Rapid advances in high-per-formance (supercomput-ing) simulations are revo-

lutionizing biomedicine in both theresearch and industrial context.Scientists and engineers now runpatient-specific computationalfluid dynamics (CFD) and finiteelement analysis (FEA) simula-tions at unprecedented levels ofresolution and accuracy. A drivingforce behind these advances is

growing interest on the part ofboth industry and the Food andDrug Administration (FDA) inusing computer modeling and sim-ulation to support medical deviceinnovation and validation. As newcapabilities to better incorporatesimulation into engineering prac-tice emerge, these can have atransformative impact on medicaldevice engineering and medicine.For example, a medical device de-

signer could have access to early,accurate feedback on device per-formance and be able to exhaus-tively explore many design itera-tions. In this way, simulation couldreduce the time it takes to reachbench tests and animal trials, makethese trials more efficient and ef-fective, and, in time, overtakethese methods as the primary eval-uative approach in device design.To realize this potential will re-quire tackling several difficult re-

search challenges.

A group of University of Min-nesota researchers have begun acollaboration to work toward a vi-sion of an immersive design envi-ronment composed of coupledcomponents for running simula-

Supercomputing Institutefor Advanced Computational Research

Medical Devices

Medical Device Invention and EvaluationThrough Simulation, Visualization, and Interactive Design

Volume 26, Number 3

Also in This Issue

Fall 2010 Research Bulletin

a unit of the Office of the Vice President for Research

Figure 1. A new data-intensive medical device design workflow is made possibleby rapidly advances in high-performance supercomputing. The system designshown here couples simulation, visualization, and interaction with the goal of im-proving early design feedback and evaluation and, eventually, leading to im-proved design of safe and effective medical devices.

2010 MSI Intern Program . . . .5GPU Computing Conference . .82011 Research Exhibition . . . .8New Supercomputer, Koronis .9Viñals Welcome . . . . . . . . . . . .9Outreach Activities . . . . . . . . .10Research Reports . . . . . . . . . .12Email notification sign-up . . .18

tions, visualizing and comparingmassive numbers of results, andinteracting directly with the pa-rameter space to explore new de-vice designs. A schematic of thisimmersive simulation-based virtu-al design environment can be seenin Figure 1. In this vision, all ofthe components are backed bydatabases composed of pre-exist-ing device models, patient-specificanatomies, and tissue properties.This design environment wouldenable a fundamentally new data-intensive workflow for device en-gineers to create initial designsand interactively refine them withthe informed context provided byaccurate simulation results. Inpartnership with the MinnesotaSupercomputing Institute, threegroups across campus have startedto explore the research challengesassociated with this new biomed-ical workflow and immersive envi-

ronment vision: the Interactive Vi-sualization Lab in the Departmentof Computer Science and Engi-neering, the St. Anthony FallsLaboratory (SAFL), and the Med-ical Devices Center. Members ofthe team include: Dane Coffey(Computer Science), Trung Le(SAFL), Vamsi Konchada (Com-puter Science), Nicholas Malbraat-en (Computer Science), Chi-LunLin (Mechanical Engineering), YiSun (Mechanical Engineering),Molly Staker (Mechanical Engi-neering), Iman Borazjani (SAFL),Victoria Interante (Computer Sci-ence), Daniel Keefe (ComputerScience), Fotis Sotiropoulos (Di-rector, SAFL), and Arthur Erdman(Mechanical Engineering; Direc-tor, Medical Devices Center). MSIstaff who have contributed to thisresearch include Nancy Rowe and

H. Birali Runesha.

A high-performance simulation

framework has been developed tocouple computational fluid dynam-ics (CFD) simulations with ad-vanced fluid-solid interaction(FSI) models in order to simulate aheartbeat and the resulting openingand closing of mechanical valvesimplanted in the heart. Resultsfrom this work have established anew standard in physiologicallyaccurate cardiovascular simulation.Figure 2 shows a visualization ofsimulated blood flow through apatient-specific model of the leftventricle and aorta extracted fromCT imaging data. The researchersenvision that the new power pro-vided by simulations such as thesecan form the backbone of the in-teractive design environment out-lined in Figure 1. In this vision ofthe future, where fast, accuratesimulation is coupled with engi-neering design tools, the results ofmultiple simulations could be

Medical Devices

Supercomputing Institute Research Bulletin Fall 20102

Figure 2. Groundbreaking fluid-solid interaction (FSI) models now make simulating accurate time-varying blood flow in pa-tient specific geometries possible. The simulation describes flow through a synthetic heart valve as it opens and closes withthe beat of the heart inside of a patient-specific model of the left ventricle and aorta.

Medical Devices

Fall 2010 Supercomputing Institute Research Bulletin 3

compared using visualization tounderstand the impact of differentdesign parameters on valve func-tion and the three-dimensionalgeometry of the valve could be ed-

ited interactively by engineers.

To employ this style of simula-tion-based design workflow, newtechniques for visualizing large,complex datasets are needed.Rapid increases in complexity andresolution of CFD simulation dataparallel the exponential advancesin supercomputing resources.However, a major bottleneck ex-ists in conveying the informationthat results from these visualiza-tions to users. Traditional desktop-based data visualizations struggleto convey the complex spatial rela-tionships and other complexities inthe data. In contrast, emerging

techniques for visualizing datausing immersive virtual reality(VR) provide new opportunitiesfor insights and discoveries thatmay have otherwise been missed.Using visualization environments,such as the MSI PowerWall shownin Figure 3 (located in theLCSE/MSI Visualization Labora-tory), scientists and engineers canview simulation results from theperspective of a blood cell, investi-gating small-scale data features indetail. Interactive VR environ-ments, such as this one, combinestereoscopic vision with three-di-mensional head tracking to pro-duce three-dimensional views ofthe data that update, recalculatingthe correct perspective projectionof the three-dimensional scene, asscientists walk through the virtual

environment. In addition to room-sized VR environments, the teamis also investigating the potentialof smaller scale, more affordableVR environments constructedusing commercially availablethree-dimensional televisions,which may provide the engineer-

ing workbench of the future.

