Curriculum Vitae forARIEH WARSHEL

PERSONALBorn: 20 November 1940, Kibbutz Sde-Nahum, IsraelMarried: Tamar Warshel, 1966; Two daughters (Merav and Yael)Military Service: Israel Defense Army; 1958-1962; Rank, CaptainCitizenships: USA and Israel Contact: Tel: 213.740.4114; Fax: 213.740.2701; E-mail: warshel@usc.eduWeb: http://laetro.usc.edu/

EDUCATIONTechnion, Israel Institute of Technology, Haifa BS 07/1966 ChemistryWeizmann Institute, Rehovot MS 08/1967 Chemical PhysicsWeizmann Institute, Rehovot PHD 01/1969 Chemical Physics

1962 - 66 BSc, Chemistry; The Technion, Israel Institute of Technology, Haifa, Israel1966 - 67 MSc, Chemical Physics; The Weizmann Institute of Science, Rehovot, Israel1967 - 69 PHD, Chemical Physics; The Weizmann Institute of Science, Rehovot, Israel Thesis

advisor: S. Lifson

PROFESSIONAL POSITIONS1970 - 72 Research Associate, Harvard University, Cambridge, MA1972 - 73 Research Scientist, Weizmann Institute of Science, Rehovot1973 - 76 Senior Scientist, Weizmann Institute of Science, Rehovot1976 - 79 Assistant Professor of Chemistry, University of Southern California, Los Angeles1977 - 78 Associate Professor, Weizmann Institute of Science, Rehovot1979 - 84 Associate Professor of Chemistry, University of Southern California, Los Angeles1984 - Professor of Chemistry, University of Southern California, Los Angeles1991 - Professor of Chemistry and Biochemistry, University of Southern California, Los Angeles1996 - Distinguished Professor of Chemistry, University of Southern California, Los Angeles2004 - Member, USC Norris Comprehensive Cancer Center, Los Angeles2011 - Distinguished Professor, University of Southern California, Los Angeles2013 - Nobel laureate, Nobel Committee for Chemistry2014 –

2016 -

Dana and David Dornsife Chair in Chemistry, University of Southern California, Los AngelesDistinguished Professor at Large, The Chinese University of Hong Kong, Shenzhen

HONORS AND AWARDS1965 Technion Award, Best Third-year Student in Chemistry, Technion, Israel Institute of

Technology1966 BS. Summa Cum Laude, Technion, Israel Institute of Technology1969 Mifal Hapais Prizes for the Arts and Sciences, Israel1975 EMBO Fellow, MRC Laboratory of Molecular Biology1978 Alfred P. Sloan Fellowship, Alfred P. Sloan Foundation1981 USC Associates Award for Creativity in Research, University of Southern California1981 EMBO Senior Fellowship, Weizmann Institute of Science1991 The Inaugural Becton, Dickinson Memorial Lecture, Duke University1992 USC Faculty Recognition Award for the book, “Computer Modeling of Chemical Reactions

in Enzymes and Solutions”, University of Southern California1993 Annual Award of the International Society of Quantum Biology and Pharmacology,

International Society of Quantum Biology and Pharmacology

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2000 Elected Fellow of the Biophysical Society, Biophysical Society2002 Brown and Williams Scholars Lectures, University of Louisville2003 The Habermann Lecture, Marquette University2003 Tolman Medal, American Chemical Society2006 President’s Award for Computational Biology, International Society of Quantum Biology

and Pharmacology2008 Elected Fellow of the Royal Society of Chemistry, Royal Society of Chemistry2008 Molecular Frontiers Symposium, Royal Swedish Academy of Science2009 Elected Member, National Academy of Sciences2010 The Lifson Memorial Lecture, The Weizmann Institute2010 Chevy Goldstein Distinguished Lecture, California State Polytechnic University2011 Appointed Distinguished Professor of Chemistry and Biochemistry, University of Southern

California2012 Soft Matter and Biophysical Chemistry Award, Royal Society of Chemistry2012 Elected Fellow of the AAAS, American Association for the Advancement of Science2013 The Nobel prize for chemistry, Nobel Committee for Chemistry2014 Founders Award, Biophysical Society2014 Honorary Fellow (HonFRSC), Royal Society of Chemistry2014 ISC Gold Medal, Israeli Chemical Society2014 Doctor of Philosophy, Honoris Causa, Bar Ilan University2014 Honorable Professor, Kazakh National Agrarian University2014 The Jubilee Medal “80 years of Al-Farabi Kazakh University”, Al-Farabi Kazakh University2014 Honorary Doctor, Al-Farabi Kazakh National University2014 Doctor Scietiae et honoris causa, Pontifical Catholic University of Chile2015 Doctor of Science, honoris causa, Uppsala University201520152016

Doctor Honoris Causa, Lodz University of TechnologyDoctor Honoris Causa, Israel Institute of TechnologyThe Birch lecture at UNSU, Canberra

20162016

Emerson Center Lectureship Award, Emory UniversityDiploma for Distinguish Service to Life Science, CIS Union of Physiological Society and the Russian Biochemical Society.

EDITORAL BOARDS Proteins: Structure, Function and Genetics Computational Molecular Bioscience Israel Journal of Chemistry QRB discovery

NAMED AND KEYNOTE LECTURES1991 The Inaugural Becton Dickinson Memorial Lecture, Duke University, [How do Enzymes

Really Work?].2002 The Brown and Williamson Scholar Lectures, The University of Louisville, [[a) How do

Enzymes Really Work? b) Computer Simulations of the Dynamics of Biological Processes].2003 The Habermann Lecture, Marquette University, [Computer Simulations of Biological

Processes: Towards Quantitative Structure Function Correlation in Biology].2005 Keynote Speaker, 3rd Chinese Theoretical and Computational Chemistry Conference, Hong

Kong, [Computer Simulation of the Function of Biological Molecules].2006 The 2006 President’s Award Lecture, ISQBP President’s Meeting, Strasburg, [Computer

Simulations of the Function of Biological Molecules; What has been Accomplished and Where we are Going].

2009 The CUSO Lecture Series in Switzerland, [Frontiers in Biophysical Simulations].

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2010 The Lifson Memorial Lecture, The Weizmann Institute of Science, [Computer Simulations of the Functions of Biological Systems; What has been Accomplished and Where we are Going]. The Chevy Goldstein Distinguished Lecture in Chemistry, Cal Poly Pomona, [Electrostatic Basis of Biological Functions].

2012 Distinguished Lecture in Computational Biology, UC Irvine, [Advances in Modeling of Biological Functions].RSC Award in Soft Matter and Biophysical Chemistry Lecture Tour, Newcastle, Sheffield, Bath, November, [Advances in Modeling Biological Functions].

2013 Opening Lecture in Modeling Interaction in Biomolecules VI, Marianské Lazně, Czech Republic, [Multiscale Modeling of the Function of Biological Systems].Nobel Lecture, Stockholm, December, [Computer Simulations of Biological Functions; From Enzymes to Molecular Machines].

2014 Opening Lecture, Federation of Israeli Experimental Biology (ILANIT), Eilat, Israel, February, [Multiscale Modeling of Complex Biological Systems and Processes]. The 4th Annual Vladimir Zelman M.D., Ph.D. Endowed Lecture, University of Southern California, [Computer Simulations of Biological Function].The Annual George A. Olah Lecture in Chemistry, University of Southern California, [Multiscale Modeling of Complex Biological Systems and Processes].BIT’s 5th World Gene Convention, Haikou, China, Keynote Lecture, [Multiscale Modeling of the Functions of Biological Molecules].CHAINS 2014, Eindhoven. The Netherlands, Keynote Lecture, [Multiscale Modeling of the Functions of Biological Molecules].

2015 Inaugural Keynote Lecturer at the10th International Symposium on Bio-organic Chemistry (IUPAC), Indian Institute of Science Education and Research, Pune, India, [Computer Simulations of the Action of Biological Molecules].7th International Science Youth Forum, Singapore, [Computer Simulations of the Action of Biological Molecules].The Almløf-Gropen Lecture Department of Chemistry, Oslo, June [ Multiscale modeling of the function of biological systems].The Almløf-Gropen Lecture center for theoretical and computational chemistry Tromso, June [Multiscale modeling of the function of biological systems].Franklin Memorial Lecture at Rice University, September [ How to Model the Action of Complex Biological Systems on a Molecular Level?].

2016 Global Young Scientists Summit, Singapore, [How to Model the Action of Complex Biological Systems?].

BIT’s 7th World DNA and Genome Day, Dalian, China, [Modeling the Action of Complex Biological Systems on a Molecular Level].

EMBO Conference on Biocatalysts, Oulu, Finland, [Electrostatic in Biocatalysts]. The Birch lecture at UNSU, Canberra, Australia, [Modeling the Action of Complex Biological

Systems on a Molecular Level]. ICPOC-23, Sydney Australia, [ How Do Enzymes Work and How Do They Not Work:

Advances in Simulations and Computer Aided Enzyme Design].Opening the academic year, Chinese University of Hong Kong (CUHK).The Emerson Center Award Lecture, Emory University, [How to Model the Action of Complex Biological Systems on a Molecular Level]. V Baku International Humanitarian Forum, Baku, Azerbaijan, [Using Computer Modeling in Biological Medicine].The V Congress of the Russian Biochemical Society, Sochi, Russia, [How to Model the Action of Complex Biological Systems and to Advance Molecular Medicine].Youth Forum, Sochi, Russia, October [Modeling Biological Molecules Keynote Speech].The Xingda Lectureship, Peking University, Beijing, China, [Modeling the Action of Complex Biological Systems on a Molecular Level].BIT’s 14th Annual Congress International Drug Discovery Science & Technology, Nanjing, China, [Computer Modeling of Complex Biological Systems].Instituto Politecnico Nacional, Mexico City [From Kibbutz to Nobel on Modeling Complex

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Chemical Systems].

REVIEW COMMITTEES (Since 2001)2001 Special review of theoretical chemists from Sweden for a senior position.2002 Study section of theoretical chemistry in Sweden (2002).2003 Search for a chair in Computational Biophysics in Denmark 2004 NIH Special emphasis panel for a program project on ikb/NF kB recognition (March).2004 NIH study section for National Centers for Biocomputing (May).2005 NIH study sections for National Centers for Biocomputing (May).2006 NIH study section ZRG1 BCMB-Q (90) (February).2006 NIH study section ZRG1 BCMB-Q (90) (June).2008-13 European Review Panel.2010 NAS Review committee of molecular dynamics proposals.2011 NAS Review committee of molecular dynamics proposals.2012 NAS Review committee of molecular dynamics proposals.

INVITED LECTURES1973 Farkas Memorial Symposium on Structure and Dynamics of Excited States, Jerusalem,

[Calculations of Excited State Properties of Conjugated Molecules].1974 Intercongress Symposium on Intra- and Intermolecular Forces, International Union for

Crystallography, University Park, Pennsylvania, [Incorporation of Inter- and Intra-Molecular Interactions in Calculations of Equilibrium Geometries & Lattice Vibrations of Molecular Crystals].

1976 Gordon Research Conference, Biopolymers, New Hampshire, [Theoretical Studies of the Catalytic Reaction of Lysozyme].

1977 Symposium on Simulation of Enzymatic Reactions, Bilthoven, The Netherlands, [The Theory of Enzyme Catalysis].

1978 Symposium on Local Modes in Molecules, APS Annual Meeting, San Francisco, [General Anharmonicity Treatments of Large Molecules and the Local Modes Description].Fourth West Coast Protein Workshop, Asilomar, [Charge Stabilization and Enzymatic Reactions].Symposium on Sickle Cell Anemia, San Diego, [Energy/Structure Correlation in Metalloporphyrins and Hemoglobin].ACS Symposium on Solvent Effect on Molecular Structure and Energetics, Indianapolis, [Microscopic Models for Calculations of Solvent Effects in Chemistry].Sanibel Symposia, Palm Coast, Florida, [Quantitative Calculations of Ionic Reactions in Aqueous Solutions and in Enzyme Active Sites].Ionic Reactions in Aqueous Solutions and in Enzyme Active Sites, Gordon Research Conference on The Visual Pigment, New Hampshire, [Charge Stabilization Mechanism in Rhodopsin and Bacteriorhodopsin].Frontiers of Biological Energetics, 50th Anniversary of Johnson Research Foundation and 65th Birthday of Briton Chance, Philadelphia, [Energy Structure Correlation in Metalloporphyrins and Hemoglobin].Sixth International Biophysics Congress, Kyoto, Japan, [Theoretical Studies of the Origin of Enzyme Catalysis].Symposium on Visual Pigment and Purple Membrane, Kyoto, Japan, [Charge Stabilization Mechanism in Rhodopsin and Bacteriorhodopsin].

1979 The Third International Symposium on Oxidases and Related Oxidation Reduction Systems, Albany, [Theoretical Studies of Electron Transfer in Cytochromes].Symposium on Structure-Function Relationships in Proteins, Nucleic Acids and Viruses, Minneapolis, [Theoretical Studies of Enzyme Catalysis].Lectures on Biological and Chemical Physics, A Symposium in Honor of Shneior Lifson on his 65th Birthday, The Weizmann Institute of Science, Israel, [The Energetics of Enzyme Catalysis].Workshop on Simulation of Enzymatic Reactions, Orsay, France, [A Valence Bond Approach for Calculations of Enzymatic Reactions].

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The Lighthouse Conference on Enzyme Mechanism, Oregon, [Electrostatic Effects in Biological Reactions].SECAM Discussion on Protein-Protein Interactions, Brussels, [Electrostatic Effects in Subunits Interactions].

1980 Symposium on Interaction between Iron and Proteins in Oxygen and Electron Transport, Airlie House, Virginia, [Electrostatic Contributions to Cooperativity in Hemoglobin].Conference on Quantum Chemistry in Biomedical Sciences, The New York Academy of Sciences, NY, [Valence Bond Calculations of Enzymatic Reactions].Gordon Research Conference on Visual Transduction, Tilton School, New Hampshire, [Theories for the Reaction Pathway in Visual Pigment Photochemistry].Eighth International Congress on Photobiology, Strasbourg, France, [The Dynamics of the First Step of the Vision Process].The VIIth International Conference on Raman Spectroscopy, Ottawa, Canada, [Panel Discussion on the Visual Pigments].West Coast Protein Crystallography Workshop, Asilomar, [Energetics of Cooperativity in Hemoglobin].Gordon Research Conference on Diffraction Methods in Molecular Biology, Andover, New Hampshire, [Molecular Dynamics in Rhodopsin].

1981 Resonance Light Scattering in Solid States and Biomolecular Systems, Arizona State University, March, [Resonance Raman in Protein Active Sites]. Oholo Biological Conference on Biomimetic Chemistry and Transition State Analogs: Approaches to Understanding Enzyme Catalysis, Israel, March, [Correlation X-ray Structures of Enzymes with Their Activity].Fourth American Conference on Theoretical Chemistry, Boulder, June, [Molecular Dynamics of Reactions in Solutions and Proteins]. Discussion Meeting on Visual Pigments. Montreal, Canada, October, [Energy Storage and Reaction Pathway in the First Step of the Vision Process].CECAM Discussion Meeting on Simulation of Small Molecules Binding to Proteins, Bilthoven, The Netherlands, October, [Correlation of Geometry Changes and Energetics of Ligand Binding in Proteins].

