changes Key Words water gas shift iron oxide catalyst microkinetic modeling

p 34 of 44

30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

p 35 of 44

31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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30 Exploring The Phase Behaviour Of A Simple Model Protein Using Molecular Simulation

Thomas W Rosch Jeffrey R Errington University at Buffalo State University of New York Buffalo NY 14620 E-mail jerringbuffaloedu Many neurological diseases cataracts and sickle-cell diseases are linked to protein phase separationaggregation At the heart of these phenomena are protein-protein interactions It is known that these interactions are influenced by numerous physiological factors such as salt concentration pH and temperature The variation of any of these factors can lead to significant changes in protein phase stability and behavior yet to this day a systematic approach to quantitatively predict these changes a priori in conjunction with a comprehensive understanding of molecular level interaction is currently unavailable It has been found by George and Wilson1 that there exists a small range of protein-protein attraction leading to crystallization It has also been found by ten Wolde and Frankel2 that protein crystallization and nucleation may be enhanced by liquid-liquid phase separation In light of these recent advances we perform Grand Canonical Monte Carlo simulations to probe protein phase stability using a simple model introduced by Carlsson et al3 Lysozyme is modeled as a spherical protein with embedded charged residues that are pH dependent This model incorporates experimental information from the Protein Data Bank to create realistic charge as well as the location of these residues in hopes of gaining insight into molecular level protein-protein interactions that cause macrostate phenomena References 1 George A Wilson W W Predicting Protein Crystallization from a Dilute-Solution Property Acta Crystallographica Section D-Biological Crystallography 1994 50 361-365 2 tenWolde P R Frenkel D Enhancement of protein crystal nucleation by critical density fluctuations Science 1997 277 (5334) 1975-1978 3 Carlsson F Malmsten M Linse P Monte Carlo simulations of lysozyme self-association in aqueous solution Journal of Physical Chemistry B 2001 105 (48) 12189-12195

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31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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31 Orthogonal Polynomial Method to Compute the Density of States

Tai Boon Tan David A Kofke Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 httpwwwcbebuffaloedu E-mail taitanbuffaloedu Density of states (DOS) is a property in statistical physics that quantifies how populated energy levels are in a physical system The accuracy and efficiency in computation for the DOS are important because it prepares a path to obtain the thermodynamic quantities such as energy entropy and free energy Previously the histogram reweighting method has been employed for density-of-states calculation This method can be used in multidimensional form eg to relate simulation data at different temperatures and chemical potentials With the motivation of further improving the computational accuracy we aim to develop a new method to calculate the DOS through the implementation of an orthogonal-basis representation In this approach the DOS is represented by an arbitrary set of functions that are orthogonal over the states of interest The basis coefficients are given by simple ensemble averages from the simulation We will also investigate combining orthogonal basis representations into a biased reweighting scheme to produce a wide-spanning DOS similar in nature to that done in conventional histogram reweighting method As a test case we carry out our implementation using an orthogonal basis applied to Monte Carlo simulations of a 3-D Yukawa model In order to demonstrate the accuracy and the validity of this method the results from the orthogonal polynomial computation are compared with single histogram method and histogram reweighting methods With this improved method we expect to have more simplified data representation than the single histogram and better information over a range of values of DOS

p 36 of 44

32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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32 Computer Simulations in Complex Fluids

Jie Feng Eli Ruckenstein Chemical and Biological Engineering Department State University of New York at Buffalo Buffalo New York 14260 E-mail jiefengbuffalo feaelirubuffaloedu Three kinds of complex fluids namely polymer melts polyelectrolytes and nano particles have been investigated by computer simulations Because the morphologies of block copolymer melts become disordered at long range without external fields the control of the formation and orientation of the nano-structures to generate long-range ordered structures is important from both fundamental and technological points of view By applying Monte Carlo simulation and Cell Dynamics the nano-structures of the block copolymer melts under short-range (eg surface field) and long-range fields (eg electric and shear fields) have been predicted The conformations and phase behavior of polyelectrolytes are important issues from a fundamental point of view as well as because of their numerous potential applications to nano-materials drug delivery etc By employing Monte Carlo simulations the self-assembly in systems of polyelectrolytes with opposite charges as well as the complexes of charged particles and polyelectrolytes have been investigated Additionally the collective interactions between identical charged particles have been examined via Monte Carlo simulations The results have shown that when the number of charges per particle and the particle volume fraction were sufficiently large the pair long-range electrostatic repulsion generated an effective attractive interaction between identically charged particles because of many-body effects Disordered liquid like structures and ordered crystal like structures have been found in the simulations Key Words Computer Simulation Monte Carlo Cell Dynamical System Complex Fluids Polymer polyelectrolytre Nano particle