In addition to the challenge ofvisualizing complex datasets, thenew data-intensive workflow envi-sioned by the team also raises sig-nificant challenges for human-computer interaction, as the suc-cess of these visualizations de-pends heavily on the ability of en-gineers to explore their data, test-ing hypotheses and forming newhypotheses as they work. To bettersupport visualization at the work-bench scale, the team is new data

Figure 3. Immersive virtual reality (VR) visualizations provide scientists and engineers with new detailed views of complexanatomical geometries and data. Using the MSI PowerWall, results of a blood flow simulation through an aorta and synthet-ic heart valve can be explored interactively.

exploration interfaces that leverageemerging technologies, such asmulti-touch input. Figure 4 showsa semi-immersive VR environmentthat is coupled with a large multi-touch table display. This environ-ment makes it possible to explorecomplex three-dimensional data-sets in using a variety of new in-teraction metaphors. For example,in the figure, the user navigatesthrough complex three-dimension-

al data from a blood flow simula-tion using rich multi-touch ges-tures made on top of an interactiveshadow of the data displayed onthe table. In addition to supportingrich input, the table display surfacealso provides a large visual surfacecapable of organizing and display-ing additional information. In thefuture, the researchers expect thatinteractive visual data explorationenvironments such as this one will

serve as the a medical device de-signer’s workbench, enabling newmodes of refining design itera-tions, spinning off high-resolutionsimulations, and organizing mas-sive amounts of data, and, ulti-mately, leading to improved inno-vation and design of safe and ef-fective medical devices.

4 Supercomputing Institute Research Bulletin Fall 2010

Medical Devices

Figure 4. New human-computer interfaces are needed to support data exploration. Here a multi-touch table display is cou-pled with a VR display to provide new possibilities for interacting with data, such as manipulating three-dimensional datathat appears (through stereoscopic projection) to float above the table by manipulating its shadow.

The Supercomputing Insti-tute’s Undergraduate Intern-ship Program, now in its

20th year, gives undergraduatesthe opportunity to experienceworking in a research environ-ment. The interns get to participatein a challenging and enriching ed-ucational experience that helpsthem decide whether they want topursue graduate or professionaleducation and research. The pro-gram encompasses digital simula-tion and advanced computationand all aspects of high-perform-ance computing and scientificmodeling and simulation, as wellas graphics, visualization, infor-matics, and high-performance net-work communications. Internswork with Principal Investigatorsat the Supercomputing Instituteand their research groups on theirprojects. They give a presentationabout their research to the interngroup as well as the faculty and

other researchers and also prepare

a written report.

The Summer 2010 program in-cluded 11 interns who worked onprojects in a wide variety of fields.They were selected from over 100applicants at colleges and universi-ties in the United States and Puer-to Rico. Eight of the internsworked on projects sponsored bythe Supercomputing Institute’s Re-search Experiences for Undergrad-uates (REU) grant from the Na-tional Science Foundation (NSF),two were sponsored by internalMSI funds, and one was sponsoredby his faculty mentor’s NSF grant.

Bjorn K. Berntson, a Universi-ty of Minnesota physics and math-ematics double major, workedwith Professor Christopher J.Cramer, Department of Chemistryand MSI Fellow. Mr. Berntson’sproject was titled “ElectronicStructure Characterization of the(bpy)2MO2 Catalyst.”

University of Minnesota chem-istry major Erik M. Fritz workedwith Professor Steven A. Kass,Department of Chemistry and Su-percomputing Institute Fellow. Mr.Fritz, who was also in the 2009 in-tern program in the Kass group,worked on a project called “Ener-gy Barriers and Relative Basicity.”

Timothy M. Hecht was in theresearch group of Professor J.Woods Halley, Department ofPhysics and Supercomputing Insti-tute Fellow. Mr. Hecht is a physicsmajor with mathematics and busi-ness minors at Brigham YoungUniversity in Provo, Utah. Hisproject was entitled “ElectronicSpin Structures of Pt, O, and HWith Possible Catalysis Applica-

tions.”

Michelle S. Lenz, from BethelUniversity in St. Paul, Minnesota,worked with the research group ofRegents Professor Donald G.Truhlar, Department of Chemistry

2010 Undergraduate Internship Program

5Fall 2010 Supercomputing Institute Research Bulletin

Supercomputing Institute Programs

Michelle Lenz, Tim Hecht, Erik Fritz, and Bjorn Berntson at the intern program Welcome Luncheon.

and Supercomputing Institute Fel-low. Ms. Lenz is an engineeringscience major with an emphasis inbiomedical engineering, and herproject was “ElectrochemicalProperties of Ruthenium Catalysts

in Solution.”

University of Minnesota neuro-science major Aatif Mansoor

worked with Assistant ProfessorElizabeth A. Amin, Department ofMedicinal Chemistry and Super-

computing Institute Associate Fel-low. His project was “AnthraxToxin Lethal Factor Inhibitors: InSilico Design Approaches.”

Brendan A. Murphy, a Univer-sity of Minnesota biomedical engi-neering major, worked with Assis-tant Professor Tay I. Netoff, De-partment of Biomedical Engineer-ing. His project was “Deep BrainStimulation and Neuronal Syn-chrony.”

Adam M. Novak, who attendsHarvey Mudd College in Clare-mont, California, worked withProfessor Victor Barocas, Depart-ment of Biomedical Engineeringand Supercomputing Institute Fel-low. Mr. Novak is a double majorin computer science and biology,and his project was “Multi-scaleModeling on the GPU.”

University of Minnesota mathe-matics major David A. Sanchez

worked with Professor David A.Yuen, Department of Geology andGeophysics and SupercomputingInstitute Fellow. His project was“2D and 3D Mantle Convection onthe GPU.”

Ashwin P. Srikrishna, who at-tends North Carolina State Univer-sity in Raleigh, North Carolina,worked with Assistant ProfessorKevin Dorfman, Department ofChemical Engineering and Materi-als Science and SupercomputingInstitute Associate Fellow. Mr.Srikrishna majors in chemical en-gineering with a minor in nuclearengineering. Mr. Srikrishna’s proj-ect was entitled “Parallelization ofa Brownian Dynamics Simulation

Supercomputing Institute Programs

6 Supercomputing Institute Research Bulletin Fall 2010

Andrew Wesson gives his presentation.

Left to right: Andrew Wesson, Bjorn Berntson, Erik Fritz, Aatif Mansoor, Adam Novak, Michelle Lenz, Alexandra Zudova,Tim Hecht, Aaron Erdman, and Ashwin Shrikrishna.

Supercomputing Institute Programs

7Fall 2010 Supercomputing Institute Research Bulletin

of DNA Electrophoresis in a Non-homogeneous Electric Field.”