1982 Gordon Research Conference on Biopolymers, New Hampshire, July, [The Dynamics of Enzymatic Reactions].International Conference on Time Resolved Vibrational Spectroscopy, Lake Placid, NY, August, [Semiclassical Trajectory Studies of Vibronic Processes in Large Molecules].NSF Workshop on Time Resolved Vibrational Spectroscopy, Minnowbrook, NY, August. The Lighthouse Conference on Structure and Mechanism, Oregon, August, (could not attend).Biological Structure and Coupled Flows, Rehovot, Israel, June, [Electrostatic Basis for Vectorial Light-Induced Charge Separation in Photobiological Systems].

1983 West Coast Protein Crystallography Workshop, Asilomar, March, [Dynamics of Enzymatic Reactions].Molecular Mechanics Symposium, Indiana University, June, [Extending Molecular Mechanics to Studies of Chemical and Biological Reactions]. International Conference on Nonlinear Electrodynamics in Biological Systems, Loma Linda, June, [Dynamics of Enzymatic Reactions and the Role of Electrostatic Fluctuations].CECAM Workshop on Nucleic Acids, Orsay, France, July, [Electrostatic Interactions in Nucleic Acids].ACS Symposium on Biomolecules, Washington D.C., August, [Computer Simulation of Enzymatic Reactions].A Symposium on Biochemistry and Mechanism of Enzyme Reactions in the West Coast Conference on Chemistry and Spectroscopy, Pasadena, October, [Electrostatic Basis of Structure-Function Correlation of Enzymatic Reactions].A Symposium on Molecular Dynamics in the West Coast Conference on Chemistry and Spectroscopy, Pasadena, October, [Simulating the Dynamics of Biological Reactions].

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Pontifical Academy of Science Study Group on Specificity in Biological Interactions, The City of Vatican, November, [Correlating the Catalytic Activity of Enzymes with Their Structure and Dynamics].A Workshop on Nonlinear Wave Phenomena in Electromagnetic Interactions with Tissue, Univ. of Maryland, November, (Could not attend).

1984 A Meeting on the Mechanism of Protein Folding, Santa Cruz, February, [Folding Energy and Enzyme Catalysis].International Symposium on Structure and Dynamics of Nucleic Acids, Proteins and Membranes, Rome, April, [Symposium Chairperson].A Workshop on Molecular Dynamics of Proteins, University of North Carolina, Chapel Hill, May, [Electrostatic Energy in Solutions and Proteins].A Workshop on Molecular Dynamics of Proteins, University of North Carolina, Chapel Hill, May, [Dynamics of Enzymatic Reactions].Meeting on Molecular Basis of Cancer, Buffalo, May, [Electrostatic Aspects of Biological Recognition].The 8th International Biophysics Congress, Bristol, England, August, [How to Calculate Electrostatic Energies in Proteins].International Symposium on Biomolecular Structure and Interactions, Bangalore, India, December, [Dynamics of Proton Transfer Reactions in Proteins] (Invited, had to cancel due to last minute problems).

1985 Gordon Research Conference on Protons and Membranes Reactions, Santa Barbara, February, [The Energetics and Dynamics of Light Induced Proton Transfer Across Membranes].Conference on Protein Structure: Molecular and Electronic Reactivity, Philadelphia, April, [The Dynamics of Electron Transfer Reactions in Proteins].The Emil-Warburg-Symposium on Time Resolved Vibrational Spectroscopy, Bayreuth, Germany, June, [Exploring the Molecular Origin of Vibronic Line Shapes in Anharmonic Molecules by a Quantized Semiclassical Trajectory Approach].Symposium on Quantum Chemistry of Biological Systems, Hunter College, New York, August, [Modeling Enzymatic Reactions].The 5th International Congress on Quantum Chemistry, Montreal, Canada, August, [Simulating the Dynamics of Enzymatic Reactions].International Workshop on Intramolecular Vibrational Redistribution and Quantum Chaos, Rochester, NY, October, [Simulating Intramolecular Dynamics of Radiative and Radiationless Processes].US/Japan Seminars on Time Resolved Vibrational Spectroscopy, Honolulu, November, [Simulating Radiationless Transitions].International Workshop on Molecular and Biotechnology, Madars, India, August, (could not participate because of overlap with the meeting in Canada).International Workshop on Structure and Function of Rhodopsin, Szegeb, Hungary, September, [Electrostatic Effects in Proteins; Light Driven Charge Motion in Rhodopsin, BR and Photosynthetic Systems]. Biophysical Society, Baltimore, Session Chairman, [Microscopic and Macroscopic Models for Calculations of Electrostatic Energy].

1986 ACS Symposium on Theory of the Solvent Role in Charge Transfer Reactions, New York, April, [Simulating the Energetics and Dynamics of Electron Transfer and Proton Transfer Reactions in Polar Solvent].Sanibel Symposia on Quantum Biology and Quantum Pharmacology, Marineland, Florida, March, [Toward Computer Simulation of Site Directed Mutagenesis of Enzymatic Active Site].The first EBSA Workshop on Structure Dynamics and Functions of Biomolecules, Saltsjobaden, Sweden, July, [Simulating the Functions of Designer Enzymes].The 10th International Conference on Raman Spectroscopy, Eugene, Oregon, September, [Incorporating Protein and Solvent Environments in Resonance Raman Calculations].ACS Symposium on Theory at the Interface Between Chemistry and Biology, Anaheim, September, [Towards Computer Aided Enzymes Design].

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Gordon Research Conference on Biopolymers, Holderness School, New Hampshire, June, [Correlating Structure, Energy and Function in Solvated Proteins].Symposium on Three-Dimensional Structure and Drug Action, Tokyo, Japan, September, [Towards Computer Simulation of Site-directed Mutagenesis of Enzyme Active Sites].

1987 The Thirty-First Annual Meeting of the Biophysical Society, New Orleans, February, [Towards Quantitative Structure Function Correlation in Proteins].American Physical Society, Symposium on Computational Approaches to Protein Structure and Dynamics, New York, March, [Simulating Enzymatic Reactions].ACS Symposium on Biological Electron Transfer, Denver, April, [Simulating the Energetics and Dynamics of Electron Transfer in Proteins].The Fifth Conversation in Biomolecular Stereodynamics, Albany, June, [Computer Simulation of Designer Enzymes].World Congress of Theoretical Organic Chemist, Budapest, Hungary, August, [Simulating Organic Reactions in Solutions and Proteins].ACS Symposium on Free Energy Perturbation Methods, New Orleans, September, [Quantitative Evaluation of Catalytic Free Energies in Genetically Modified Proteins].The Microscopics of Enzyme Catalysis, Barga, Italy, October, [Simulating the Dynamics of Enzymatic Reactions in Genetically Modified Proteins].NATO Workshop on Structure of Photosynthetic Bacterial Reaction Centers, Cadarache, France, September, [Crystallography and Optical Spectroscopy] (Invited but could not attend).

1988 Sanibel Symposia, Marineland, Florida, March, [Simulating the Dynamics and Energetics of the Primary Event in Bacterial Photosynthesis].Workshop on Molecular Mechanics and Molecular Dynamics, Tallahassee, April, [Force Fields for Chemical Reactions in Solutions and Proteins].Colloquium on Computer Simulations in Protein Engineering and Drug Design, Amsterdam, Netherlands, [Free Energy of Reaction Pathways in Designer Enzymes].Macromolecular Dynamics Workshop of the ONR, Las Vegas, May, [The Dynamics of the Primary Event in Photosynthesis].Gordon Research Conference on Physico-Chemical Aspects of Photosynthesis, Holderness School, New Hampshire, July, [Computer Simulation of the Primary Charge Separation Process in Bacterial Photosynthesis].NATO ASI on The Enzyme Catalysis Process: Energetics, Structure and Dynamics, Barga, Italy, July, [A Series of Three Lectures on Simulation of Enzymatic Reactions].OHOLO Conference on Computer Assisted Modeling of Receptor-Ligand Interactions, Eilat, Israel, April, [Computer Aided Enzyme Design].Gordon Research Conference on Proteins, Newport, Rhode Island, June, [Computer Simulation of Genetically Modified Serine and Cystein Proteases; Correlating Sequence and Catalysis].Workshop on Molecular Basis of Biological Recognition Saltsjobaden, Stockholm, Sweden, September, [Simulation of the Primary Event in Bacterial Photosynthesis].Rosentiel retreat meeting on Anticipatory Design Strategies, Greenwich. October, [Computer Aided Protein Design: How to Optimize Electrostatic Microenvironments].Nobel Symposium on Structure and Dynamics of Biological Systems, Lund, Sweden, December, [Simulating Electrostatic Energies in Solvated Proteins: A Semiquantitative Correlation of Structure and Function]The Third Annual Alliant Users Conference, San Diego, October, [Computer Aided Enzyme Design, The Molaris System]

1989 UCLA Symposium on Protein and Pharmaceutical Engineering, Park City, Utah, January, [Enzyme Catalytic Mechanism a CAD Approach].ACS Symposium on Computational Modeling of Molecular Systems, Dallas, Texas, April, [Simulations of Chemical Reactions in Solutions and in Enzymes]The 22nd Jerusalem Symposium on Perspectives in Photosynthesis, May, [Microscopic Simulation of Quantum Dynamics and Energetics in Bacterial Reaction Centers]The 23rd European Symposium on Bio-Organic Chemistry, Gregynog, Wales, May, [The Microscopic Dielectric Constant in Macromolecules and the Origin of Enzyme Catalysis]

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The 2nd Symposium of Protein Engineering, Kobe, Japan, August, [Computer Aided Enzyme Design]The 44th International Meeting of Physical Chemistry on Modeling Molecular Structures, Nancy, France, September, [Electrostatic Basis of Protein Functions].The 3rd Alliant Chemistry Colloquium, Tokyo, Japan, October, [Reaction Pathways in Designer Enzymes].MSI Symposium on Protein Chemistry, Minneapolis, Minnesota, October, [Simulation of Quantum Dynamics of Electron Transfer Processes in Bacterial Photosynthesis].International Chemical Congress of Pacific Basin Societies, Honolulu, Hawaii, December, [Computer Simulation of Electron Transfer in Bacterial Reaction Centers].

1990 ONR Meeting on Molecular Recognition, Charleston, January, [Molecular Recognition in Metalloenzymes Catalysis].UCSF Conference on Protein and Drug Design and Delivery, San Francisco, February, [Design Principles of Metalloenzymes, Insight from Electrostatic Calculations].Joint U.S.-Israel Workshop on Light Energy Conversion, February, [Microscopic Simulations of the Energetics and Dynamics of Light Induced Charge Separation in Bacterial Photosynthesis].Symposium of Structure Function of Bacterial Reaction Centers, Feldafing, Germany, March, [Simulations of Reorganization Energies in Native and Mutant Proteins].Gordon Research Conference on Biocatalysts, Plymouth State College, NH, June, [Mutagenesis Calculations]. Gordon Research Conference on Enzymes, Coenzymes and Metabolic Pathways, Kimball Union Academy, NH, July, [Computer Simulation of the Key Role of Electrostatic Energy in Enzyme Catalysis]The 10th International Biophysics Congress, Vancouver, Canada, August, [The Energetics and Dynamics of Ion Channels]IUPAB Satellite Symposium on Expanding Frontiers in Polypeptide and Protein Structural Research, Whistler, Canada, July, [Calculations of Free Energies of Macromolecules]American Conference on Theoretical Chemistry, San Diego, August, [Simulation of Quantum Dynamics in Proton Transfer Process].ACS Symposium on Electron Transfer Reactions in Chemistry and Biology, Washington D.C., August, [Computer Simulations as Microscopic Probes of Electron Transfer in Solutions and Photosynthetic Proteins].ACS Symposium on Challenges in Computational Chemistry, North Carolina State University, September, [Computer Simulations of Chemical Reactions in Solutions and Proteins].

1991 Sanibel Symposia, St. Augustine, March, [Computer Simulations of Bacterial Photosynthesis].International Symposium on Computer Simulation of Biomolecular Systems and Mechanisms, Menton, France, June, [Computer Simulations of Enzymatic Reactions].NATO Workshop on the Role of Computational Models and Theories in Biotechnology, Sant Feliu, Spain, June, [Computer Aided Enzyme Design and the Key Role of Electrostatic Energies].ACS Symposium on Biological Electron Transfer, New York, August, [Computer Simulations of the Quantum Dynamics of Electron Transfer Processes in Solutions and Bacterial Reaction Centers].

1992 ACS Symposium on Computer Simulations in Chemical Systems, Anaheim, October, [Computer Simulations of Chemical Reactions in Solutions and Proteins].U.S.-Japan Joint Seminar on the Biophysical Chemistry of Retinal Proteins, Hawaii, January, [Simulating the Dynamics of the Primary Event in Bacteriorhodopsin].Workshop on High Performance Computing and Grand Challenges in Structural Biology, Tallahassee, Florida, January, [Computer Simulations of Enzymatic Reactions]. The Biophysical Society Meeting, Symposium on Quantum Effects in Proteins, Houston, Texas, February, [Simulations of Quantum Dynamics in Proton Transfer and Hydride Transfer Reactions in Proteins].

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Royal Society of Chemistry Discussion of Structure and Activity of Enzymes, Cambridge, England, April, [Computer Simulation of Enzymatic Reactions: Examination of Linear Free Energy Relationships and Quantum Mechanical Corrections in the Initial Proton Transfer Step of Carbonic Anhydrase].Meeting on Modeling Organic Reactivity in Solutions, Spain, June, (Was invited but could not participate).NATO Workshop on the Photosynthetic Bacterial Reaction Center, Cadarache, France, May, (Was invited but could not participate).Gordon Research Conference on Computational Chemistry, New Hampton, June, [Computer Simulation of Chemical Processes in Proteins and Solution].Workshop on Activated Dynamics in Condensed Matter, Telluride, Colorado, July, [Evaluation of Quantum Mechanical Rate Constants for Processes in Solutions].The IXth International congress on Photosynthesis, Nagoya, Japan, August 30 - September 5, [Computer Simulations of Charge Separation Processes in Model Compounds and Bacterial Reaction Centers].NSF-DOE Institute in Computational Biology, Argonne National Laboratory, December, [Computer Simulations of Biological Processes; Studies of Enzyme Catalysis, Electron Transfer, Ion channels and Other Systems].