p 37 of 44

33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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33 Modeling Of Industrial Pressure Swing Adsorption Process For Fuel Ethanol Production

Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1

1 Dept of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 E-mail msimo2buffaloedu 2 Thermal Kinetics Systems LLC 667 Tifft St Buffalo NY 14220 E-mail cjbthermalkineticsnet Dehydration of ethanol on 3Aring molecular sieves is successful alternative to the conventional separation techniques for breaking the ethanol-water azeotrope In the production process aqueous ethanol from fermentation is concentrated in the distillation columns In order to achieve gt995 purity the final purification of ethanol is done by pressure swing adsorption (PSA) using hydrophilic zeolite A simulation package for the PSA process based on the data from an operating plant has been developed Adiabatic dispersed plug flow model includes variation of axial velocity and pressure drop Adsorption equilibrium data were provided by adsorbent manufacturer Linear driving force mass-transfer-rate coefficient was used to describe adsorption and desorption kinetics The set of governing partial differential equations has been solved via method of lines using a high order approximation scheme The resulting system of stiff differential equations has been integrated by the GEARrsquos method The model has been used to investigate current operating conditions of the plant and also the transient start-up of PSA unit It was found that the flowrate of purge stream has significant effect on the overall performance Key Words pressure swing adsorption fuel ethanol production water adsorption 3A zeolite method of lines

p 38 of 44

34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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34 Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu Solder Using Transition Path Sampling

Michael S Sellers1 Katherine R Schadel David A Kofke2 Cemal Basaran3

1 Department of Chemical Engineering University at Buffalo 514 Furnas Hall E-mail msellersengbuffaloedu 2 Department of Chemical Engineering University at Buffalo 306 Furnas Hall E-mail kofkeengbuffaloedu 3 Department of Civil Engineering Electronics Packaging Laboratory 102 Ketter Hall E-mail cjbengbuffaloedu The cracking and subsequent failure of solder joints in integrated circuit devices is caused by an electrical current induced diffusion of metal ions dubbed electromigration In the normal use of todayrsquos lead-free electronics this process manifests itself over a period of years Microprocessors continue to shrink and increase in speed however as we move into the age of nanotechnology Already we are beginning to see a decrease in the conducting surface area of the solder ball and an increase in the current needed to power these faster nano-scale devices This physical scaling produces large current densities in excess of 10E6 Ampcm2 that in combination with the lead-free solder can expedite this process and create observable bulging and void formation at opposite ends of the solder ballmdasha recipe for quick failure of the interconnect An ongoing collaborative effort with Prof Basaranrsquos Electronic Packaging Laboratory is in place to study electromigration and create a computational model to understand this failure process Grain boundaries are thought to allow for diffusion that is four to six orders of magnitude larger than volume type diffusion creating a ldquoshort circuitrdquo path for metal atoms to traverse Accordingly the present state of our effort is to provide Basaran with diffusion coefficients and activation energies of Sn Cu and Ag along grain boundaries in the solder alloy We intend to simulate diffusion through different types of grain boundaries using Baskesrsquo Modified Embedded Atom Method as an interatomic potential and Chandler et alrsquos Transition Path Sampling technique to induce the rare event of an atom hop Key Words electromigration grain boundary MEAM transition path