Andrew J. Wesson attendsCarnegie Mellon University inPittsburgh, Pennsylvania, where heis a physics major. He worked inthe research group of ProfessorThomas W. Jones, Department ofAstronomy, Supercomputing Insti-tute Fellow, and Interim Directorof the Institute until August 1,2010. His project was “RadiativeCooling in Astrophysical Magne-to-Hydrodynamic Simulations.”

Alexandra M. Zudova, a Uni-versity of Minnesota chemical en-gineering major with a chemistryminor, worked with ProfessorDavid D. Thomas, Department ofBiochemistry, Molecular Biology,and Biophysics and MSI Fellow.Her project was “Molecular Dy-namics Simulation of a Spin-la-beled Membrane Protein.”

While not a member of the for-mal program, Aaron Erdman, astudent at Century College inWhite Bear Lake, Minnesota, par-ticipated in many of the intern pro-gram’s activities during the sum-mer. Mr. Erdman is a student inthe Telecommunication Technolo-gy program at Century. He workedwith MSI Scientific ComputingConsultant Nancy Rowe on sever-al projects at the LCSE-MSI Visu-alization Laboratory during thesummer.

See the sidebar on this page forthe announcement about nextyear’s intern program.

Summer 2011

Undergraduate Internship Program

The Supercomputing Institute is pleased to announce its Under-graduate Internship Program for Summer 2011. Appointments are forfull-time, 10-week internships, and will run from June 6 through Au-gust 12, 2011. A student interested in becoming an intern must stillbe an undergraduate in August 2011 and must be a citizen or perma-nent resident of the United States or its possessions. Interns will bepaid a stipend of $5,000. Room and board at the University resi-dence hall are free to the interns. If interns wish to live elsewhere,they will receive a per-diem food allowance and can request reim-bursement for housing costs.

All applications are evaluated competitively based on the qualifi-cations of the applicant and the availability of a suitable project.Projects are available in the following disciplines:

Aerospace Engineering and MechanicsAstronomy

BiochemistryBiomedical Engineering

Chemistry Computer Science

Geology and GeophysicsMedicinal Chemistry

Physics

Complete application information, application forms, and projectlists are available on the Supercomputing Institute website at:

www.msi.umn.edu/programs/undergraduateinternship.html

Applications, transcripts, and letters of recommendation can beemailed, faxed, or mailed as shown below.

Email: uip@msi.umn.eduFax: 612-624-8861Mail: Undergraduate Internship Coordinator

University of Minnesota Supercomputing Institute599 Walter117 Pleasant Street SEMinneapolis, MN 55455

Phone: (612) 624-2330

All applications and letters of recommendation must be

received by February 28, 2011.

MSI Research Exhibition 2011

MSI will host a Research Exhibition poster session on April 29, 2011. AllMSI researchers will be invited to present posters of their work using MSI re-

sources. Prizes will be awarded to the outstanding posters.

The Call for Posters will be sent out in early February. We will post more in-formation as it becomes available on the Research Exhibition 2011 website

(www.msi.umn.edu/events/researchexhibition2011.html).

Supercomputing Institute Research Bulletin Fall 20108

Events

International Workshop on GPU Computing

David A. Yuen (Geologyand Geophysics and MSIFellow) was on the organ-

izing committee for the 2010 In-ternational Workshop of GPU So-lutions to Multiscale Problems inScience and Engineering, whichwas held in Harbin, China duringSummer 2010. The two-day work-shop included over 100 attendeesfrom colleges, universities, and re-search centers from around theworld. The attendees discussedsuch topics as GPU solutions tomulti-scale problems, focusing onhigh-performance computingmethods and algorithms, efficientsoftware implementation tech-nique, the construction of the sci-entific computing environment,and mainstream development

trends. Besides Professor Yuen, at-tendees from the University ofMinnesota included MSI ScientificComputing Consultant Dr. ShuxiaZhang (shown above, giving a

presentation), MSI Summer 2010Undergraduate Intern David A.Sanchez (see article, page 5), andMSI Summer 2009 UndergraduateIntern Robin Weiss.

Supercomputing Institute News

Fall 2010 Supercomputing Institute Research Bulletin 9

MSI was recently awardedan NIH grant that is al-lowing us to purchase a

new supercomputing system,which has been named “Koronis”after a lake in central Minnesota.Koronis features an SGI Altix UV1000 supercomputer that has ashared-memory architecture inwhich each core can access all 3.1terabytes of memory directly. Ko-ronis also includes high-perform-ance visualization workstationsand high-performance and -fidelitydata storage. This system will beused by MSI researchers workingon a number of NIH-funded proj-ects in the areas of multi-scalemodeling, chemical dynamics,bioinformatics and computationalbiology, and biomedical imaging.The Principal Investigator on thegrant is Professor Darrin York(Chemistry, MSI Fellow). Other

major users of Koroniswill include Jiali Gao(Chemistry, MSI Fel-low), Donald Truhlar(Chemistry, MSI Fel-low), George Karypis(Computer Science andEngineering, MSI Asso-ciate Fellow), DavidLargaespada (Genetics,Cell Biology, and De-velopment), Kelvin Lim(Psychiatry), and BinHe (Biomedical Engi-neering). Koronis willalso be available toother MSI researcherswho have NIH funding.

Koronis was deliv-ered in early October and is under-going acceptance testing. It shouldbe available for full-scale use inJanuary 2011. Up-to-date informa-tion can be found on the MSI web-

site as it becomes available:

www.msi.umn.edu/hardware/

New Supercomputer, “Koronis”

Welcome Reception for MSI Director

On September 14, MSI held a reception to formally welcome Jorge Viñals as the new Director of the Su-percomputing Institute. Attendees included MSI researchers and staff, members of the staff of the Officeof the Vice President for Re-

search, supercomputing vendors, andother members of the MSI extendedcommunity. In the picture at right,Vice President for Research TimMulcahey makes a few welcoming re-marks. Left to right: Jorge Viñals, H.Birali Runesha (MSI Assistant Direc-tor of Scientific Computing), TimMulcahey, Mike Balak (IT Director,CFANS), and Brian Ropers-Huilman(MSI Assistant Director of HPC Oper-ations). At far right, back to camera,Mark Nelson (MSI HPC Systems Ad-ministrator).