1993 ACS Workshop on Protein Dynamics and Thermodynamics, Jerusalem, Israel, March, [Computer Simulation of Enzymatic Reactions and Other Biological Processes].Special lecture series in Molecular Biology, University of Uppsala, Sweden, April, [Computer Simulation of Enzymatic Reactions and the Origin of Biological Catalysis].The 26th Jerusalem Symposium on Quantum Chemistry and Biochemistry: Reaction Dynamics in Clusters and Condensed Phases, Jerusalem, Israel, [Simulations of Electrons and Proton Transfer Reactions in Condensed Phases].Symposium on Dynamics and Function of Biomolecules of the Hungarian Academy of Sciences, Szeged, Hungary, August, [Computational Methods in Biology].NATO workshop on Photoinduced Electron Transfer Reactions, Hotel Alfa Mar, Portugal, September, [Computer Simulations of Photoinduced Electron Transfer in Solutions and Proteins].American Chemical Society National Meeting, Chicago, August, [Computer Simulation of Electron Transfer and Proton Transfer in Proteins and Solutions].The 2nd Conference on Recent Trends in Computational Chemistry, Jackson, Mississippi, November, [Computations Modeling of Chemical Processes in Solutions and Proteins].The 2nd Britton Chance Research Discussion Meeting on Photosynthesis, November, [Discussion leader].

1994 New York Academy of Science Symposium on Modeling Proteins in Solutions, New York, February, [Modeling Proteins in Solution].Sanibel Symposium, Verda Beach, Florida, February, [Simulation of Electron Transfer Processes in Proteins; Energetics, Dynamics, and Reliable Boundary Conditions].Gordon Research Conference on Isotopes, Oxnard, California, March, [Computer Simulation of Quantum Mechanical Tunneling in Enzymatic Reactions].ACS Symposium on Structure and Reactivity in Aqueous Solutions, San Diego, California, March, [Semiempirical and Ab Initio Approaches for Simulation of Chemical Processes in Solution].The 27th Jerusalem Symposium on Quantum Chemistry and Biochemistry, Jerusalem, Israel, May, [Computer Simulation of Enzyme Catalysis and the Action of Metallo-Enzymes].Protein Engineering and Design: Pfizer-Beckman Institute Symposium, Univ. of Illinois at Urbana-Champaign, June, [Computer Modeling as an Analytical Tool in Structure-function Correlation of Proteins].Hungarian Chemical Society Symposium on Molecular Modeling in Genetic and Protein Engineering, Sopron, Hungary, June, [Computer Aided Enzyme Design].The 8th International Congress of Quantum Chemistry, Prague, Czech Republic, June, [Computer Simulation of Enzyme Catalysis and Other Biological Processes].

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International Workshop on Electronic Structure Methods for Truly Large Systems: Moving the Frontiers in Quantum Chemistry, Braunlage, Germany, August, [Quantum Chemical Modeling of Reactions in Solution].Gordon Conference on Photosynthesis: Biological Aspects, New Hampton, New Hampshire, August, [Computer Simulations of the Electron Transfer Processes in Bacterial Reaction Centers: The Importance of Proper Treatments of Electrostatic Energies in Solvated Macromolecules].ACS Symposium on Theoretical Modeling of Biological Systems, New York, August, [Energetics and Quantum Dynamics of Enzymatic Reactions].European Research Conference: Modeling Photochemical Reactivity, San Feliu de Guixols, Spain, September, [Computer Simulation of Photochemical Processes in Proteins].Workshop on Algorithms for Macromolecular Modeling, Lawrence, Kansas, October, [Calculation of Electrostatic Energies in Proteins].Bimolecular Recognition at ONR Meeting, Berkeley Springs, West Virginia, November, [On the Design of Biocatalysts].

1995 The III Feldafing Workshop on Reaction Center of Photosynthetic Bacteria Structure and Dynamics, Feldafing, Germany, March, [The Dynamics of the Primary Event in Bacterial Reaction Centers].A Symposium in Honor of Martin Karplus, Cambridge, MA, March, [Computer Simulations of Enzymatic Reaction and the Mechanism of DNA Polymerases].Workshop on Quantum Mechanical Simulation Methods for Studying Biological Systems, Les Houches, France, May, [Semiempirical and Ab-Initio Approaches for Simulation of Chemical Processes in Solution and Proteins].CECAM Workshop on Developing Hybrid Quantum and Classical Mechanical Methods for Simulation of Biopolymers in Solution, Lyon, France, May, [Semiempirical and Ab-Initio Methods for Simulating Chemical Processes in Solution and in Proteins].CCPI Study Group on Quantum Mechanics of Large Systems: Dynamics and Hybrid Methods, St. Andrew, Scotland, June, [Calculating Chemical Processes in Solution and Proteins].The 2nd International Symposium on Biological Physics, Munich, Germany, July, [Electrostatic Energies and Macromolecular Functions].ACS Symposium on Proton Transfer, Chicago, August, [Computer Simulation of Proton Transfer in Enzymes and the Electrostatic Nature of Catalytic Hydrogen Bonds].The Fifth International Conference Taipei (ICCT) on Structure and Dynamics of Biological Macromolecules, Tsing Hua University, Taiwan, December, [Computer Modeling on Enzymatic Reactions and the Mechanism of G-Protein].Pacifichem ‘95 Symposium of Solvation Dynamics from Ions to Protein, Honolulu, Hawaii, December, [Simulating Quantum Dynamics of Charge Transfer Reactions in Solutions and Proteins].

1996 Beckmann Institute Workshop on Protein Folding, Caltech, February, [Chair of Theory Session].ACS Symposium on Transition States in Electron Transfer Reaction, New Orleans, March, [Simulating Transition States of Chemical Reactions in Solutions].NATO Advanced Study Institute on Biomolecular Structure and Dynamics, Loutraki, Greece, May, [(a) Computer Simulation of Enzymatic Reactions, (b) Structure and Dynamics of Biological Excited States].Fourth World Congress of Theoretical Oriented Chemists, Jerusalem, Israel, July, [Semiemprical and Ab Initio Approach for Simulation of Chemical Processes in Solution and Proteins].Gordon Research Conference on Protolytic Enzymes and Their Inhibitors, Colby-Sawyer, New Hampshire, July, [Energy Considerations Show that LBHB are Anticatalytic].ACS Symposium on Biophysical Chemistry, Orlando, August, [Organizer and Chair of the Section on Ion Channels and Protein Pumps].ACS Symposium on Performance on Quantum Chemical and Molecular Modeling Codes for Complex Chemical Systems, Orlando, August, [Ab-Initio Calculations of Chemical Reactions in Solutions and Proteins].

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EMBO-Workshop on Nucleotide and Phosphoryl Transfer in the Protein and RNA World, Xanten, Germany, September, [Energetics of Phosphate Hydrolysis in Proteins and Solution].Brazilian Chemical Society Meeting on Methods of Computer Simulation, As Applied to Chemistry, Biochemistry and Materials Sciences, Sao-Carlos, Brazil, November, [Semiempirical and Ab Initio Simulations of Chemical Reactions in Solutions and Proteins].

1997 Annual Biophysical Meeting, New Orleans, March, [Calculations of Electrostatic Energies in Proteins and Solutions by Simplified Dipolar Models].NATO Meeting on Molecular Modeling and Dynamics of Biological Molecules Containing Metal Ions, San Miniato, Italy, March, [Computer Simulation of the Action of Metalloenzymes].Symposium on Theoretical Chemistry in Biology; From Molecular Structure to Functional Mechanisms, Savannah, Georgia, June, [Approaches for Simulation of Chemical Processes in Solutions and Proteins].NIH Eleventh Meeting of Groups Studying the Structure of AIDS-related Systems and Their Application to Targeted Drug Design, Bathesda, June, [Structure Function Analysis of the Origin of Drug Resistance in HIV Proteases].CERCA/Chemistry-Industry Workshop, Montreal, Canada, June, [Computer Simulation of Enzymatic Reactions].Modeling ‘97, Erlangen, Germany, September, [Evaluation of Solvent Effects in Chemical and Biological Systems].ACS Symposium on Methods and Applications of Hybrid QM/MM Methods, Las Vegas, September, [Ab initio QM/MM Approaches of Studying Reactions in Proteins and Solutions: Strategies, Problems, and Perspectives].ACS Symposium on the Role of Electrostatics in Chemistry, Las Vegas, September, [Consistent Calculation of Electrostatic Energies in Proteins and Solutions].National Academy of Science Colloquium on Computational Biomolecular Science, Irvine, California, September, [Computer Simulation of Enzymatic Reactions and Other Biological Processes; Finding out What was Optimized by Evolution].

1998 ACS Symposium on Transition State Modeling for Catalysis, Dallas, March, [Elucidating the Origin of Transition State Stabilization in Enzymatic Reactions].ACS Symposium on Large Scale Electronic Structure Calculations, Dallas, March, [Electronic Structure Calculations of Chemical Reactions in Proteins and Solutions].Sanibel Symposium, St. Augustine, February, [Ab-Initio Simulations of Enzymatic Reactions].CECAM Workshop on Implicit Solvent Models for Biomolecular Simulations, Lyon, May, [The Relationship Between Explicit and Implicit Models for Evaluation of Electrostatic Energy in Macromolecules].Dahlem Workshop on Simplicity and Complexity in Proteins and Nucleic Acids, Berlin, May, [What is the Relationship Between Dynamical Effects and Biological Function?].The XIVth ICPC International Conference on Phosphorous Chemistry, Cincinnati, July, [Mechanistic Alternatives in Phosphate Ester Hydrolysis, the Use of Computer Simulations to Obtain More Unique Interpretation of Experiments].Gordon Conference on Computational Chemistry, Tilton, July, [Simulations of Binding and Catalysis: Ab Initio QM/MM-FEB Approaches and Electrostatic Models].

1999 Quantum Bioinorganic Chemistry 99, Warwick, England, July, [Computer Simulations of Metalloenzymes] The 5th World Congress of Theoretically Oriented Chemists, London, England August, [Computer Simulation of Enzymatic Reactions (Plenary Lecture)]ACS Symposium on QM/MM Methods, New Orleans, August, [Simulations of Chemical Reactions in Proteins and Solutions by Ab-Initio and Related Approaches]ACS Symposium on Bioenergetics, New Orleans, August, [Simulating Proton Translocations in Proteins: Probing Proton Transfer Pathways in the Rhodobacter Sphaeroides Reaction Center]

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2000 ACS Symposium on Potential Energy Surfaces from Polyatomic to Macromolecules, San Francisco, March, [Implicit and Explicit Models for Calculations of Electrostatic Energies in Macromolecules and Solutions]Symposium in Tribute to W. W. Parson, The Weizmann Institute of Science, Israel, April, [Do We Have Any Dynamical Contributions to Enzyme Catalysis?] International Society of Quantum Biology and Pharmacology, New Orleans, August, [Computer Simulations of Proton Transfer Processes in Proteins]ACS Symposium on Proton Transfer in Liquids, Solids and Proteins, Washington, August, section chairman The 3rd European Biophysics Congress, Munich, Germany, September, [Simulating Proton Translocations in Proteins: Probing Proton Transfer Pathways in the Rhodobacter Sphaeroides Reaction Center]Understanding Protein Electrostatics, Karolinska Institute, Stockholm, Sweden, September, (Plenary Lecture) [Microscopic and Macroscopic Approaches to Understanding the Nature of Electrostatic Energies in Proteins]Workshop on Macromolecular Modeling, New York University, October, [How Important are Entropy Contributions to Enzyme Catalysis?] The 2000 International Chemical Congress of Pacific Basin Societies, Honolulu, Hawaii, December, [Modeling the Energetics and Dynamics of Chemical Processes in Solutions and Clusters by Ab-initio Models of the Complete Solute Solvent System].

2001 The 11th International Conference on Second Messengers and Phosphoproteins, Melbourne, Australia, April, [How Does GAP Catalyze the GTPase Reaction of Ras: Insight from Computer Simulation Studies].ACS Symposium on Computational Studies of Enzymes, San Diego, April, [Using Computer Simulations to Elucidate the Origin of Enzyme Catalysis].CECAM Workshop: Mixed or Hybrid Quantum/Classical Methods, Lyon, France, June, [Pushing the Frontiers of QM/MM Simulations].Applied Biocatalysis 1980-2020, Trondheim, Norway, June, [The Origin of Biocatalysis: What are the Catalytic Principles that Really Work?].ACS Symposium on QM/MM methods, Chicago, August, [Pushing the Frontiers of QM/MM Calculations].

2002 Chemical Physics of Biological Systems, Lifson Memorial Lecture, The Weizmann Institute, Israel, February, [From Force Fields to Function of Biological Systems].ACS Symposium on Modern Aspects of Structure Function Correlation of Biomolecules: Signal Transduction, Orlando, Florida, April, [How Does GAP Catalyze the GTPase Reaction of Ras?]ACS Symposium on Modern Aspects of Structure-Function Correlation of Biomolecules: Electrostatic Aspects, Orlando, Florida, April, [Electrostatic Aspects of Structure-function Correlation in Biomolecules; From pKa Calculations to Studies of Signal Transduction and Ion Channels].The Sixteenth Symposium of the Protein Society, August, San Diego, [Searching for the Origin of the Catalytic Power of Enzymes: What Has Been Learned from Computer Simulation Approaches].The Second Conference of Quantum Bioorganic Chemistry (QBIC-2), Örenäs, Sweden, July, [Recent Advances in QM/MM and Related Approaches; More QM and More Configurational Sampling].Gordon Research Conference on Mutagenesis: Bates College, Main, August, [General Factors in Enzyme Catalysis and Their Specific Contributions to the Fidelity of DNA Polymerases].European Research Conference on “Computational Biophysics: Integrating Theoretical Physics and Biology”, San Feliu de Guixols, Spain, September, [Computer Simulations of Biophysical Reactions: Balancing First Principles with Completeness].

2003 The Enzyme Mechanism Conference, Galveston, Texas, January, [Using Computer Simulations to Elucidate the Molecular Origin of Enzyme Catalysis].

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American Physical Society Symposium on Physical Models of Ions/Protein Interactions, Austin, Texas, March, [Probing the Origin of the Selectivity of the KcsA Channel by Calculating Ion Currents with Realistic Protein Models].American Chemical Society symposium on Structure Function Correlation of Biological Channels, New Orleans, March, [Ion Selectivity in Ion Channels as a Challenge for Electrostatic Modeling of Proteins].American Chemical Society Symposium on Biological Applications of Implicit Solvent Models, New Orleans, March, [Implicit and Explicit Electrostatic Models for Structure Function Correlation of Biomolecules]. American Chemical Society Symposium on Understanding Physical Chemistry of Biomolecular Motors, New Orleans, March, [The Energetics of ATP synthase/Converting Conformational Changes to Electrostatic Energies].Seventh Annual Conference of the Structural Biology Network (SBNet), Tallberg, Sweden, June, [Challenges in Computer Simulations of Biological Molecules].The Applied Statistical Physics: Molecular Engineering Conference 9Astrtphys-Mex-2003), Puerto Valletta, Mexico, August, [Probing the Origin of Ions and Protons Selectivity in Realistic Models of Biological Channels].Modeling Chemical Reactivity: From Gas Phase to Solutions and Enzymes, Nancy, France, July, [Computer Simulations of Enzymatic Reactions: Exploring and Quantifying Catalytic Principles].