p 39 of 44

35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

• Biological Engineering
• In Silico Simulation Of Genome-Scale Intracellular Flux Mode
• • Zachary L Fowler William Gikandi and Mattheos AG Koffas
  • • Engineering Escherichia Coli For Plant Pharmaceutics Product
    • • Effendi Leonard and Mattheos Koffas
      • • Mutasynthesis Of Novel Unnatural Flavonoids
        • • Joseph A Chemler Mattheos Koffas
          • • Engineering The E Coli UDP-Glucose Synthesis Pathway For An
            • • Zhen Li Yajun Yan and Mattheos Koffas
              • • Engineering Plant Pigment Biosynthesis In Escherichia Coli
                • • Yajun Yan Zhen Li and Mattheos Koffas
                  • • Exploring Metabolons For Improvement In Plant-Specific Flava
                    • • Kok Hong Lim Effendi Leonard and Mattheos AG Koffas
                      • • Recycling Acetate For Improvement Of Flavonoid Productions F
                        • • Phanee Saw Kok-Hong Lim Effendi Leonard Mattheos Koffas
                          • • Characterization Of Bone Marrow Derived Smooth Muscle Cells
                            • • Hao Fan Peng Jin Yu Liu Lan Yao and Stelios T Andreadis
                              • • Purification Of Recombinant Retrovirus For Gene Therapy
                                • • Deepa Makkar Stelios T Andreadis
                                  • • Involvement Of The CCAATEnhancer-Binding Proteins In The In
                                    • • Juhee Han Piyush Koria and Stelios T Andreadis
                                      • • Distinct CCAATEnhancer Binding Protein Isoforms Mediate Ker
                                        • • Piyush Koria amp Stelios T Andreadis
                                          • • EGFR Signaling Pathways Affect Retroviral Gene Transfer To E
                                            • • Raghvendra Singh Stelios T Andreadis
                                              • • The Role Of The JNK Pathway In Lentiviral Transduction Proce
                                                • • Meng Horng Lee and Stelios T Andreadis
                                                  • • A Synthetic Sugar As A Potential Anti-Inflammatory Drug
                                                    • • Dhananjay D Marathe1 E V Chandrasekaran2 J Xue2 Khush
                                                      • • Solution Structure Of Human Von Willebrand Factor Studied Us
                                                        • • Indrajeet Singh Sriram Neelamegham
                                                          • • From Ligand Binding To Transcription An Integrated Model Fo
                                                            • • Gang Liu and Sriram Neelamegham
                                                              • • Anti-PF4 Antibodies Recognize Neutrophil Surface Bound Plate
                                                                • • Zhihua Xiao1 Gian Paolo Visentin2 Sriram Neelamegham1
                                                                  • • Exploring Intercellular Channels With A Hindered Diffusion M
                                                                    • • Anshu Verma1 Bruce J Nicholson2 Johannes M Nitsche1
                                                                      • • A Computational Model Of Transient DrugChemical Diffusion T
                                                                        • • Yuri Dancik1 Gerald B Kasting2 and Johannes M Nitsche1
                                                                          • • Propagation Of Pluripotent Embryonic Stem Cells Under Serum-
                                                                            • • Daniel E Kehoe and E S Tzanakakis
                                                                              • • Effects Of Flavonoids On Pancreatic -Cell Insulin Regulatio
                                                                                • • Lye T Lock M Koffas and E S Tzanakakis
                                                                                  • • Crosstalk Between Wnt Signaling And Insulin Regulatory Netwo
                                                                                    • • Dong Hui Jing and E S Tzanakakis
                                                                                      • • Nanoscale Materials Science and Engineering
                                                                                        • Synthesis of Zinc Sulfide Nanaparticles by Spray Pyrolysis
                                                                                        • • Hongwang Zhang1 Ken-Tye Yong2 and Mark T Swihart3
                                                                                          • • Synthesis of Tellurium Dioxide Nanoparticles by Spray Pyroly
                                                                                            • • Hongwang Zhang and Mark T Swihart
                                                                                              • • Control Mechanisms For The Molecular Assembly Of Amphiphiles
                                                                                                • • Christopher L Wirth Marina Tsianou Paschalis Alexandridis
                                                                                                  • • Water Gas Shift Over Iron Oxide Catalysts
                                                                                                    • • Rainee VanNatter Carl RL Lund
                                                                                                      • • Adsorption of Ethanol and Water Vapors on 3Aring and 4Aring Zeolites
                                                                                                        • • Daniel M Leo1 Marian Simo1 Christopher J Brown2 and Vlad
                                                                                                          • • Polymer Conformation In Water And Polar Organic Solvents
                                                                                                            • • Eleftheria Antoniou Carlos Buitrago Marina Tsianou Pascha
                                                                                                              • • Molecular and Multiscale modeling
                                                                                                                • Water Gas Shift Over Iron Oxide Catalysts Microkinetic Mode
                                                                                                                • • John S Coleman Carl RF Lund
                                                                                                                  • • Exploring The Phase Behaviour Of A Simple Model Protein Usin
                                                                                                                    • • Thomas W Rosch Jeffrey R Errington
                                                                                                                      • • Orthogonal Polynomial Method to Compute the Density of State
                                                                                                                        • • Tai Boon Tan David A Kofke
                                                                                                                          • • Computer Simulations in Complex Fluids
                                                                                                                            • • Jie Feng Eli Ruckenstein
                                                                                                                              • • Modeling Of Industrial Pressure Swing Adsorption Process For
                                                                                                                                • • Marian Simo1 Christopher J Brown2 Vladimir Hlavacek1
                                                                                                                                  • • Atomistic Modeling Of Grain Boundary Diffusion In Sn-Ag-Cu S
                                                                                                                                    • • Michael S Sellers1 Katherine R Schadel David A Kofke2
                                                                                                                                      • • A Computational Study Of The Properties Of Water Near A Prot
                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
                                                                                                                                          • • Relationship Between The Thermodynamics And Dynamics Of A Mo
                                                                                                                                            • • Ravi Chopra Jeffrey R Errington
                                                                                                                                              • • Determining Contact Angles From Molecular Simulation
                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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35 A Computational Study Of The Properties Of Water Near A Protein Surface With Added Solute