Outreach Activities

10 Supercomputing Institute Research Bulletin Fall 2010

Supercomputing Institute Outreach

MSI at the Minnesota State Fair

On September 2, 2010, MSIwas at the Minnesota State Fairwith the Medical Devices Cen-ter. Visitors to the University ofMinnesota’s building that daygot to “fly through” a three-di-mensional visualization of aheart. In the picture at right,MSI Visualization SpecialistMike Knox (right, in yellowshirt) talks to a fair visitorabout what she’s seeing on-screen. The visitor is wearing3D glasses to view the image.

Math and Science Family Fun

Fair

MSI participated in the College of Sci-ence and Engineering’s Math and Sci-ence Family Fun Fair on Saturday, No-vember 13. MSI staff members YectliHuerta and Samantha Thomas and MSIPI Carlos Sosa and his son Danielshowed the visiting kids and their par-ents how supercomputers help re-searchers. The children were able tobuild model molecules and see howscientists use computers to make ani-mated molecule simulations.

On October 14, two groups ofmiddle-school students from theWashington Technology Magnetschool in St. Paul, Minnesota vis-ited the lab. These students arepart of the BioSMART (Biologi-cally focused Science, Math, Aca-demic Rigor, and Technology)Program. The students watchedthree-dimensional visualizationson the LMVL’s large screen andlearned how doctors and scientistsuse these visualizations.

11Fall 2010 Supercomputing Institute Research Bulletin

Supercomputing Institute Outreach

On October 21, students participating in “Body Forward,” the 2010 Minnesota FIRST LEGO League roboticscompetition, visited the LMVL as part of the University of Minnesota Research Workshop. At left, Assistant Pro-

fessor Matt Johnson (Biomedical En-gineering, MSI Principal Investigator)shows the students how doctors canlook at CAT scans in three dimen-sions. The students also got to partici-pate in some hands-on virtual realitybrain surgery. The University of Min-nesota Research Workshop is hostedby the College of Science and Engi-neering. More information aboutFIRST LEGO League can be found atwww.firstlegoleague.org.

On November 12, Dave Plescia, a repre-sentative from Johnson & Johnson, visit-ed the University of Minnesota to discusscollaboration possibilities with Universityresearchers involved in medical-devicedevelopment. Professors Dan Keefe(Computer Science and Engineering),Fotis Sotiropoulos (Director, SAFL), andArt Erdman (Mechanical Engineering;Director, Medical Devices Center) andsome of their students attended the pres-entation about Johnson & Johnson’s med-ical devices. Mr. Plescia (pictured atright) also watched some of the visualiza-tions currently being created using MSI resources.

Visitors to the LCSE-MSI Visualization Laboratory

Names of Supercomputing Institute principal investigators appear in bold type. This

list contains reports entered into the reports database during August–November 2010.

Aerospace Engineering

and Mechanics

2010/137 Dynamic k-Equation Model forLarge Eddy Simulation of Com-pressible FlowsX. Chai and K. Mahesh

2010/138 Euler-Lagrangian Simulation ofBubble Migration in a TurbulentBoundary LayerM. Mattson and K. Mahesh

2010/139 Simulations of High Speed Turbu-lent Jets in CrossflowX. Chai and K. Mahesh

2010/140 Transition of Hypersonic FlowPast Flat Plate With Roughness El-ementsP.S. Iyer, S. Muppidi, and K. Ma-

hesh

2010/191 DNS of Transition in SupersonicBoundary LayersS. Muppidi and K. Mahesh

Agronomy and

Plant Genetics

2010/131 and CB 2010-44 An Integrative Approach to Ge-nomic Introgression MappingA.J. Severin, G.A. Peiffer, W.W.Xu, D.L. Hyten, B. Bucciarelli,J.A. O’Rourke, Y.-T. Bolon, D.Grant, A.D. Farmer, G.D. May,C.P. Vance, R.C. Shoemaker, andR.M. Stupar

2010/146 and CB 2010-49 Transcriptome Analysis of the Bar-ley–Deoxynivalenol Interaction:Evidence for a Role of Glutathionein Deoxynivalenol DetoxificationS.A. Gardiner, J. Boddu, F.Berthiller, C. Hametner, R.M. Stu-

par, G. Adam, and G.J.Muehlbauer

2010/147 and CB 2010-50The Genetics of Barley Low-Tiller-ing Mutants: Low number ofTillers-1 (lnt1)T. Dabbert, R.J. Okagaki, S. Cho,S. Heinen, J. Boddu, and G.J.

Muehlbauer

2010/148 and CB 2010-51Structural and Functional Charac-terization of a Winter Malting Bar-leyM. Munoz-Amatriain, L. Cistue, Y.Xiong, H. Bilgic, A.D. Budde,M.R. Schmitt, K.P. Smith, P.M.Hayes, and G.J. Muehlbauer

2010/172 and CB 2010-63 Transcript Profiling of CommonBean (Phaseolus vulgaris L.) Usingthe GeneChip Soybean GenomeArray: Optimizing Analysis byMasking Biased ProbesS.S. Yang, O. Valdes-Lopez, W.W.Xu, B. Bucciarelli, J.W. Gron-

wald, G. Hernandez, and C.P.

Vance

2010/173 and CB 2010-64 Transcript Profiling of Two AlfalfaGenotypes With Contrasting CellWall Composition in Stems Using aCross-Species Platform: Optimiz-ing Analysis by Masking BiasedProbesS.S. Yang, W.W. Xu, M. Tesfaye,J.F.S. Lamb, H.J.G. Jung, K.A.VandenBosch, C.P. Vance, andJ.W. Gronwald

Animal Science

2010/134 and CB 2010-45 Genome-Wide Association Analysisof Total Cholesterol and High-Den-sity Lipoprotein Cholesterol LevelsUsing the Framingham HeartStudy DataL. Ma, J. Yang, H. B. Runesha, T.Tanaka, L. Ferrucci, S. Bandinelli,and Y. Da

Biochemistry, Molecular

Biology, and Biophysics

2010/89 and CB 2010-34 Structural Insight Into Methyl-Coenzyme M Reductase ChemistryUsing Coenzyme B AnaloguesP.E. Cedervall, M. Dey, A.R. Pear-son, S.W. Ragsdale, and C.M.