2004 Telluride Workshop on Non-Adiabatic Dynamics, Telluride, August, [Simulating Non-Adiabatic Transitions in Photobiological Processes; How Many Trajectories are Actually Passing through Conical Intersections]Telluride Workshop on Translocations of Protons in Biological Systems, August, [What Really Controls Proton Transport in Proteins: Grotthuss Versus Electrostatics]American Chemical Society Symposium on Quantum Classical Calculations, Philadelphia, August, [Challenges and Advances in QM/MM Methods for Studies of Biological Systems]American Chemical Society Symposium on the Molecular Origin of Replication and Translation of Nucleic Acids, Philadelphia, August, [Simulating Phosphate Hydrolysis in Key Biological Reactions]International Symposium on Retinal Proteins, Heidelberg, September, [Computer Simulations of Photobiological Reactions: Advances and Problems]Triangle Biophysics Symposium – Electrons to Proteins: Coupling and Linkage in Biology, North Carolina, November, [Computer Simulations of Biological Functions]

2005 The 3rd Chinese Theoretical and Computational Chemistry Conference, Hong Kong, January, Keynote Speaker [Computer Simulation of the Function of Biological Molecules]The 7th Congress of the World Association of Theoretically Oriented Chemists, Cape Town, South Africa, January, [How do Enzymes Really Work; Using Computer Simulations to Examine and Eliminate Catalytic Proposals].Quantum Chemistry Applied; From H3 to Biochatlysis, An International Conference for the 60th Birthday of Per Siegbahn, June, Stockholm, [Simulating Proton Transport in Enzymes, Channels and Pumps].Conference on Quantum Atomic and Molecular Tunneling, Santiago de Compostela, Spain, July, [Nuclear Quantum Mechanical Contributions to Enzyme Catalysis: Critical Test of a Popular Hypothesis].ACS National Meeting, Washington DC, August, [Using Computer Simulations to Establish the Key Role of Electrostatic Preorganization in Enzyme Catalysis].The 1st International NorStruct Workshop in Structural Biology, Tormso, Norway, October, [Elucidation the Origin of Enzyme Catalysis by Computer Simulations; How to Exclude/Validate Catalytic Proposals].Royal Society meeting on Quantum Catalysis in Enzymes –Beyond the Transition State Theory Paradigm, London, November, [Transition State Theory Provides a Quantitative Framework for Analyzing Enzyme Catalysis; It is All in the Activation Free Energy]Workshop on Multiscale Modeling in Soft Matter and Biophysics, IPAM, UCLA, September, [Multiscale Modeling of Biological Functions].

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Bridging Time Length and Scale in Material Science and Biophysics Culminating Workshop, Lake Arrowhead, CA, December, [QM/MM Modeling].Symposium on Proton Transport Pacificame 2005, Honolulu, Hawaii, December, [Simulation Proton Transport in Biological Systems: The EVB as an Effective Strategy for Modeling PTR Processes].

2006 Gordon Research Conference on Protons and Membranes Reactions, Ventura, March, [Computer Simulations of Proton Transport in Proteins].Seventh Meeting of the Swedish Theoretical Chemists, Stockholm, Plenary lecture, May 5, [Capturing the Nature of Biochemical Processes by Molecular Simulations].ISQBP President’s meeting Strasburg, June, the 2006 Presidents Award Lecture, [Computer Simulations of the Function of Biological Molecules: What Has Been Accomplished and Where We are Going].Urobic8, Avero, Portugal, July, plenary lecture, [Computer Simulations of the Action of Metalloenzymes: Methods and Insights].ACS National Meeting, San Francisco, September, [From Macroscopic to Microscopic Descriptions of Electron Transfer and Proton Transfer Reactions: Quantifying Marcus Parabolas].Gordon Conference on Computational Chemistry, Les Diablerets, Switzerland, October, [Recent Advances in Simulation of Biological Functions].A Symposium on Enzyme Catalysis of the SFBM, Uppsala, October, [Computer Simulations as a Powerful Tool for Probing the Origin of Enzyme Catalysis].

2007 APS National Meeting, Bolder, March, [Quantitative Results in QM/MM Calculations of Biological Systems].ACS National Meeting, Chicago, March, [On Accuracy and Reliability in Simulations of Enzyme Catalysis].ACS National Meeting, Chicago, March, [Challenges in Calculations of Electrostatic Energies in Macromolecules].John Stauffer Symposium, USC, April, [How do Enzymes Really Work?]ICTP Workshop on From Physical Understanding to Novel Architectures of Fuel Cells, Trieste, May, [Effective Strategies for Unraveling Microscopic Energetic and Dynamics of Proton Transport in Complex Systems: From QM/MM to Monte Carlo EVB Based Models].Isotopes 2007, Benicassim, Spain, May, [Looking for Key Factors in Enzyme Catalysis: Some Recent Confirmation of the Electrostatic Idea].The Fritz Haber Center for Molecular Dynamics Conference on Conductance in Molecules, Jerusalem, August, [Simulating Proton Transport and Ion Transport]EMBO Workshop on the Chemistry and Biochemistry of Catalysis by Biological Systems, Hamburg, June, [Looking for Key Factors in Enzyme Catalysis: Some Recent Confirmation of the Electrostatic Idea and Additional Evidences that Enzyme Catalysis Does Not Involve Dynamical Effects].Gordon Research Conference on Computer Aided Drug Design, Tilton, August, [Simulating Drug Resistance].ACS National Meeting, Boston, August, [Computer Simulations of Photobiological Reactions: Advances and Problems].ACS National Meeting, Boston, August, [Consistent and Effective Sampling in Ab Initio QM/MM Simulations]. Symposium on 40 Year of Structural Molecular Biology (Levitt 60th Birthday) Stanford, September, [Modeling Enzyme Catalysis].

2008 Gordon Research Conference on Isotopes in Biological and Chemical Sciences, Ventura, February, [Computer Simulations Can Bridge Between Experimental Studies of Enzymes and Their Interpretation: Recent Confirmations of the Electrostatic Idea an Additional Evidences That Enzyme Catalysis Does Not Involve Dynamical Effects]Wenner-Gren Foundation Symposium on Theoretical Biochemistry, Stockholm, May, [Computer Simulations of Biological Functions].Molecular Frontiers Symposium, Royal Swedish Academy of science, Stockholm, May, [Electrostatic Basis of Biological Energy Conversion and the Fuel of Biological Motors].

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Workshop on protein Electrostatics, Telluride, Colorado, July, [Electrostatic Basis for Structure Function Correlation in Proteins: Examples, Validations and Challenges].Molecular Dynamics of Non-Adiabatic Processes, Institute of Physics, London, July, [Computer Simulations of Photobiologoical Reactions, Advances and Problems] (Had to cancel in the last minute).WATOC Congress, Sydney, Australia, September, [Computer Simulations of Biological Functions].ESF-EMBO Symposium on Protein Design and Evolution for Biocatalysis, San Feliu, Spain, October, [Hidden Principles of Enzyme Design].

2009 The R.B Woodward Lectures in Chemical Science, Harvard University, February, [How Do Enzymes Really Work and How They Do Not Work; What Has Been Learned from Computer Simulations].ACS National Meeting, A Symposium on Functional Motions in Enzyme Catalysis, Salt Lake City, March, [Dynamical Coupling Between Conformational and Chemical Motions Does Not Contribute to Catalysis].The CUSO lecture series, Switzerland, May, [(a) Modeling Proton Transfer and Electron Transfer Reactions in Chemistry and Biology, Bern; (b) Multilevel Modeling in Biophysics and Chemistry, Geneva; (c) Modeling Light Induced Photochemical and Photobiological Reactions, Geneva; (d) How do Enzymes Really Work and How do They Not Work: What Has Been Learned from Computer Simulation Studies?, Lausanne; (e) On the Nature of Proton Transport in Biological Systems - What Can Be Learned from Consistent Simulation Studies and Who is Grotthuss Anyhow?, Basel].ISOTOPES 2009, Cluj-Napoca, Romania, May, [How Do Enzymes Work and How Do They Not Work: What Has Been Learned from Computer Simulation Studies?].Workshop on Electrostatics in Proteins, Telluride, Colorado, July, [How to Study Electrostatic Energies in Proteins].ACS National Meeting, Symposium on Protein Dynamics and Functions, Washington, August, [Dynamical Effects are Important in Ultrafast Reactions but not in Enzyme Catalysis: Advances in Modeling long time Enzyme Dynamics].Faraday Discussion on Physical Organic Chemistry, Cardiff, September, [The EVB as a Quantitative Tool for Simulating and Analyzing Biological and Chemical Reactions].Modeling09, Erlangen, Germany, September, [Multiscale Modeling of Biological Functions].International Research of Collaborative Research Center on Protein Cofactors Interactions in Biological Systems, Berlin, September, [Simulating Proton Transfer and Electron Transfer in Biology].Goethe University Frankfurt, September, [How Do Enzymes Really Work and How They Do Not Work; What Has Been Learned from Computer Simulations].Symposium on Protein Structure and Function, Shanghai, October, [Computer Simulations of the Functions of Biological Molecules, What Has Been Accomplished and Where We are Going].Multiscale Modeling and Simulations in Science, the Royal Institute of Technology, Stockholm, Sweden, November, [(a) Multiscale Modeling of Protein Functions on Long Time Scale; (b) Multiscale Strategies in QM/MM Modeling; (c) Coarse Graining Approaches in Studying Proton Transport and Ion Transport].

2010 The Lifson Memorial Lecture, The Weizmann Institute, March, [Computer Simulations of the Functions of Biological Systems; What Has Been Accomplished and Where We are Going]. National Academy of Science, Section 29, Washington DC, April, [Computer Simulations of Biological Functions]. The Chevy Goldstein Distinguished Lecture in Chemistry, Cal Poly Pomona, May, [Electrostatic Basis of Biological Functions].Conference on Computational Molecular Science (CMS) 2010, Royal Agricultural College, Cirencester, June, [Multiscale Modeling of Biological Functions].Quantum Systems in Chemistry and Physics (qscp) xv, Cambridge, England, September, [Multiscale Modeling in Chemistry and Biology].

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The XVth QAMTS Conference, Darmstadt, Germany, September, [Using Consistent Simulations to Examine Proposals about the Origin of Enzyme Catalysis].Telluride Workshop on Proton Transfer in Biology, Telluride, August, [What Does it Take to Simulate Reliably and Effectively Proton Transfer Processes in Membrane Proteins].Workshop on Water in Biology, Chicago, September, [The Role of Water in Biological Systems].Pacificahem 2010, Honolulu, December, [Challenges and Advances in QM/MM Methods and Multi Scale Modeling for Studies of Biological Functions].

2011 ACS Symposium on Membrane Proteins, Structure and Function, Anaheim, March, [Coarse Grained Renormalization studies of the Functions of Membrane Proteins].ThioBio 2011 Madeira, Portugal, June, [Renormalization and Other CG Approaches for Long Time Simulations of Biological Systems].Royal Swedish Academy Symposium on “Proton Transport Across Biological Membranes”, Stockholm, June, [The Constraints on the Efficiency of Coupled Electron Transfer /Proton Transfer Biological Pumps, and What Does it Take to Relate the Structure of Cytochrome c Oxidase to its Actual Function].Stanford-Sweden Workshop, Uppsala, June, [Renormalization and Other CG approaches for Long Time Simulations of Biological Systems].WATOC 2011, Santiago de Compostela, Spain, July, [Reference Potentials and CG Approaches for Simulations of Biological Systems].IUPAC Symposium on Enzyme Catalysis, Porto Rico, August, [How Do Enzymes Work and How Do They Not Work: Advances in Simulations and Computer Aided Enzyme Design]. WRM-ACS Meeting on Understanding Chemical Reactivity Through Computational Chemistry, Pasadena, November, [Advances in Simulations and Computer Aided Enzyme Design].

2012 Gordon Research Conference on Protein Folding and Dynamics, Ventura, January, [Multiscale Modeling of Protein Functions]. Gordon Research Conference on Protons and Membrane Reactions, Ventura, February, [Coarse Grained Modeling of Proton Translocation, Ion Current and Voltage Effects in Membrane Proteins].Stauffer Symposium, USC, April, [Simulating the Action of Molecular Motors and Elucidating the Molecular Meaning of Single Molecule].In Silico Enzyme Design and Screening Conference, Trieste, Italy, May, [Advances in Quantitative Computer Aided Enzyme Design].The X Girona Seminar, Girona, Spain, July, [Advanced Modeling of Biological Functions; Some Recent Highlights]. Telluride workshop on Proton Transfer, Telluride, July, [Gaining Deeper Insight on Proton Transport in CcO and Related Systems].ACS Symposium on “Electron and Energy Transfer Phenomena: At the Intersection of Electronic Structure Theory and Chemical Dynamics”, Philadelphia, August, [Modeling the Dynamics and Energetics of Electron Transfer and Proton Transfer Reactions in Chemistry and Biology].Cold Spring Harbor China, Meeting on Small GTPases at Different Scales: Proteins, Membranes, Cells Suzhou, China, September, [The Nature of the Activation of GTPaes – Simulating the Allosteric Action of G-Proteins].Distinguished Lecture in Computational Biology, UC Irvine, November, [Advances in Modeling of Biological Functions].RSC Award in Soft Matter and Biophysical Chemistry Lecture Tour, Newcastle, Sheffield, Bath, November, [Advances in Modeling Biological Functions].

2013 Research Workshop on Computational Biology; Then and Now, The Weizmann Institute, Israel, May, [Progress in Modeling of Biological Functions from Then to Now]. Albany 2013: The 18th Conversation, June, [Exploring the Role of Dynamical Effects in Biology and Modeling Complex Molecular Machines] Conference in Honor of the 90th Birthday of Rudolph Marcus, Nanyang Technological University, Singapore, July, [Using Coarse Grained and Multiscale Models in Realistic Elucidations of Vectorial Processes of Motors and Other Complex Biological Systems].

16

ACS National Meeting, Symposium on Electrostatics and Polarization Effects in Biophysical Chemistry, Indianapolis, September, [Challenges and Advances in Calculations of Electrostatic Energies in Macromolecules].Opening lecture in Modeling Interaction in Biomolecules VI, Marianské Lazně, Czech Republic, September, [Multiscale Modeling of the Function of Biological Systems].Molecular Frontiers Symposium, Korea University, Seoul, Korea, October, [Multiscale Modeling of Complex Biological Systems and Processes]. The III Baku International Humanitarian Forum, Baku, Azerbaijan, November.Nobel Lecture, Stockholm, December, [Computer Simulations of Biological Functions; from Enzymes to Molecular Machines].Uppsala University, Post Nobel Lecture, Uppsala, December, [Computer Simulations of Biological Functions; from Enzymes to Molecular Machines].Chalmers University, Post Nobel Lecture, Gutenberg, December, [Computer Simulations of Biological Functions; from Enzymes to Molecular Machines].Lund University, Post Nobel Lecture, Lund, December, [Computer Simulations of Biological Functions; from Enzymes to Molecular Machines].