Eric C Cichowski Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo New York 14260-4200 In this presentation we describe a project involving the use of molecular dynamics simulations to obtain a better understanding of the behavior of proteins in aqueous solution The current focus of the project is aimed at relating kinetic thermodynamic and structural properties of water molecules in the vicinity of a protein As a start to the project a five to ten amino acid chain will be simulated We have developed a molecular dynamics simulation program that enables us to examine the system described above The simulation uses the CHARMM force field and the parameters associated with it Properties of interest in this study are the diffusive and rotational mobility of water as it nears the peptide surface and how these properties are decoupled Through the use of this simulation it is hoped to gain a better understanding of the kinetics involved between water and a peptide and how these relate to the stability of the peptide Key Words molecular dynamics water simulations CHARMM protein simulations

p 40 of 44

36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

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                                                                                                                                        • • Eric C Cichowski Jeffrey R Errington
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                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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36 Relationship Between The Thermodynamics And Dynamics Of A Molecular Fluid

Ravi Chopra Jeffrey R ErringtonDepartment of Chemical and Biological Engineering University at Buffalo State University of New York Buffalo New York 14260-4200 Transport coefficients of liquids such as diffusion and viscosity are not only important for understanding liquid structures and thermophysical behaviors of liquids but also studying the flow behaviors in practical engineering applications Despite the importance there are currently no rigorous relationships connecting thermodynamic and transport properties of a liquid However a number of empirical scaling relationships have been developed which relate the two Rosenfeld [Phys Rev A 15 2545 (1977)] proposed a lsquouniversalrsquo corresponding-states relationship for the dimensionless transport coefficients of dense fluids as functions of the reduced configurational entropy more then twenty five years ago Dzugutov [Nature 381 137 (1996)] proposed an alternative entropy scaling approach using the atomic diffusion collision frequency We use the entropy scaling relationship developed by Rosenfeld to understand the relationships between the transport properties excess entropy and the relaxation dynamics of the extended simple point charge model of water This is performed using molecular dynamics and transition-matrix Monte Carlo simulations Our study is motivated by previous work [Phys Rev Lett 96 177804 (2006) J Chem Phys 125 0761402 (2006) J Phys Chem B 110 18147 (2006)] which clearly illustrates the robust relationship between diffusion coefficients and excess entropy of atomistic fluids We suspect for a molecular system the component of the excess entropy will scale with its corresponding type of motion We can also expect comparable values for the macroscopic viscosity from the microscopic structural relaxation time (alpha relaxation time) If this is the case then the relationship between thermodynamics and dynamics will be greatly simplified Key words Excess entropy scaling Molecular dynamics transition-matrix Monte Carlo molecular fluid