Wilmot

2010/90 and CB 2010-35Structural Features PromotingDioxygen Production byDechloromonas aromatica ChloriteDismutaseB.R. Goblirsch, B.R. Streit, J.L.DuBois, and C.M. Wilmot

2010/91 and CB 2010-36Kinetic and Structural Analysis ofSubstrate Specificity in Two Cop-per Amine Oxidases FromHansenula polymorphaC.M. Chang, V.J. Klema, B.J.Johnson, M. Mure, J.P. Klinman,and C.M. Wilmot

2010/92 and CB 2010-37In Crystallo PosttranslationalModification Within a MauG/Pre-Methylamine Dehydrogenase Com-plexL.M.R. Jensen, R. Sanishvili, V.L.Davidson, and C.M. Wilmot

2010/149 and CB 2010-52 Phosphorylation-Induced Structur-al Changes in Smooth MuscleMyosin Regulatory Light ChainD. Kast, L.M. Espinoza-Fonseca,C. Yi, and D.D. Thomas

12 Supercomputing Institute Research Bulletin Fall 2010

Research Reports

13Fall 2010 Supercomputing Institute Research Bulletin

Research Reports

2010/169 and CB 2010-60Synthesis, Properties, and Applica-tions of Diazotrifluropropanoyl-Containing Photoactive Analogs ofFarnesyl Diphosphate ContainingModified Linkages for EnhancedStabilityM.L. Hovlid, R.L. Edelstein, O.Henry, J. Ochocki, A. DeGraw, S.Lenevich, T. Talbot, V.G. Young,A.W. Hruza, F. Lopez-Gallego,N.P. Labello, C.L. Strickland, C.

Schmidt-Dannert, and M.D. Dis-

tefano

2010/200 and CB 2010-80 LTQ-iQuant: A Freely AvailableSoftware Pipeline for Automatedand Accurate Protein Quantifica-tion of Isobaric Tagged PeptideData From LTQ InstrumentsG. Onsongo, M.D. Stone, S.K. VanRiper, J. Chilton, B. Wu, L. Hig-gins, T.C. Lund, J.V. Carlis, andT.J. Griffin

BioTechnology Institute

2010/145 and CB 2010-48 Switching From an Esterase to aHydroxynitrile Lyase MechanismRequires Only Two Amino AcidSubstitutionsS.K. Padhi, R. Fujii, G.A. Legatt,S.L. Fossum, R. Berchtold, andR.J. Kazlauskas

Center for Drug Design

2010/93 and CB 2010-38 Dual Inhibitors of InosineMonophosphate Dehydrogenaseand Histone Deacetylase Based ona Cinnamic Hydroxamic Acid CoreStructureL. Chen, R. Petrelli, G. Gao, D.J.Wilson, G.T. McLean, H.N. Ja-yaram, Y.Y. Sham, and K.W.Pankiewicz

2010/168 and CB 2010-59 N-3 Hydroxylation of Pyrimidine-2,4-diones Yields Dual Inhibitors ofHIV Reverse Transcriptase and In-tegraseJ. Tang, K. Maddali, C.D. Dreis,Y.Y. Sham, R. Vince, Y. Pommier,and Z. Wang

Chemical Engineering

and Materials Science

2010/104 Koopmans’ Condition for Density-functional TheoryI. Dabo, A. Ferretti, N. Poilvert, Y.Li, N. Marzari, and M. Cococcioni

2010/113 Dynamics of Surface StructureEvolution in Colloidal Adsorption:Charge Patterning and Polydisper-sityD.D. Brewer, M. Tsapatsis, and S.

Kumar

2010/133 Accurate and Efficient Calcula-tions on Strongly Correlated Min-erals With the LDA+U Method:Review and PerspectivesM. Cococcioni

2010/136 Tuning the Charge-Transport Pa-rameters of Perylene Diimide Sin-gle Crystals via End and/or CoreFunctionalization: A Density Func-tional Theory InvestigationM.C. Ruiz Delgado, E.-G. Kim,D.A. da Silva Filho, and J.-L.Bredas

2010/174 Existence, Stability, and NonlinearDynamics of Detached BridgmanGrowth States Under Zero GravityA. Yeckel and J.J. Derby

2010/176 and CB 2010-67Free Energy Profile of the Interac-tion Between a Monomer or aDimer of Protegrin-1 in a SpecificBinding Orientation and a ModelLipid BilayerV. Vivcharuk and Y. Kaznessis

2010/177 and CB 2010-66Antimicrobial Mechanism of Pore-forming Protegrin Peptides: 100Pores to Kill E. coliD. Bolintineanu, E. Hazrati, H.T.Davis, R.I. Lehrer, and Y.N. Kaz-

nessis

2010/192Quasiharmonic Thermal Elasticityof Crystals: An Efficient AnalyticalApproachZ. Wu and R.M. Wentzcovitch

2010/193 The Hubbard U Correction forIron-Bearing Minerals: A Discus-sion Based on (Mg,Fe)SiO3 Per-ovskiteH. Hsu, K. Umemoto, M. Cococ-

cioni, and R.M. Wentzcovitch

2010/194 Thermodynamic Properties ofMgSiO3 Majorite and Phase Tran-sitions Near 660-km Depth inMgSiO3 and Mg2SiO4: A FirstPrinciples StudyY.G. Yu, R.M. Wentzcovitch, V.L.Vinograd, and R.J. Angel

2010/195 Effect of the d Electrons on PhaseTransitions in Transition-MetalSesquioxidesK. Umemoto and R.M. Wentzcov-

itch

Chemical Engineering,

UMD

2010/197 Combined Gravitational and Ther-mocapillary Interactions of Spheri-cal Drops With IncompressibleSurfactantM.A. Rother

Chemistry

2010/95 and CB 2010-41 Equilibrium Mercury Isotope Frac-tionation Between Dissolved Hg(II)Species and Thiol-Bound HgJ.G. Wiederhold, C.J. Cramer, K.Daniel, I. Infante, B. Bourdon, andR. Kretzschmar

2010/96 and CB 2010-40High Tg Aliphatic Polyesters bythe Polymerization of SpirolactideDerivativesG.L. Fiore, F. Jing, V.G. Young, Jr.,C.J. Cramer, and M.A. Hillmyer

14 Supercomputing Institute Research Bulletin Fall 2010

Research Reports

2010/97 Prediction of SAMPL2 AqueousSolvation Free Energies and Tau-tomeric Ratios Using the SM8,SM8AD, and SMD Solvation Mod-elsR.F. Ribeiro, A.V. Marenich, C.J.