2014 Federation of Israeli Experimental Biology (ILANIT), Eilat, Israel, February (Keynote), [Multiscale Modeling of Complex Biological Systems and Processes].Biophysical Society (The Founder Award Lecture), San Francisco, February, [Multiscale Modeling of Biological Systems].

Hidden Connections Conference, Nanyang Technology University, Singapore, March, [Unraveling the Complexity of Biological Function by Computer Simulations] Honorary Degree Lecture, Bar Ilan University, Israel, May, [Multiscale Modeling of Biological Systems and Processes]A Symposium Commemorating Lifson's 100th Birthday, Honoring the 2013 Nobel Laureates in Chemistry, Weizmann Institute of Science, Israel, May, [Multiscale Modeling of Biological Systems and Processes]Al-Farabi Kazakh National University, Almaty, Kazakhstan, May, [Computer Simulations of Biological Molecules]ATPase Workshop, Tokyo, Japan, June, [Elucidating the Origin of the Directionality of Molecular Motors: Converting the Structure of ATPases to Free Energy Landscape]Helmholtz University, Munich, Germany, June, [Multiscale Modeling of the Function of Biological Systems]64th Lindau Nobel Laureate Meetings, Lindau, Germany, [Multiscale Simulations of the Functions of Biological Molecules]WATOC 2014, Santiago, Chile, October, [Multiscale Modeling of Complex Biological Systems and Processes]Holland Research School of Molecular Chemistry, Amsterdam, November 20, [Multiscale Modeling of the Functions of Biological Molecules]

2015 eSSENCE Workshop on Frontiers in Computational Biomedicine, Uppsala, Sweden, January, [Perspective on Computer Modeling of Biological Systems and Processes].7th International Science Youth Forum, Singapore, January, [Master Class on Computer Modeling].The Almløf-Gropen Lecture Department of Chemistry, Oslo, June [ Multiscale modeling of the function of biological systems].The Almløf-Gropen Lecture center for theoretical and computational chemistry Tormso, June [Multiscale modeling of the function of biological systems].65th Lindau Nobel Laureate Meeting, Lindau, June [ How to Model the Action of Complex Biological Systems on a Molecular Level?].World Science Conference the Hebrew University of Jerusalem, August [Modeling the Action of Complex Biological Systems on a Molecular Level?].Franklin Memorial Lecture at Rice University, September [ How to Model the Action of Complex Biological Systems on a Molecular Level?].

2016 Global Young Scientists Summit, Singapore, January [How to Model the Action of Complex Biological Systems].Keynote speaker at BIT’s 7th World DNA and Genome Day, Dalian, China, April [Modeling

17

the Action of Complex Biological Systems on a Molecular Level]. Keynote lecture at the EMBO Conference on Biocatalysts, Oulu, Finland, June

[Electrostatic in Biocatalysts]. The Birch lecture at UNSU, Canberra, Australia, June [Modeling the Action of Complex

Biological Systems on a Molecular Level]. Plenary lecture ICPOC-23, Sydney Australia, July [How Do Enzymes Work and How Do

They Not Work: Advances in Simulations and computer Aided Enzyme Design]. Opening the academic year, Chinese University of Hong Kong (CUHK).The Emerson Center Award Lecture, Emory University, [How to Model the Action of Complex Biological Systems on a Molecular Level]. V Baku International Humanitarian Forum, Baku, Azerbaijan, [Using Computer Modeling in Biological Medicine].The V Congress of the Russian Biochemical Society, Sochi, Russia, [How to Model the Action of Complex Biological Systems and to Advance Molecular Medicine].Youth Forum, Sochi, Russia, October [Modeling Biological Molecules Keynote Speech].The Xingda Lectureship, Peking University, Beijing, China, [Modeling the Action of Complex Biological Systems on a Molecular Level].BIT’s 14th Annual Congress International Drug Discovery Science & Technology, Nanjing, China, [Computer Modeling of Complex Biological Systems].

Instituto Politecnico Nacional, [From Kibbutz to Nobel on Modeling Complex Chemical

INVITED SEMINARS 1976 Department of Biophysics, University of California, Los Angeles, May, [Theoretical Studies

of Enzymatic Reactions].ACS Centennial Meeting, San Francisco, [Calculations of the Effect of Inter- and Intra-Molecular Interactions on Properties of Organic Molecules in Crystal and Solution Phases].Department of Pharmaceutical Chemistry, University of California, San Francisco, [Theoretical Studies of Enzymatic Reactions].Department of Chemistry and Biology, University of Illinois, Urbana, [Bicycle-Pedal Model for the First Step of the Vision Process].School of Medicine, Washington University, St. Louis, [Electrostatic Stabilization in Enzymatic Reactions].

1977 Department of Chemistry, University of California, San Diego, [Computer Simulation of Enzymatic Reactions].Fifth Structure-Energy Relationship Conference, Santa Barbara, [Direct Calculations of Ionic Reactions in Solution].Department of Chemistry, University of California, Riverside, [Dynamical Models for the First Step of the Vision Process].Fifth American Peptide Symposium, San Francisco, [How do Enzymes Really Work?].Department of Chemistry, University of California, San Diego, [Energy Structure Correlation in Metalloporphyrins].University of Nijmegen, The Netherlands, [Dynamical Models for the First Step of the Vision Process].The Weizmann Institute of Science, Israel, [The Secret of Enzymatic Reactions].Department of Biology, Columbia University, [The Secret of Enzymatic Reactions].Department of Chemistry, Princeton University, [The Secret of Enzymatic Reactions].Dept. of Molecular Biology & Dept. of Chemistry, Stanford University, [How do Enzymes Really Work?].IBM Laboratories, San Jose, [How to Calculate Equilibrium and Dynamical Properties of Molecular Crystals].

1978 University of California, San Francisco, [What’s Going on in the First Step of the Vision Process?].University of California, Berkeley, [What’s Going on in the First Step of the Vision Process?].California Institute of Technology, [Charge Stabilization Mechanism in Rhodopsin and Bacteriorhodopsin].

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California State University, Northridge, [Energetics of Enzyme Catalysis].University of California, Irvine, [Energetics of Enzyme Catalysis].University of California, Los Angeles, [What’s Going on in the First Step of the Vision Process?].Waseda University, Tokyo, [Charge Stabilization Mechanism in Rhodopsin].

1979 The Johnson Research Foundation, [The Energetics of Proton Pumps].The National Institutes of Health, [The Energetics of Enzyme Catalysis].Florida State University, [The Energetics of Enzyme Catalysis].The University of Chicago, [The Energetics of Enzyme Catalysis].California State University, Los Angeles, [The Energetics of Enzyme Catalysis].NRC Laboratory of Molecular Biology, Cambridge, England, [Electrostatic Contributions to Cooperativity in Hemoglobin].CECAM Workshop on Calculations of Enzymatic Reactions, Orsay, France, [Electrostatic Control of Cooperativity in Hemoglobin].CECAM Workshop on Sudden Polarization, Orsay, France, [A New View on the Dynamics of cis-trans Photoisomerization].The Max-Planck Institute, Gottingen, West Germany, [Electrostatic Effects in Proteins].

1980 Department of Chemistry, Columbia University, [The Dynamics of cis-trans Photoisomerization].Department of Biophysics, Yale University, [Electrostatic Control of Enzyme Catalysis].Department of Chemistry, Princeton University, [What is the Molecular Origin of Cooperativity in Hemoglobin?].West Coast Theoretical Chemistry Conference, California Institute of Technology, Pasadena [The Dynamics of cis-trans Photoisomerization].Department of Chemistry, University of Strasbourg, France, [How do Enzymes Really Work].IBM, San Jose, [The Dynamics of cis-trans Photoisomerization and the First Step of the Visual Process].Department of Chemistry, University of Southern California, Los Angeles, [The Dynamics of the First Step of the Visual Process].

1982 Department of Chemistry, Ben-Gurion University, Ber-Seva, Israel, January, [Electrostatic Basis for Light-Induced Charge Separation in Photobiology]. Department of Chemistry, Tel Aviv University, Israel, February, [Electrostatic Basis for Light-Induced Charge Separation in Photobiology].The Weizmann Institute of Science, Rehovot, Israel, February, [The Dynamics of Electron Transfer Reactions].Department of Biochemistry, Univ. North Carolina. Chapel Hill. March, [Electrostatic Basis for Structure Correlation in Proteins].Department of Biochemistry, Duke University, Durham, NC, March, [Structure Function Correlation in Proteins].National Institutes of Health, Bethesda, Maryland, March, [Structure Function Correlation in Proteins].Bell Laboratories, Murray Hill, NJ, March, [Electrostatic Basis for Structure Function Correlation in Proteins].Department of Chemistry, Israel Institute of Technology, Haifa, April, [The Molecular Dynamics of the First Step of the Vision Process]. Department of Chemistry, Imperial College, London, May, [Structure Function Correlation in Proteins]Department of Crystallography, Birkbek College, London, May, [Electrostatic Basis for Structure Function Correlation in Proteins].Department of Biochemistry, MIT, Cambridge, May, [Electrostatic Basis of Enzyme Catalysis].Department of Chemistry, Technical Univ. Munich, Germany, May, [Molecular Basis for Light Induced Charge Separation Across Membranes].Medical Research Council, Cambridge, England, May, [Molecular Basis for Light Induced Charge Separation in Photobiology].

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Laboratory of Molecular Biophysics, Oxford University, Oxford, England, May, [Structure Function Correlation in Proteins].Fritz-Haber Institute, Berlin, W. Germany, May, [Molecular Basis for Light Induced Charge Separation Across Membranes in Photobiological Systems].Max Planck Institute, Munich, Germany, May, [Structure Function Correlation in Proteins].Department of Chemistry & Biology, The Hebrew University, Jerusalem, May, [Electrostatic Basis for the Action of Proteins; From Enzyme Catalysis to Photosynthesis].Department of Chemistry, University of Southern California, October, [Computer Simulation of the Dynamics of Enzymatic Reactions].

1983 Department of Chemistry, Rutgers University, March, [The Dynamics of Enzymatic Reactions].Department of Biology, Univ. of Pennsylvania, March, [The Dynamics of Enzymatic Reactions].Department of Biochemistry, University of California-Riverside, May, [Structure Function Correlation in Enzymatic Reaction].Chemical Physics Seminar, University of Southern California, May, [Semi classical Approaches to Studies of Dynamics of Unimolecular Processes].

1984 Departments of Chemistry & Biophysics, University of California-Berkeley, January, [Dynamics of Proton Transfer Reactions in Solutions and Proteins].Departments of Physics & Chemistry, Arizona State, Tempe, February, [Dynamics of Fundamental Reactions in Solutions and Proteins].Department of Chemistry, University of California-Irvine, April, [Dynamics of Proton Transfer Reactions in Solutions and Proteins].National Institutes of Health, Bethesda, Maryland, May, [Electrostatic Effects in Proteins].National Institutes of Health, Bethesda, Maryland, June, [Dynamics of Enzymatic Reactions].Department of Physics, Johns Hopkins Univ. School of Medicine, May, [Electrostatic Basis of Enzyme Catalysis].The Max-Planck Institute for Biochemistry, Munich, July, [Electrostatic Basis for the Efficiency of Light Induced Charge Separation Across Membranes].The Technical University of Munich, July, [The Dynamics of Proton Transfer Reactions].

1985 CALTECH, In a special topic series of lectures on Electron Transfer Reactions. Series organized by Gray, Hopfield and Marcus, [Simulating Electron Transfer Reactions].Department of Chemistry, Cal State-Pomona, January, [Dynamics of the First Step of the Vision Process].Department of Chemistry, Cal State-Fullerton, February, [Simulating the Dynamics of Enzymatic Reactions].University of Southern California-Medical School, February, [How do Enzymes Really Work?].Biophysical Society, February, [Microscopic and Macroscopic Models for Calculations of Electrostatic Energy].West Coast Protein Crystallography Workshop, Asilomar, March, [How to Evaluate Electrostatic Energies in Proteins].ETH, Department of Physics, Zurich, June, [Electrostatic Interactions in Proteins].Department of Chemistry, Univ. of Konstanz, June, [Dynamics of Enzymatic Reactions].Argonne National Laboratory, October, [The Dynamics of Electron Transfer Reactions].Upjohn Laboratory, October, [Toward Computer Aid in Site-Directed Mutagenesis].University of Southern California-Medical School, December, [Toward Computer Aid in Enzyme Design].Department of Biophysics, UC-Irvine, December, [Simulating the Dynamics of Electron Transfer in Proteins].Department of Chemistry, Cal. State Long Beach, December [The Molecular Dynamics of the First Step of the Vision Process].

1986 Gordon Research Conference on Metals in Biology, January, [Calculating the Redox Potentials of Proteins].

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Biophysical Society Meeting, San Francisco, February, [What is the Dielectric Constant of Proteins (with F. Sussman)].Biophysical Society Meeting, San Francisco, February, [Computer Aided Site Directed Mutagenesis of Proteins (with F. Sussman)].Biophysical Society Meeting, San Francisco, February, [How to Calculate Solvation Energies in Proteins (with G. King)].Pomona College, Dept. of Chemistry, January, [Simulating the Dynamics of Enzymatic Reactions].University of Washington, Dept. of Chemistry, Seattle, May, [Simulating Chemical Reactions in Solutions].University of Washington, Dept. of Biochemistry, Seattle, May, [How do Enzymes Really Work?].Tokyo Research Laboratories, Tokyo, Japan, September, [Simulating the Action of Proteins].

1987 University of California Berkeley, Dept. of Chemistry, Berkeley, February, [Towards Quantitative Evaluation of Activation Barriers in Designer Enzymes].Gordon Research Conference on Enzymes, Coenzymes and Metabolic Pathways, Kimball Union Academy New Hampshire, July, [poster on The Effect of Mutations on the Energetics and Dynamics of Subtilisin Catalysis].Colorado State University, Dept. of Chemistry and Biochemistry, Fort Colinse, May, [Computer Simulation of Designers Enzymes].New York University, Dept. of Chemistry, New York, October, [Computer Simulation of Designer Enzymes].California State University, Dept. of Chemistry, Northridge, October, [Computer Simulation of Electron Transfer Reactions in Solutions and Proteins].West Coast Protein Crystallography Workshop, Asilomar, March, [Effect of Mutation of Catalytic Rate of Enzymes (Poster with F. Sussman)].West Coast Protein Crystallography Workshop, Asilomar, March, [How to Calculate Electrostatic Free Energies in Solutions and in Proteins, (Poster with G. King)].West Coast Protein Crystallography, Workshop, Asilomar, March, [Electron Transfer in Proteins (Poster with J-K. Hwang)].University of California San Francisco, Dept. of Biophysics and Pharmaceutical Chemistry, San Francisco, November, [How do Enzymes Really work?].