p 41 of 44

37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

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                                                                                                                                                    • • Nancy Cribbin David A Kofke
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37 Determining Contact Angles From Molecular Simulation

Eric Grzelak Jeffery R Errington Department of Chemical and Biological Engineering University at Buffalo Buffalo NY 14260 The effects of surface composition and roughness on fluid wetting are studied A Lennard-Jones fluid contacts a molecularly defined wall under conditions that allow coexistence between a liquid and vapor region Grand canonical transition matrix Monte Carlo simulations are carried out to generate a particle density probability distribution from which thermodynamic properties are calculated Among those properties calculated are surface tensions contact angles and spreading coefficients These values are then compared to data previously published both refining those values and proving the efficiency of this method Subsequently more and more complex surfaces are simulated to study the effect of surface roughness on wetting properties Additionally a long ranged correction to the truncated Lennard-Jones potential is analyzed for future use in rough surface wetting studies in the hopes of capturing the physical phenomenon known as prewetting transitions Key Words contact angle surface tension wetting Lennard-Jones molecular simulation Monte Carlo

Figure 1 An example probability distribution resulting from a grand canonical Monte Carlo simulation of a fluid in contact with a molecularly ordered surface From a distribution such as this the most probable regions of vapor and liquid existence are evident and the spreading coefficient can be obtained

p 42 of 44

38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

p 43 of 44

39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

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                                                                                                                                                • • Eric Grzelak Jeffery R Errington
                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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38 Assessing Crystal Free Energy

Nancy Cribbin David A Kofke State University of New York at Buffalo 303 Furnas Hall Buffalo New York 14260 Crystal morphology is a key determinant of the properties of the solid phase affecting the thermodynamic mechanical electrical optical and other physical features of the solid Prediction of the stable polymorph adopted by a molecular crystal is therefore a problem of great practical importance Current methods of predicting crystal structure are limited in two ways First the molecular models used to describe the atomic interactions are imperfect Second common practice is to minimize the overall energy of the system rather than the free energy because free energies are hard to evaluate This neglects the entropic contribution Failure to predict polymorphs correctly may result from either or both of these approximations and it is important to be able to separate these effects To address this problem we are developing a method for estimating free energies of solids and apply it to polymorph prediction problems The method is based on harmonic analysis of the crystal with a molecular simulation based correction that assumes independent normal modes but which can be systematically improved Applications include organic molecules organic crystals and potentially protein and other biological crystals Key Words polymorph free energy crystals

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39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

p 44 of 44

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                                                                                                                                                  • • Assessing Crystal Free Energy
                                                                                                                                                    • • Nancy Cribbin David A Kofke
                                                                                                                                                      • • Grand Canonical Monte Carlo Simulations Of Water Adsorption

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39 Grand Canonical Monte Carlo Simulations Of Water Adsorption On Graphite Surface

Wai Keong Choong Jeffrey Errington Department of Chemical and Biological Engineering University at Buffalo The State University of New York Buffalo NY The objective of this work is to examine the efficacy of a new simulation technique for determining the surface thermodynamic properties of water in contact with a graphite substrate such as the contact angle and various interfacial tensions The new technique makes use of grand canonical transition matrix Monte Carlo simulations to directly evaluate the spreading coefficient from which other interfacial properties are deduced The Lennard-Jones potential is used to describe the interaction energy between water molecules and carbon atoms in the graphite surface We use the extended simple point charge (SPCE) water model to describe the interaction energy between water molecules The results from these simulations will be compared with the work of Warder et al [J Phys Chem B 107 (2003) 1345] in which molecular dynamics (MD) simulations where used to determine the contact angle of water droplets

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