Cramer, and D.G. Truhlar

2010/126Enolates in 3-D: An Experimentaland Computational Study of De-protonated 2-AdamantanoneM.M. Meyer and S.R. Kass

2010/127 and CB 2010-43An Infrared Multiphoton Dissocia-tion Spectroscopy Study of Proto-nated p-Aminobenzoic Acid: DoesElectrospray Ionization Afford theAmino- or Carboxy-ProtonatedIon?J. Schmidt, I. Spector, M.M.Meyer, and S.R. Kass

2010/135 and CB 2010-46Internal Proton Transfer in the Ex-ternal Pyridoxal 5’-PhosphateSchiff Base in Dopa DecarboxylaseY. Lin and J. Gao

2010/152 and CB 2010-54Tunneling in Enzymatic andNonenzymatic Hydrogen TransferReactionsD.G. Truhlar

2010/153 Tests of the RPBE, revPBE, τ-HC-THhyb, wB97X-D, and MOHLYPDensity Functional Approximationsand 29 Others Against Representa-tive Databases for Diverse BondEnergies and Barrier Heights inCatalysisK. Yang, J. Zheng, Y. Zhao, andD.G. Truhlar

2010/154 Density Functional Study of COand NO Adsorption on Ni-dopedMgO(100)R. Valero, J.R.B. Gomes, D.G.

Truhlar, and F. Illas

2010/155 and CB 2010-53Kinetics of Hydrogen-Transfer Iso-merizations of Butoxyl RadicalsJ. Zheng and D.G. Truhlar

2010/156 Binding Energy of d10 TransitionMetals to Alkenes by Wave Func-tion Theory and Density Function-al TheoryB.B. Averkiev, Y. Zhao, and D.G.

Truhlar

2010/157 and CB 2010-55Density Functional Calculations ofE2 and SN2 Reactions: Effects ofthe Choice of Density Functional,Basis Set, and Self-Consistent Iter-ationsY. Zhao and D.G. Truhlar

2010/158 On the Performances of the M06Family of Density Functionals forElectronic Excitation EnergiesD. Jacquemin, E.A. Perpete, I.Ciofini, C. Adamo, R. Valero, Y.Zhao, and D.G. Truhlar

2010/159 and CB 2010-56Communication: Energetics of Re-action Pathways for Reactions ofEthenol With the Hydroxyl Radical:The Importance of Internal Hydro-gen Bonding at the Transition StateO. Tishchenko, S. Ilieva, and D.G.

Truhlar

2010/161 Density Functional Approximationsfor Charge Transfer ExcitationsWith Intermediate Spatial OverlapR. Li, J. Zheng, and D.G. Truhlar

2010/162 Sorting Out the Relative Contribu-tions of Electrostatic Polarization,Dispersion, and Hydrogen Bondingto Solvatochromic Shifts on Verti-cal Electronic Excitation EnergiesA.V. Marenich, C.J. Cramer, andD.G. Truhlar

2010/163 Computational Thermochemistry:Scale Factor Databases and ScaleFactors for Vibrational Frequen-cies Obtained From ElectronicModel ChemistriesI.M. Alecu, J. Zheng, Y. Zhao, andD.G. Truhlar

2010/164 and CB 2010-57Direct Dynamics Implementation ofthe Least-Action Tunneling Trans-mission Coefficient. Application tothe CH4/CD3H/CD4 + CF3 Ab-straction ReactionsR. Meana-Paneda, D.G. Truhlar,and A. Fernandez-Ramos

2010/167 and CB 2010-58 Density-Functional ExpansionMethods: Evaluation of LDA, GGAand Meta-GGA Functionals andDifferent Integral ApproximationsT.J. Giese and D.M. York

2010/169 and CB 2010-60Synthesis, Properties, and Applica-tions of Diazotrifluropropanoyl-Containing Photoactive Analogs ofFarnesyl Diphosphate ContainingModified Linkages for EnhancedStabilityM.L. Hovlid, R.L. Edelstein, O.Henry, J. Ochocki, A. DeGraw, S.Lenevich, T. Talbot, V.G. Young,A.W. Hruza, F. Lopez-Gallego,N.P. Labello, C.L. Strickland, C.

Schmidt-Dannert, and M.D. Dis-

tefano

2010/170 and CB 2010-61Selective Labeling of PolypeptidesUsing Protein Farnesyltransferasevia Rapid Oxime LigationM. Rashidian, J.K. Dozier, S.Lenevich, and M.D. Distefano

2010/171 and CB 2010-62Evaluation of Alkyne-Modified Iso-prenoids as Chemical Reporters ofProtein PrenylationA.J. DeGraw, C. Palsuledesai, J.D.Ochocki, J.K. Dozier, S. Lenevich,M. Rashidian, and M.D. Distefano

2010/160 Free-Energy Surfaces for Liquid-Phase Reactions and Their Use ToStudy the Border Between Concert-ed and Nonconcerted α,b-Elimina-tion Reactions of Esters andThioestersY. Kim, J.R. Mohrig, and D.G.

Truhlar

15Fall 2010 Supercomputing Institute Research Bulletin

Research Reports

2010/181 and CB 2010-68A Non-Orthogonal Block-LocalizedEffective Hamiltonian Approachfor Chemical and Enzymatic Reac-tionsA. Cembran, A. Payaka, Y. Lin,W. Xie, Y. Mo, L. Song, andJ. Gao

2010/182 Generalized X-Pol Theory andCharge Delocalization StatesJ. Gao, A. Cembran, and Y. Mo

2010/183 and CB 2010-69On the Interfragment Exchange inthe X-Pol MethodA. Cembran, P. Bao, Y. Wang,L. Song, D.G. Truhlar, and J. Gao

2010/184 and CB 2010-70Internal Dynamics of an Analyti-cally Coarse-Grained ProteinM.J.M. Mazack, A. Cembran, andJ. Gao

2010/185 and CB 2010-71The Opsin Shift and Mechanism ofSpectral Tuning in RhodopsinR. Rajamani, Y. Lin, and J. Gao

2010/186 and CB 2010-72Energy Decomposition AnalysisBased on Block-Localized Wave-Function and Multistate DensityFunctional TheoryY. Mo, P. Bao, and J. Gao

2010/196 CB 2010-78 Active Participation of Mg2+ Ion inthe Reaction Coordinate of RNASelf-Cleavage Catalyzed by theHammerhead RibozymeK. Wong, T.S. Lee, and D.M. York