1988 Cal State University, Los Angeles, March, [Simulation of Electron Transfer in Solutions and Proteins].Department of Chemistry, The University of Chicago, February, [Computer Simulation of Charge Separation Reaction in Solutions and Proteins].Department of Molecular Systems, Merck Sharp and Dohme, Rahway, New Jersey, June, [Computer Aided Protein Design].Department of Chemistry, UC Santa Cruz, October, [Computer Simulation of Electron-Transfer Reactions in Solutions and Photosynthetic Proteins].

1989 Ardent Computer Symposium of Scientific Supercomputing for Biotechnology, San Diego, March, [Effective Calculations of Free Energy for Protein Design].Ardent Computer Seminars on Chemical Computing, New Jersey, Schaumburg, San Mateo, May, [New Methods Computer-Aided Enzyme Design].

1990 NRC Lecture Series; NRC Research Institute for Biotechnology, Montreal, Canada, March, [How do Serine Proteases Really Work?].Battelle Pacific Northwest Labs, Richland, Washington, December, [Computer Simulations of Enzymatic Reactions].Department of Biochemistry, USC School of Medicine, October, [How do Enzymes Really Work?].

1991 Department of Chemistry and Biochemistry, Utah State University, Logan January, [Computer Simulations of Enzymatic Reactions].Department of Chemistry, The University of Utah, Salt Lake City, January, [How do Enzymes Really Work?].

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Department of Biochemistry, Loma Linda University School of Medicine, February, [Computer Simulations of Enzymatic Reactions and the Origin of Enzyme Catalysis].Department of Physics, University of California, San Diego, April, [Electrostatic Energy and Macromolecular Functions].Molecular Simulations Inc. Users Meeting, Princeton, May, [Computer Simulations with Polaris and Enzymix Programs].

1992 Department of Biophysics, Mount Sinai Medical School, New York, August, [Computer Simulation of Chemical Reactions].National Cancer Institute, Frederick, Maryland, September, [On the Mechanism of Ras p21].

1993 Department of Chemistry, UC Irvine, February, [Simulating the Dynamics of the Primary Events in Photosynthesis and Vision].Department of Chemistry, Technical University of Munich, Munich, Germany, July, [Computer Simulation of Biological Processes].Department of Chemistry, University of South Alabama, Mobile, Alabama, November, [How do Enzymes Really Work?].Agouron Pharmaceuticals Inc., San Diego, [Computer Modeling of Binding and Catalysis in Proteins and the Origin of Biological Specificity].ISIS Pharmaceuticals Inc., Carlsbad, July, [Computer Simulation of Catalysis and Binding of DNA, RNA and Related Molecules].

1994 Department of Chemistry, New York University, February, [Computer Simulation of the Dynamics of Photobiological Processes].Department of Theoretical Physics, University of Munich, Germany, July, [Computer Modeling of Metalloenzymes].Department of Chemistry, Freie Universitat Berlin, Germany, July, [The Treatment of Long-Range Electrostatic Interactions in Molecular Simulations].Institute of Biophysical Chemistry, Hannover Medical School, Hannover, Germany, August, [The Structure-Function Correlation of Ras p21].Department of Chemical Physics, University Autonoma de Barcelona, Spain, December, [Computer Modeling of Enzymatic Reactions].

1995 Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, March, [Substrate Assisted Catalysis is the Mechanism of GTP Hydrolysis in ras-P21].Merck Research Labs, New Jersey, March, [Computer Aided Drug Design].Department of Chemical Physics, California Institute of Technology, [Computer Simulations of Chemical Reactions in Solutions and in Enzymes].Max Planck Institute for Biophysik (Professor Hartmut Michel), Frankfurt, Germany, [Simulation of Proton Transfer Reactions in Proteins (Enzymes and Proton Pumps)].Max-Planck Institute of Physics, Stuttgart, Germany, [Computer Simulation of Chemical Reactions in Enzymes].Max-Planck Institute for Molecular Physiology (Prof. A. Wittinghefer), Dortmund, Germany, [Computer Simulations of the Action of G-Proteins].Max-Planck Institute for Biochemistry (Prof. R. Huber), Munich, Germany, [Computer Simulation of Ligand Bonding to Proteins and the Action of ras-P21].Department of Chemistry, The University of Michigan, Ann. Arbor, [Computer Simulation of Chemical Processes in Solutions and Proteins].Department of Chemistry and Biochemistry, University of Michigan, October, [Computer Simulation of Enzymatic Reactions].

1996 Scripps Research Institute, March, [Computer Simulation of Enzymatic Reactions].Center for Advanced Research in Biotechnology (AARB), Maryland, March, [Computer Modeling of Enzymatic Reaction and the Role of Electrostatic Energies].DuPont, Wilmington, March, [Calculating Binding Affinities of Ligands to Proteins: In Search of Optimal Strategies].Department of Molecular Biophysics and Biochemistry, Yale University, March, [Computer Simulation of Enzymatic Reactions and the Action of G-Protein].Department of Biochemistry, Albert Einstein College of Medicine, Bronx, June, [Computer Simulation of Enzymatic Reactions and the Action of G-Protein].

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Department of Biophysics, Johns Hopkins School of Medicine, Baltimore, November, [Computer Simulation of Enzymatic Reactions and the Action of G-Proteins].Department of Chemistry and Biochemistry, California State University at Fullerton, November, [Computer Simulation of Enzymatic Reactions and the Action of G-Proteins].

1997 Department of Chemistry and Biochemistry, University of Maryland, June, [Computer Simulation of Enzyme Reactions and the Origin of Enzyme Catalysis].Biology Department, Brookhaven National Lab, July, [Computer Simulations of Enzymatic Reactions; What is the Origin of Enzyme Catalysis].Department of Chemistry and Biology, University of California, Santa Barbara, October, [Probing the Catalytic Power of Enzymes by Computer Simulation Approaches].

2000 Department of Biochemistry and Biophysics, University of Pennsylvania, February, [Computer Simulations of Enzyme Catalysis; Finding Out What was Optimized by Evolution].Department of Biochemistry, Tufts Medical School, February, [Computer Simulations of Enzymatic Reactions].Department of Biochemistry and Molecular Biology, University of Tennessee, April, [Computer Modeling of Enzymatic Reactions].Department of Chemistry, Biochemistry and Molecular Biology, Florida State University, Tallahassee, October, [How Do Proteins Work: Computer Simulations of Protein Functions].Department of Chemistry and Biochemistry, UC Santa Cruz, November, [Finding Out What Was Optimized by Evolution in Enzyme Catalyzed Reactions].

2001 Keck School of Medicine, University of Southern California, Los Angeles, February, [How does GAP Catalyze the GTPase Reaction of Ras?: Insights from Computer Simulation Studies].Department of Molecular Biology, University of Southern California, March, [Computer Simulations of Enzymatic Reactions: Finding Out What Was Optimized by Evolution].Department of Chemistry, California State University, Northridge, October, [Computer Simulations of the Dynamics of Biological Processes].

2002 The Brown and Williamson Scholar Lectures, The University of Louisville, March, [a)How do Enzymes Really Work? b) Computer Simulations of the Dynamics of Biological Processes]IBM Thomas Watson Research Center, New York State, June, [Computer Simulations of Biological Processes: Maximizing the Benefits form the Available Computer Power by Using Effective Simulation Approaches].Department of Chemistry and Biochemistry Texas A&M University, October, [Computer Simulations of Enzymatic reactions: What are the Catalytic Principles that Really Work?].

2003 The 2003 Habermann Lecture, Department of Chemistry Marquette University, September, [Computer Simulations of Biological Processes: Toward Quantitative Structure Function Correlation in Biology].Department of Chemistry and Biochemistry of Iowa, October, [How Enzymes Really Work? Voodoo Formulations vs. Energy Based Considerations and Computer Simulations].University of Pittsburgh Scholl of Medicine, October, [Computer Simulations of Protein Functions: From Enzymes to Ion Channels and Other Functioning Biological Systems].

2004 Department of Chemistry, University of California Davis, March, [Simulating Proton Transport in Proteins and Who is Grotthuss Anyhow?]Theoretical and Computational Biophysics, University of Illinois at Urbana Champaign, April, [How do Enzymes Really Work; Using Computer Simulations to Examine and Eliminate Catalytic Proposals].Department of Chemistry university of California San Diego, November, [Simulating Proton Transport in Proteins and Who is Grotthuss Anyhow?]Department of Chemistry, The Johns Hopkins University, October, [Computer Simulations of Proton Transport in Gramicidin, Aquaporin and Other Biological Systems: What is Going on and Who is Grotthuss AnyHow?].

2005 Department of Chemistry Washington State University, March, [How do Enzymes Really Work: What Has Been Found By Computer Simulation Approaches].

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Department of Chemistry University of New Mexico, September, [Computer Simulations of Enzymatic Reactions: Finding Out What are the Catalytic Principles that Really Work?].

2006 Department of Chemistry University of Alberta, Edmonton, February 2, [Computer Simulations of Enzymatic Reactions; Finding Out What are the Catalytic Principles that Really Work?].Department of Chemistry, University of Calgary, Calgary, February 3, [Computer Simulations of Enzymatic Reactions: Finding Out What are the Catalytic Principles that Really Work?]. Department of Chemistry, University of Wisconsin, Madison, March 7, [Computer Simulations of Enzymatic Reactions: Finding Out What are the Catalytic Principles that Really Work?].Chalmers University, April, [Molecular Dynamics Simulations of Biological Functions: Finding Out What Dynamical Effects Where Actually Optimized by Evolution?].Lund University, May 2005, [Molecular Dynamics Simulations of Biological Functions: Finding Out What Dynamical Effects Where Actually Optimized by Evolution?].Uppsala University, May, [Molecular Dynamics Simulations of Biological Functions: Finding Out What Dynamical Effects Where Actually Optimized by Evolution?].

2007 Department of Chemistry, Ljubljana, Slovenia, May, [Simulating Enzyme Catalysis]ETH Kolloquium für Physikalische Chemie, Zurich, Switzerland, June, [Computer Simulations of Very Fast and Extremely Slow Biological Processes]ETH Organic Chemistry Seminar, Zurich, June, [Computer Simulations of Enzymatic Reactions].University of Zurich Department of Chemistry, Zurich, Switzerland, June, [Advanced Methods for Modeling Enzymatic Reactions].University of Pennsylvania Department of Biochemistry and Biophysics, September, [Computer Simulation of Biological Functions].

2008 Stockholm University, Stockholm, Sweden, February, [On the Nature of Proton Transport in Cytochrome c Oxidase and Other Biological Systems: What Can Be Learned from Consistent Simulation Studies].Uppsala University, Sweden, February, [Computer Simulations of Phosphate Hydrolysis in Biology: Facts Fictions and Open Questions].Max Planck Institute for Biophysics, Frankfurt, March, [On the Nature of Proton Transport in Cytochrome c Oxidase and other Biological Systems: What Can Be Learned from Consistent Simulation Studies].Department of Biophysics, Johns Hopkins University, Baltimore, April, [On the Nature of Proton Transport in Cytochrome c Oxidase and Other Biological Systems: What Can Be Learned from Consistent Simulation Studies].Department of Computational Biology, University of Pittsburg School of Medicine, April, [Dynamical Contributions to Enzyme Catalysis: Critical Tests of a Problematic Hypothesis].California Institute of Quantitative Biomedical Research (Invitational Speakers Series), UCSF, San Francisco, April, [On the Control of Proton Transport and Ion Transport in Biology: What Can Be Learned from Consistent Simulations].Department of Chemistry Chalmers University, Gothenburg, Sweden, May, [Electrostatic Control of Bioenergetics].Department of Chemistry, University of California, Davis, June, [Dynamical Contributions to Enzyme Catalysis: Critical Tests of a problematic Hypothesis].

2009 The R.B Woddward Lectures in Chemical Science, Harvard University, February, [How do Enzymes Really Work and How They Do Not Work: What Has Been Learned from Computer Simulations].

2010 Department of Chemistry California Institute of Technology, April, [ Multiscale Simulations of Complex Biological Systems: Exploring Problematic Dynamical Proposals and Quantifying Enzyme Catalysis]. Department of Chemistry Oxford University, June, [Multiscale Modeling of Biological Functions].

2012 Department of Chemistry & Biology, The Hebrew University, Jerusalem, June, [Progress in Modeling of Biological Functions].

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2013 Department of Biophysics, City College New York, April, [Computer Modeling of Molecular Machines]Department of Physiology and Biophysics, Weill Medical College of Cornell, New York, April, [Computer Modeling of Molecular Machines].Department of Biophysics Stockholm University, Sweden, May, [Computer Modeling of Molecular Motors and Other Systems].Department of Molecular Biology, Uppsala, Sweden, May, [Computer Modeling Molecular Motors and Other Systems].Department of Chemistry and Biosciences, Chalmers University, Gothenburg, Sweden, May, [Computer Modeling of Molecular Motors and Other systems].Departments of Chemistry and Biophysical Chemistry, Lund University, Sweden. May, [Advances in Modeling Biological Functions].

2014 Department of Chemistry and Biochemistry, University of California, Los Angeles, April, [Multiscale Modeling of the Function of Biological Systems].

2015 Department of chemistry University of Illinois at Urbana-Champaign, IL [Multiscale modeling of the function of biological systems].Department of Chemistry, Technion [Multiscale modeling of the function of biological systems].

RESEARCH ACTIVITIESMy general research area is computer simulation and interpretation of the properties of large molecules, with special emphasis on the function of biological systems. My main topics are:

1) Theoretical studies of enzymatic reactions, and computer aided enzyme design.2) Electrostatic effects in biological systems. 3) Studies of proton transport, ion transport and electron transfer in biology.4) Modeling molecular motors 5) Dynamics and mechanisms of photobiological reactions. 6) Simulation of chemical reactions in solutions.7) Simulation and analysis of protein folding.8) Calculations of spectroscopic properties of biological molecules.

RESEARCH GRANTS1973 - 75 Theoretical Study of the First Steps in the Visual Process and Development of a Dynamic

Model for the Photoisomerization Reaction in Retinal. Israel National Academy of Sciences and Humanities.

1974 - 77 Development of Theoretical Models for Interpretation of the Resonance Raman Spectra of Biological Systems. The U.S.-Israel Bi-National Science Foundation.

1976 - 79 Theoretical Study of the Vision Process. National Eye Institute (EY01766A) ($65,000).1976 - 79 Theoretical Studies of Enzymatic Reactions. Petroleum Research Foundation ($9,000).

Grant was given back.1978 - 80 Theoretical Studies of Enzymatic Reactions. National Institutes of Health (GM 24492)

($103,210).1980 - 82 Theoretical Studies of Enzymatic Reactions. National Institutes of Health (GM 24492)

($80,000).1978 - 80 Alfred P. Sloan Fellowship ($19,800).1978 - 82 Theoretical Studies of the Vision Process. National Eye Institute (EY 01766) ($103,030).1981 - 86 Biomolecular Computer Graphics (Regional Center, joint with R. Dickerson, D. Eisenberg

(UCLA) and others).1983 - 86 Theoretical Studies of Enzymatic Reactions. National Institutes of Health (GM 24492)

($140,000).1983 - 87 Theoretical Studies of the Primary Event in the Vision Process. National Science

Foundation (PCM 8303385) ($135,000).1986 - 89 Theoretical Studies of Enzymatic Reactions. National Institutes of Health (GM 24492)

($240,000).

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1985 - 88 Hydrophilic and Hydrophobic Forces in Membrane Proteins. National Science Foundation (CHE-8519194) ($150,000).

1987 - 90 Computer Simulation of Chemical-Reactions in Synthetic Model Compounds and Genetically Engineered Active Sites. Office of Naval Research (N00014-87-K-0507) ($312,000).

1988 - 93 Computer Simulation of Electron Transfer Reactions. National Institute of Health (GM40283) ($373,000).

1988 - Biomolecular Simulation Center (joint with a group of molecular biologists). National Science Foundation ($420,000).

1985 - 87 Time on the NSF supercomputer (DMB 303385) (150 hours).1987 - 89 Time on the NSF supercomputer (CHE-8519194) (250 hours).1989 - 94 Theoretical Studies of Enzymatic Reactions. National Institutes of Health (GM 24492)

($519,000).1991 - 94 Computer Simulation of Chemical-Reactions in Synthetic Model Compounds and

Genetically Engineered Active Sites. Office of Naval Research (N00014-91-5-1318) ($300,000).

1993 - 96 Simulation of Entropic Effects. AASERT ($97,200).1993 - 97 Computer Simulation of Electron Transfer Reactions. National Institute of Health (GM

40283) ($566,000)1994 - 96 Structure Function Correlation for Ras p21 and the Molecular Origin of Cancer. Department

of Energy (DE-F603-94ER61945) ($259,000).1994 - 98 Structure Function Correlation of Ras p21 and Its Mutants. Tobacco Related Diseased

Research Program (4RT-0002) ($170,000).1994 - 98 Theoretical Studies of Enzymatic Reactions. National Institutes of Health (GM 24492)

($1,043,385).1997 - 01 Computer Simulation of Electron Transfer Reactions. National Institute of Health (GM

40283) ($906,501).1998 - 02 Theoretical Studies of Enzymatic Reactions. National Institutes of Health (GM 24492)

($1,085,594).1998 – 01 Structure Function Correlation of G-Proteins. National Institute of Science (MCB-9808638)

($330,000).2001 - 04 Structure Function Correlation in G-Proteins, National Institute of Science (MCB-9808038)

($330,000).2001 - 05 Computer Simulation of Electron Transfer Reactions, National Institute of Health (GM

40289) ($760,000).2002 - 06 Theoretical Studies of Enzymatic Reactions, National Institute of Health (GM 24492)

($1,293,700).2004 - 08 The Origin of the Fidelity of DNA Polymerase-Fidelity Mechanism: Theory and Experiment,

a program projects with Myron Goodman and Sam Wilson, NCI ($3,577,717).2004 - 09 Structure Function Correlation in G-Proteins, National Institute of Science, (MCB-9808038)

($440,000).2005 - 09 Computer Simulation of Electron Transfer Reactions, National Institute of Health (GM

40289) ($1,300.000).2006 - 10 Theoretical Studies of Enzymatic Reactions, National Institute of Health (GM 24492)

($1,400.000).2008 - 13 The Origin of the Fidelity of DNA Polymerase-Fidelity Mechanism: Theory and Experiment,

a program projects with Myron Goodman and Sam Wilson, NCI ($5,350,186).2009 - 13 Structure Function Correlation in G-Proteins, National Institute of Science (MCB-0342276)

($788,000).2009 - 13 Computer Simulation of Electron Transfer and Proton Transfer Reactions. National Institute

of Health (GM 40289) ($1,320.000). 2010 - 14 Theoretical Studies of Enzymatic Reactions, National Institute of Health (GM 24492)

($1,356.337).2013 - 17 Structure Function Correlation in G-Proteins, National Institute of Science (MCB-1243719)

($873,317).

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2013 - 17 Computer Simulation of Electron Transfer and Proton Transfer Reactions. National Institute of Health (GM 40289) ($1,257.600).

2013 - 2018 The Origin of the Fidelity of DNA Polymerase-Fidelity Mechanism: Theory and Experiment, a program projects with Myron Goodman and Sam Wilson, NCI ($5,350,186).

2014 - 2018 Theoretical Studies of Enzymatic Reactions, National Institute of Health (GM 24492) ($1,300.000).

2017 – 2021 Structure Function Correlation of G-Proteins, National Science Foundation, MCB-1707167, ($1,017,745)

2017 – 2022 Multiscale Simulations of Biological Systems and Processes, National Institute of Health (R35 GM122472), ($2,524,291).

PATENTS2014 Arieh Warshel, Spyridon Vicatos, “Production of Stable Proteins,” U.S. Patent 8855936- B2,

October 7, 2014.

LIST OF PUBLICATIONS1. A Consistent Force Field for Calculation on Conformations, Vibrational Spectra and

Enthalpies of Cycloalkanes and n-Alkane Molecules, S. Lifson and A. Warshel, J. Chem. Phys. 49, 5116-5129 (1968).

2. An Empirical Function for Second Neighbor Interactions and its Effect on Vibrational Modes and Other Properties of Cyclo- and n-Alkanes, A. Warshel and S. Lifson, Chem. Phys. Lett. 4, 255-256 (1969).

3. Consistent Force Field for Calculation of Vibrational Spectra and Conformations of Some Amides and Lactam Rings, A. Warshel, M. Levitt and S. Lifson, J. Mol. Spectrosc. 33, 84-89 (1970).

4. Consistent Force Field Calculations. II. Crystal Structure, Sublimation Energies, Molecular and Lattice Vibrations, Molecular Conformations and Enthalpies of Alkanes, A. Warshel and S. Lifson, J. Chem. Phys. 53, 582-594 (1970).

5. Oxidation of 4a, 4b-Dihydrophenanthrenes. III. A Theoretical Study of the Large Kinetic Isotope Effect of Deuterium in the Initiation Step of the Thermal Reaction with Oxygen, A. Warshel and A. Bromberg, J. Chem. Phys. 52, 1262-1269 (1970).

6. Oxidation of 4a, 4b-Dihydrophenanthrene. IV. Kinetic Isotope Effect of Deuterium in the Propagation and the Initiation Steps, A. Bromberg, K. A. Muszkat and A. Warshel, J. Chem. Phys. 52, 5952-5959 (1970).

7. Intermolecular Potentials for N2 Molecules and the Lattice Vibrations of Solid Alpha-N2, T.S. Kuan, A. Warshel and O. Schnepp, J. Chem. Phys. 52, 3012-3020 (1970).

8. Anharmonicity in Crystal Vibrations, A. Warshel, J. Chem. Phys. 54, 5324-5330 (1971).

9. Calculations of the Anharmonicity in the Vibrational Frequencies of Alkane Molecules by the CFF Functions, A. Warshel, J. Chem. Phys. 55, 3327-3335 (1971).

10. Calculation of Ground and Excited State Potential Surfaces of Conjugated Molecules. I. Formulation and Parameterization, A. Warshel and M. Karplus, J. Am. Chem. Soc. 94, 5612-5625 (1972).

11. Vibrational Structure of Electronic Transitions in Conjugated Molecules, A. Warshel and M. Karplus, Chem. Phys. Lett. 17, 7-14 (1972).

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12. Quantum Mechanical Consistent Force Field (QCFF/PI) Method: Calculations of Energies, Conformations and Vibronic Interactions of Ground and Excited States of Conjugated Molecules, A. Warshel, Isr. J. Chem. 11, 709-717 (1973).

13. Conformation of Retinal Isomers, R. Rowan III, A. Warshel, B. D. Sykes and M. Karplus, Biochemistry 13, 970-981 (1974).

14. Incorporation of Intermolecular and Intramolecular Forces in the Calculation of Crystal Packing and Lattice Vibrations, E. Huler and A. Warshel, Acta Crystallogr. B 30, JUL15, 1822-1826 (1974).

15. Examination of Intramolecular Potential Surfaces of Flexible Conjugated Molecules by Calculation of Crystal Structures. Equilibrium Geometries of Chalcones and Diphenyloctatetraene in Crystal and Gaseous State, A. Warshel, E. Huler, D. Rabinovich and Z. Shakked. J. Mol. Struct. 23, 175-191 (1974).

16. Calculation of ππ* Excited State Conformations and Vibronic Structure of Retinal and Related Molecules, A. Warshel and M. Karplus, J. Am. Chem. Soc. 96, 5677-5689 (1974).

17. Molecular Inelastic Neutron Scattering: Computational Method Using Consistent Force Fields, B. Hudson, A. Warshel and R. G. Gordon, J. Chem. Phys. 61, 2929-2939 (1974).

18. Calculations of CD and CPL Spectra as a Tool for Evaluation of the Conformational Differences Between Ground and Excited States of Chiral Molecules, J. Schlessinger and A. Warshel, Chem. Phys. Lett. 28, 380-383 (1974).

19. Theoretical Evaluation of Potential Surfaces, Equilibrium Geometries and Vibronic Transition Intensities of Excimers: The Pyrene Crystal Excimer, A. Warshel and E. Huler, Chem. Phys. 6, 463-468 (1974).

20. Calculation of Vibronic Structure of the π→π* Transitions of trans- and cis- Stilbene, A. Warshel, J. Chem. Phys. 62, 214-221 (1975).

21. Theoretical Studies of the Visual Chromophore, B. Honig, A. Warshel and M. Karplus, Accounts Chem. Res. 8, 92-100 (1975).

22. Semiclassical Trajectory Approach to Photoisomerization, A. Warshel and M. Karplus, Chem. Phys. Lett. 32, 11-17 (1975).

23. The Vibronic Structure of Crystalline Ethylene, P. Dauber, M. Brith, E. Huler and A. Warshel, Chem. Phys. 7, 108-115 (1975).

24. Theoretical Study of Excimers in Crystals of Flexible Conjugated Molecules. Excimer Formation and Photodimerization in Crystalline 1,4-Diphenylbutadiene, A. Warshel and Z. Shakked, J. Am. Chem. Soc. 97, 5679-5684 (1975).

25. Computer Simulations of Protein Folding, M. Levitt and A. Warshel, Nature 253, 694-698 (1975).

26. A Reply to News and Views, M. Levitt and A. Warshel, Nature 254, 388 (1975).

27. On the Consistent Calculation of Lattice Dynamics Using Semiempirical Potential Functions, E. Huler and A. Warshel, Chem. Phys. 8, 239-244 (1975).

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28. Theoretical Studies of Enzymatic Reactions: Dielectric Electrostatic and Steric Stabilization of the Carbonium Ion in the Reaction of Lysozyme, A. Warshel and M. Levitt, J. Mol. Biol. 103, 227-249 (1976).

29. Folding and Stability of Helical Proteins: Carp Myogen, A. Warshel and M. Levitt, J. Mol. Biol. 106, 421-437 (1976).

30. Bicycle-pedal Model for the First Step in the Vision Process, A. Warshel, Nature 260, 679-683 (1976).

31. Theoretical Studies of Drug Receptor Interaction, A. Warshel, Trends in Biochem. Sci. 1, N105-N106 (1976).

32. On the Molecular Origin of the Anomalous Polarization in the Resonance Raman of Metalloporphyrins, A. Warshel, Chem. Phys. Lett. 43, 273-278 (1976).

33. The Resonance Raman Spectrum of Azulene, R. Liang, O. Schnepp and A. Warshel, Chem. Phys. Lett. 44, 394-398 (1976).

34. The Consistent Force Field and Its Quantum Mechanical Extension, A. Warshel in Modern Theoretical Chemistry, Vol. 7, edited by G. A. Segal, Plenum Press, New York, pp. 133-172 (1977).

35. A Microscopic Dielectric Model for Reactions in Water, A. Warshel, Philos. T. R. Soc. London B – Biol. Sci. 278, 97-112 (1977).

36. Interpretation of Resonance Raman Spectra of Biological Molecules, A. Warshel, Annu. Rev. Biophys. Bioeng. 6, 273-300 (1977).

37. Calculations of Resonance Raman Spectra of Conjugated Molecules, A. Warshel and P. Dauber, J. Chem. Phys. 66, 5477-5488 (1977).

38. Energy-Structure Correlation in Metalloporphyrins and the Control of Oxygen Binding by Hemoglobin, A. Warshel, Proc. Natl. Acad. Sci. USA 74, 1789-1793 (1977).

39. The QCFF/PI+MCA Program Package Efficiency and Versatility in Molecular Mechanics, [Symposium in print on programs for Molecular Mechanics], A. Warshel, Computers and Chemistry 1, 195-202 (1977).

40. Pair-States in Alpha-Perylene Crystal. A Theoretical Study, M.D. Cohen, R. Haberkorn, E. Huler, Z. Ludmer, M. E. Michel-Beyerle, D. Rabinovich, R. Sharon, A. Warshel and V. Yakhot, Chem. Phys. 27, 211-216 (1978).

41. How Do Enzymes Really Work, A. Warshel, Peptides: Proceedings of the Fifth American Peptide Symposium, ed. M. Goodman and J. Meienhofer, John Wiley & Sons, pp. 574-576 (1977).

42. Extreme Conformational Flexibility of the Furanose Ring in DNA and RNA, M. Levitt and A. Warshel, J. Am. Chem. Soc. 100, 2607-2613 (1978).

43. Coupling of Charge Stabilization, Torsion and Bond Alternation in Light-Induced Reactions of Visual Pigments, A. Warshel and C. Deakyne, Chem. Phys. Lett. 55, 459-465 (1978).

44. A Microscopic Model for Calculations of Chemical Processes in Aqueous Solutions, A. Warshel, Chem. Phys. Lett. 55, 454-458 (1978).

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45. Charge Stabilization Mechanism in the Visual and Purple Membrane Pigments, A. Warshel, Proc. Natl. Acad. Sci. USA 75, 2558-2562 (1978).

46. Energetics of Enzyme Catalysis, A. Warshel, Proc. Natl. Acad. Sci. USA 75, 5250-5254 (1978).

47. Resonance Raman Spectrum of Azulene, R. Liang, O. Schnepp and A. Warshel, Chem. Phys. 34, 17-27 (1978).

48. On the Efficiency of Electron Transfer Reactions in Proteins, A. Warshel and R. Weiss in Frontiers of Biological Energetics, Vol. 1, ed. P.L. Dutton, J. Leigh and A. Scarpa, Academic Press, pp. 30-36, (1978).

49. On the Origin of the Red Shift of the Absorption Spectra of Aggregated Chlorophylls, A. Warshel, J. Am. Chem. Soc. 101, 744-746 (1979).

50. Conversion of Light Energy to Electrostatic Energy in the Proton Pump of Halobacterium halobium, A. Warshel, Photochem. Photobiol. 30, 285-290 (1979).