Chemistry and

Biochemistry, UMD

2010/187 and CB 2010-73 Unexpected Fluorescence Proper-ties in an Axially σ-bonded Ferro-cenyl-Containing PorphyrinP,V. Solntsev, J,R. Sabin, S,J.Dammer, N,N. Gerasimchuk, andV.N. Nemykin

2010/188 and CB 2010-74Long-Range Electronic Communi-cation in Free-Base Meso-Poly(Ferrocenyl)-Containing Por-phyrinsV.N. Nemykin, G.T. Rohde, C.D.Barrett, R.G. Hadt, J.R. Sabin,G. Reina, P. Galloni, and B. Floris

2010/189 and CB 2010-75Interpretation of the UV–vis Spec-tra of the Meso(Ferrocenyl)-Con-taining Porphyrins Using aTDDFT Approach: Is Gouterman’sClassic Four-Orbital Model Still inPlay?V.N. Nemykin and R.G. Hadt

Civil Engineering

2010/124 Reactivity of Alkyl Polyhalides to-ward Granular Iron: Developmentof QSARs and Reactivity CrossCorrelations for Reductive Dehalo-genationD.M. Cwiertny, W.A. Arnold, T.Kohn, L.A. Rodenburg, and A.L.Roberts

2010/178 Large-Eddy Simulation of Stably-Stratified Flow Over a Steep HillF. Wan and F. Porté-Agel

2010/179 Large-Eddy Simulation of Wind-turbine Wakes: Evaluation of Tur-bine Parametrisations

Y.-T. Wu and F. Porté-Agel

2010/180 Large-Eddy Simulation of a VeryLarge Wind Farm in a Stable At-mospheric Boundary LayerH. Lu and F. Porté-Agel

Computer Science

and Engineering

2010/98 Content-Based Methods for Pre-dicting Web-Site Demographic At-tributesS. Kabbur, E.-H. Han, and G.

Karypis

2010/112 GPU-Accelerated PreconditionedIterative Linear SolversR. Li and Y. Saad

2010/114 Domain-Decomposition-TypeMethods for Computing the Diago-nal of a Matrix InverseJ.M. Tang and Y. Saad

2010/115 Sparse Approximations of theSchur Complement for Parallel Al-gebraic Hybrid Solvers in 3DL. Giraud, A. Haidar, and Y. Saad

2010/200 and CB 2010-80 LTQ-iQuant: A Freely AvailableSoftware Pipeline for Automatedand Accurate Protein Quantifica-tion of Isobaric Tagged PeptideData From LTQ InstrumentsG. Onsongo, M.D. Stone, S.K. VanRiper, J. Chilton, B. Wu, L. Hig-gins, T.C. Lund, J.V. Carlis, andT.J. Griffin

Computer Science, UMD

2010/118 Computational Approaches toMeasuring the Similarity of ShortContexts: A Review of Applicationsand MethodsT. Pedersen

2010/165 Towards Improving Synonym Op-tions in a Text Modification Appli-cationJ. Burstein and T. Pedersen

Economics

2010/129 Computing Dynamic OptimalMechanisms When Hidden TypesAre MarkovK. Fukushima and Y. Waki

2010/130 Quantifying the Welfare GainsFrom Flexible Dynamic IncomeTax SystemsK. Fukushima

Electrical and Computer

Engineering

2010/100 Quantitative Analysis of Interac-tion Between Domain Walls andMagnetic NanoparticlesT. Klein, D. Dorroh, Y. Li, and J.-

P. Wang

2010/141 Simulation of Erase After Write on2.4T FeCo Solid Pole WriterM. Patwari and R.H. Victora

2010/142 and CB 2010-47Optimization of MagneticAnisotropy and Applied Fields forHyperthermia ApplicationsH. Sohn and R.H. Victora

2010/143 Calculation of Spin TransferTorque in Partially Polarized SpinValves Including Multiple Reflec-tions S. Hernandez and R.H. Victora

2010/144 Extracting Intergranular ExchangeCoupling in Perpendicular Mag-netic Recording MediaY. Dong and R.H. Victora

Finance

2010/203 Effects of Real and Financial Fric-tions on Corporate Capital Struc-ture Variation Over TimeP. Nezafat

Geology and Geophysics

2010/99 Influences of Lower-Mantle Prop-erties on the Formation of As-thenosphere in the Upper MantleD.A. Yuen, N. Tosi, and O. Cadek

2010/101 Parallel Numerical Analysis on theRheology of the Martian Ice-rockMixtureH. Jing, H. Zhang, H. Li, D.A.

Yuen, and Y. Shi

2010/109The Impact of Variability in theRheological Activation Parameterson Lower-Mantle Viscosity Stratifi-cation and Its DynamicsC. Matyska, D.A. Yuen, and H.Cizkova

2010/128 Numerical Modeling of ProtocoreDestabilization During PlanetaryAccretion: Feedbacks From Non-Newtonian Rheology and EnergyDissipationJ.-R. Lin, T.V. Gerya, P.J. Tackley,D.A. Yuen, and G.J. Golabek

Laboratory Medicine

and Pathology

2010/119 and CB 2010-42 S-MED: Sarcoma microRNA Ex-pression DatabaseA.L. Sarver, R. Phalak, V. Thayan-ithy, and S. Subramanian

Mathematics

2010/125 The Zeta Function on the CriticalLine: Numerical Evidence for Mo-ments and Random Matrix TheoryModelsG.A. Hiary and A.M. Odlyzko

Mathematics,

U of St. Thomas

2010/201 Origins of the Granite Falls, MNTornado, July 25, 2000 RevisitedD. Dokken, R. Naistat, B. Togstad,K. Scholz, K. Weise, J. Nelson, L.Edholm, and P. Shanahan

2010/202 Investigations of Cai’s Power Lawfor Strong TornadosD. Dokken, K. Scholz, and M.Shvartsman

Mechanical Engineering

2010/105 The Effects of Turbulence onNanoparticle Growth in TurbulentReacting JetsS. Das and S.C. Garrick

2010/106 Modeling and Simulation of Titani-um Dioxide Nanoparticle SynthesisWith Finite-Rate Sintering in Pla-nar JetsS.C. Garrick and G. Wang

2010/107 On the Effect of Nanoparticle Sizein Homogeneous Metal Vapor Nu-cleationJ. Liu and S.C. Garrick

2010/108 Large Eddy Simulation of TitaniumDioxide Nanoparticle Formationand Growth in Turbulent JetsJ. Loffler, S. Das, and S.C. Gar-

rick

2010/166 Particle-in-Cell and Monte CarloCollision Simulation of Positiveand Negative Corona PlasmasP. Wang, J. Chen, F.-G. Fan, andJ.A. Swift

Pharmaceutics

2010/94 and CB 2010-39 Understanding the RelationshipBetween Crystal Structure, Plastic-ity and Compaction Behaviour ofTheophylline, Methyl Gallate, andTheir 1:1 Co-crystalS. Chattoraj, L. Shi, and C.C. Sun

2010/190 and CB 2010-76 Cooperative Binding Isotherms forNearest Neighbor Interacting Lig-ands on Platonic Solids: A SimpleModel for Viral Capture Nanother-apyR.A. Siegel and J.L. Linstad

Research Reports

Supercomputing Institute Research Bulletin Fall 201016

Physics

2010/110 Magnetic Order in a Spin-1/2 In-terpolating Kagome/SquareHeisenberg AntiferromagnetR.F. Bishop, P. H.Y. Li, D.J.J. Far-nell, and C.E. Campbell

2010/111 Magnetic Order on a FrustratedSpin-1/2 Heisenberg Antiferromag-net on the Union Jack LatticeR.F. Bishop, P.H.Y. Li, D.J.J. Far-nell, and C.E. Campbell

2010/116 Non-Classical Rotational Inertia ina Two-Dimensional Bosonic SolidContaining Grain BoundariesC. Dasgupta and O.T. Valls

2010/117 Superconducting Proximity Effectsin Metals With a Repulsive PairingInteractionO.T. Valls, M. Bryan, and I. Zutic

2010/120Angular Dependence of the Super-conducting Transition Temperaturein Ferromagnet-Superconductor-Ferromagnet TrilayersJ. Zhu, I.N. Krivorotov, K. Halter-man, and O.T. Valls

2010/121 EBEX: A Balloon-Borne CMB Po-larization ExperimentB. Reichborn-Kjennerud, A.M.Aboobaker, P. Ade, F. Aubin, C.Baccigalupi, C. Bao, J. Borrill, C.Cantalupo, D. Chapman, J. Didier,M. Dobbs, J. Grain, W. Grainger,S. Hanany, S. Hillbrand, J. Hub-mayr, A. Jaffe, B. Johnson, T.Jones, T. Kisner, J. Klein, A. Ko-rotkov, S. Leach, A. Lee, L. Levin-son, M. Limon, K. MacDermid, T.Matsumura, X. Meng, A. Miller,M. Milligan, E. Pascale, D. Pols-grove, N. Ponthieu, K. Raach, I.Sagiv, G. Smecher, F. Stivoli, R.Stompor, H. Tran, M. Tristram, G.S. Tucker, Y. Vinokurov, A. Yadav,M. Zaldarriaga, and K. Zilic

2010/122 Software Systems for Operation,Control, and Monitoring of theEBEX InstrumentM. Milligan, P. Ade, F. Aubin, C.Baccigalupi, C. Bao, J. Borrill, C.Cantalupo, D. Chapman, J. Didier,M. Dobbs, W. Grainger, S.

Hanany, S. Hillbrand, J. Hubmayr,P. Hyland, A. Jaffe, B. Johnson, T.Kisner, J. Klein, A. Korotkov, S.Leach, A. Lee, L. Levinson, M.Limon, K. MacDermid, T. Mat-sumura, A. Miller, E. Pascale, D.Polsgrove, N. Ponthieu, K. Raach,B. Reichborn-Kjennerud, I. Sagiv,H. Tran, G. S. Tucker, Y. Vi-nokurov, A. Yadav, M. Zaldarriaga,and K. Zilic

2010/123 The EBEX Cryostat and Support-ing ElectronicsI. Sagiv, A.M. Aboobaker, C. Bao,S. Hanany, T. Jones, J. Klein, M.Milligan, D.E. Polsgrove, K.Raach, K. Zilic, A. Korotkov, G.S.Tucker, Y. Vinukurov, T. Matsumu-ra, P. Ade, W. Grainger, E. Pascale,D. Chapman, J. Didier, S. Hill-brand, B. Reichborn-Kjennerud, M.Limon, A. Miller, A. Jaffe, A.Yadav, M. Zaldarriaga, N. Pon-thieu, M. Tristram, J. Borrill, C.Cantalupo, T. Kisner, F. Aubin, M.Dobbs, K. MacDermid, G. Hilton,J. Hubmayr, K. Irwin, C. Reintse-ma, C. Baccigalupi, S. Leach, B.Johnson, A. Lee, H. Tran, and L.Levinson

2010/132 Observations of Large-Amplitude,Narrowband Whistlers at StreamInteraction RegionsA. Breneman, C. Cattell, S.Schreiner, K. Kersten, L.B. WilsonIII, P. Kellogg, K. Goetz, and L.K.Jian

Physics, UMD

2010/102 Pauli-Villars Regularization ofField Theories on the Light Front(presented at Light Cone 2010)J. Hiller

2010/103 Nonperturbative Calculations inLight-Front QED (presented atLight Cone 2010)S. Chabysheva

2010/198 Pauli-Villars Regularization ofField Theories on the Light Front(presented at QCD@Work 2010)J.R. Hiller

2010/199 Nonperturbative Calculations inLight-Front QED (presented atQCD@Work 2010)S.S. Chabysheva

Plant Biology

2010/175 and CB 2010-65 Network Modeling Reveals Preva-lent Negative Regulatory Relation-ships Between Signaling Sectors inArabidopsis Immune SignalingM. Sato, K. Tsuda, L. Wang,J. Coller, Y. Watanabe, J. Glaze-

brook, and F. Katagiri

Science and Mathematics,

UMM

2010/150 Alternative Syntheses and Reactivi-ty of Platinum(II) Terpyridyl Ace-tonitrile ComplexesT.M. Pappenfus, J.R. Burney,K.A. McGee, G.G.W. Lee, LarissaR. Jarvis, D.P. Ekerholm, M.Farah, L.I. Smith, L.M. Hinkle,and K.R. Mann

Research Reports

Fall 2010 Supercomputing Institute Research Bulletin 17

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