51. Kinetic and Spectroscopic Effects of Protein-Chromophore Electrostatic Interactions in Bacteriorhodopsin, A. Warshel and M. Ottolenghi, Photochem. Photobiol. 30, 291-293 (1979).

52. Calculations of Chemical Processes in Solutions, A. Warshel, J. Phys. Chem. 83, 1640-1652 (1979).

53. A New View of the Dynamics of Singlet Cis-Trans Photoisomerization, R. M. Weiss and A. Warshel, J. Am. Chem. Soc. 101, 6131-6133 (1979).

54. Electrostatic Interactions in Enzyme Catalysis, A. Warshel, R. Weiss and D. Greenberg in Molecular Structure and Dynamics, ed. M. Balaban, Balaban International Science Services, Philadelphia, p. 297 (1980).

55. An Empirical Valence Bond Approach for Comparing Reactions in Solutions and in Enzymes, A. Warshel and R. M. Weiss, J. Am. Chem. Soc. 102, 6218-6226 (1980).

56. Role of the Chlorophyll Dimer in Bacterial Photosynthesis, A. Warshel, Proc. Natl. Acad. Sci. USA 77, 3105-3109 (1980).

57. Calculations of RR Spectra as a Tool for Studying Biological Molecules, A. Warshel and R. M. Weiss in Proceedings VIIth International Conference on Raman Spectroscopy, ed. W.F. Murphy, North Holland (1980).

58. Energetics of Heme-Protein Interactions in Hemoglobin, A. Warshel and R. M. Weiss, J. Am. Chem. Soc. 103, 446-451 (1981).

59. Empirical Valence Bond Calculations of Enzyme Catalysis, A. Warshel and R. M. Weiss, Annals of the New York Academy of Sciences 367, 370-382 (1981).

60. Calculations of Enzymatic Reactions: Calculations of pKa, Proton Transfer Reactions, and General Acid Catalysis Reactions in Enzymes, A. Warshel, Biochemistry 20, 3167-3177 (1981).

61. Energetics of Light-Induced Charge Separation Across Membranes, A. Warshel, Isr. J. Chem. 21, 341-347 (1981).

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62. Calculations of Ground- and Excited- State Potential Surfaces for Conjugated Heteroatomic Molecules, A. Warshel and A. Lappicirella, J. Am. Chem. Soc. 103, 4664-4673 (1981).

63. Electrostatic Control of the Efficiency of Light-Induced Electron Transfer Across Membranes, A. Warshel and D. W. Schlosser, Proc. Natl. Acad. Sci. USA 78, 5564-5568(1981).

64. Electrostatic Basis of Structure-Function Correlation in Proteins, A. Warshel, Accounts Chem. Res. 14, 284-290 (1981).

65. Strain and Electrostatic Contributions to Cooperativity in Hemoglobin, A. Warshel and R. M. Weiss in Hemoglobin and Oxygen Binding, ed. C. Ho, Elsevier-North Holland, N.Y. (1982).

66. Optimal Protein Relaxation for Electron Transfer in Bacterial Photosynthesis, A. Warshel in Electron Transport and Oxygen Utilization, ed. C. Ho, Elsevier-North Holland, N.Y., p. 111 (1982).

67. Dynamics of Reactions in Polar Solvents. Semiclassical Trajectory Studies of Electron Transfer and Proton Transfer Reactions, A. Warshel, J. Phys. Chem. 86, 2218-2224 (1982).

68. Energy Storage and Reaction Pathways in the First Step of the Vision Process, A. Warshel and N. Barboy, J. Am. Chem. Soc. 104, 1469-1476 (1982).

69. Correlation of X-Ray Structures of Enzymes with Their Catalytic Activity; The Catalytic Reaction of Serine Proteases, A. Warshel, S. Russell and R. M. Weiss [Chemical Approaches to Understanding Enzyme Catalysis: Biomimetic Chemistry and Transition-State Analogs] Proceedings of the 26th OHOLO Conference, Israel, in Studies in Organic Chemistry, Vol. 10, eds. B. S. Green, Y. Ashani and D. Shipman, Elsevier, Amsterdam (1982).

70. Semiclassical Simulation of Vibronic Processes, A. Warshel, P. Stern and S. Mukamel in Time Resolved Vibrational Spectroscopy, ed. G. Atkinson, Academic Press, New York, p. 41 (1983).

71. On the Action of Cytochrome c: Correlating Geometry Changes Upon Oxidation with Activation Energies of Electron Transfer, A. K. Churg, R. M. Weiss, A. Warshel and T. Takano, J. Phys. Chem. 87, 1683-1694 (1983).

72. Semiclassical Calculation of Electronic Spectra of Supercooled Anharmonic Molecules, A. Warshel, P. S. Stern and S. Mukamel, J. Chem. Phys. 78, 7498-7500 (1983).

73. Converting Structural Changes upon Oxidation of Cytochrome c to Electrostatic Reorganization Energy, A. Warshel and A. K. Churg, J. Mol. Biol. 168, 693-697 (1983).

74. Dynamics of Enzymatic Reactions, A. Warshel, Proc. Natl. Acad. Sci. USA 81, 444-448 (1984).

75. Simulating the Energetics and Dynamics of Enzymatic Reactions, A. Warshel in Specificity in Biological Interactions, Pontificiae Academiae Scientiarum Scripta Varia, 55, 60-81 (1984).

76. Macroscopic Models for Studies of Electrostatic Interactions in Proteins: Limitations and Applicability, A. Warshel, S. T. Russell and A. K. Churg, Proc. Natl. Acad. Sci. USA 81, 4785-4789 (1984).

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77. Calculations of Electrostatic Interactions in Biological Systems and in Solutions, A. Warshel and S. T. Russell, Q. Rev. Biophys. 17, 283-422 (1984).

78. Modeling the Activation Energy and Dynamics of Electron Transfer Reactions in Proteins, A.K. Churg and A. Warshel in Structure and Motion: Membranes, Nucleic Acids and Proteins, eds. E. Clementi, G. Corongiu, M. H. Sarma and R. H Sarma, Adenine Press, Guilderland, N.Y., 361-374 (1985).

79. Calculations of Electrostatic Energies in Proteins; The Energetics of Ionized Groups in BPTI, S.T. Russell and A. Warshel, J. Mol. Biol. 185, 389-404 (1985).

80. Quantized Semiclassical Trajectory Approach for Evaluation of Vibronic Transitions in Anharmonic Molecules, A. Warshel and J-K Hwang, J. Chem. Phys. 82, 1756-1771 (1985).

81. Semiclassical Simulations of the Spectra of Anharmonic Molecules; Problems and Alternatives, J-K Hwang and A. Warshel, Chem. Phys. Lett. 115, 281-285 (1985).

82. A Shortcut for Multidimensional Quantization. The Average Partial Action Methods, J-K Hwang and A. Warshel, Chem. Phys. Lett. 118, 289-292 (1985).

83. Calculations of Spectroscopic Properties of Bacterial Reaction Centers, W. W. Parson, A. Scherz and A. Warshel in Antennas and Reaction Centers of Photosynthetic Bacteria, ed. M. E. Michel-Beyerle, Springer-Verlag, Berlin, p. 122-130, (1985).

84. Polarization Constraints in Molecular Dynamics Simulation of Aqueous Solutions: The Surface Constraint All Atom Solvent (SCAAS) Model, A. Warshel and G. King, Chem. Phys. Lett. 121, 124-129 (1985).

85. Simulating Solvent and Dielectric Effects, A. Warshel and S.T. Russell in Molecular Dynamics and Protein Structure, ed. J. Herman, Polycrystal Book Service, Western Springs, Illinois, 23 (1985).

86. Control of Redox Potential of Cytochrome c and Microscopic Dielectric Effects in Proteins, A. K. Churg and A. Warshel, Biochemistry 25, 1675-1681 (1986).

87. Simulation of the Dynamics of Electron Transfer Reactions in Polar Solvents: Semiclassical Trajectories and Dispersed Polaron Approaches, A. Warshel and J-K Hwang, J. Chem. Phys. 84, 4938-4957 (1986).

88. Towards Computer Aided Site-Directed Mutagenesis of Enzymes, A. Warshel and F. Sussman, Proc. Natl. Acad. Sci. USA 83, 3806-3810 (1986).

89. Correlation Between Structure and Efficiency of Light-Induced Proton Pumps, A. Warshel, Method Enzymol. 127, 578-587 (1986).

90. Theoretical Correlation of Structure and Energetics in the Catalytic Reaction of Trypsin, A. Warshel and S. Russell, J. Am. Chem. Soc. 108, 6569-6579 (1986).

91. Free Energy of Charges in Solvated Proteins: Microscopic Calculations Using a Reversible Charging Process, A. Warshel, F. Sussman and G. King, Biochemistry 25 8368-8372 (1986).

92. Computer Simulation of Enzymatic Reactions, A. Warshel, S. Russell and F. Sussman, Isr. J. Chem. 27, 217-224 (1986).

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93. Microscopic Examination of Free Energy Relationships for Electron Transfer in Polar Solvents, J-K. Hwang and A. Warshel, J. Am. Chem. Soc. 109, 715-720 (1987).

94. Spectroscopic Properties of Photosynthetic Reaction Centers. 1. Theory. A. Warshel and W. W. Parson, J. Am. Chem. Soc. 109, 6143-6152 (1987).

95. Spectroscopic Properties of Photosynthetic Reaction Centers. 2. Application of the Theory of Rhodopseudomonas Viridis, W. W. Parson and A. Warshel, J. Am. Chem. Soc. 109, 6152-6163 (1987).

96. Activation Free Energies of Enzymatic Reactions, Simulations and Experiments, A. Warshel in Structure, Dynamics and Functions of Biomolecules, ed. A. Ehrenberg, R. Rigler, A. Graslund and L. Nilsson Springer-Verlag, p. 61-64 (1987).

97. Calculations of Spectroscopic Properties and Electron Transfer Kinetics of Photosynthetic Bacterial Reaction Centers, W.W. Parson, S. Creighton, and A. Warshel in Primary Processes in Photobiology, ed. T Kobyashi, Springer-Verlag, p. 43 (1987).

98. Simulating the Dynamics of Electron Transfer Reactions in Cytochrome c, A. Warshel in Protein Structure Molecular and Electronic Reactivity, ed. R. Austin, Springer-Verlag, p. 351 (1987).

99. Semiquantitative Calculations of Catalytic Free Energies in Genetically Modified Enzymes, J. K. Hwang and A. Warshel, Biochemistry 26, 2669-2673 (1987).

100. What about Protein Polarity, A. Warshel, (News and Views) Nature 330, 15-16 (1987).

101. Simulating Rate Constants of Enzymatic Reactions and a Rational Engineering of Enzymes, F. Sussman and A. Warshel in Three Dimensional Structures and Drug Action ed. Y. Iiaka & A. Itai, University of Tokyo Press, 96 (1987).

102. Simulating the Dynamics of the Primary Charge Separation Process in Bacterial Photosynthesis, S. Creighton, J-K Hwang, A. Warshel, W.W. Parson and J. Norris, Biochemistry 27, 774-781 (1988).

103. Electron Transfer Pathways in The Primary Event of Bacterial Photosynthesis, A. Warshel, S. Creighton and W. W. Parson, J. Phys. Chem. 92, 2696-2701 (1988).

104. Simulation of Free Energy Relationships and Dynamics of SN2 Reactions in Aqueous Solutions, J-K Hwang, G. King, S. Creighton and A. Warshel. J. Am. Chem. Soc. 110, 5297-5311 (1988).

105. Effects of Solute-Solvent Coupling and Solvent Saturation on Solvation Dynamics of Charge Transfer Reactions. J-K Hwang, S. Creighton, G. King, D. Whitney, and A. Warshel, J. Chem. Phys. 89, 859-865 (1988).

106. Simulating the Energetics and Dynamics of Enzymatic Reactions in Genetically Modified Enzymes, J-K Hwang, F. Sussman, and A. Warshel in Structure and Expression, ed. R. H Sarma and M. H. Sarma, Adenine Press, New York, p. 95-106 (1988).

107. Why Ion-Pair Reversal by Protein Engineering is Unlikely to Succeed, J-K. Hwang and A. Warshel, Nature 334, 270-272 (1988).

108. Evaluation of Catalytic Free Energies in Genetically Modified Proteins, A. Warshel, F. Sussman and J-K. Hwang, J. Mol. Biol. 201, 139-159 (1988).

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109. Spectroscopic Properties and Electron Transfer Dynamics of Reaction Centers, W. W. Parson, S. Creighton, A. Warshel and J. Norris in The Photosynthetic Bacterial Reaction Center, Structure and Dynamics, ed. J. Berton and A. Vermeglio. Plenuum Press, New York, 309 (1988).

110. The Extended Ewald Method: A General Treatment of Long-Range Electrostatic Interactions in Microscopic Simulations, S. Kuwajima and A. Warshel, J. Chem. Phys. 89, 3751-3759 (1988).

111. Microscopic Free Energy Calculations of Solvated Macromolecules as a Primary Structure-Function Correlator and the MOLARIS Program, A. Warshel and S. Creighton in Computer Simulation of Biomolecular Systems, W. F. van Gunsteren and P. K. Weiner, eds., ESCOM, Leiden, p. 120 (1989).

112. How Do Serine Proteases Really Work? A. Warshel, G. Naray-Szabo, F. Sussman and J-K. Hwang, Biochemistry 28, 3629-3637 (1989).

113. Energetics of Ion Permeation through Membrane Channels. The Solvation of Na+ by Gramicidin A, J. Åqvist and A. Warshel, Biophys. J. 56 171-182 (1989).

114. Calculations of Free Energy Profiles for the Staphylococcal Nuclease Catalyzed Reaction, J. Åqvist and A. Warshel, Biochemistry 28, 4680-4689 (1989).

115. Role of Arginine-38 in Regulation of the Cytochrome c Oxidation-Reduction Equilibrium, R.L. Cutler, A.M. Davies, S. Creighton, A. Warshel, G. R. Moore, M. Smith and A. G. Mauk, Biochemistry 28, 3188-3197 (1989).

116. Calculations of Charge-Transfer Transition Energies and Spectroscopic Properties of a Molecular Crystal: Methylbacteriopheophorbide a, W. W. Parson, S. Creighton and A. Warshel, J. Am. Chem. Soc. 111, 4277-4284 (1989).

117. Consistent Calculations of Electrostatic Free Energies in Membrane Channels. The Solvation of Na+ by the Gramicidin Channel, J. Åqvist and A. Warshel, Comments Mol. Cell. Biophys. 6, 91 (1989).

118. Enzymes Work by Solvation Substitution Rather than by Desolvation. A. Warshel, J. Åqvist and S. Creighton, Proc. Natl. Acad. Sci. USA 86, 5820-5824 (1989).

119. Microscopic Simulation of Quantum Dynamics and Nuclear Tunneling in Bacterial Reaction Centers. Z. T. Chu, A. Warshel and W. W. Parson, Photosynth. Res. 22, 39-46 (1989).

120. Microscopic Simulations of Chemical Reactions in Solutions and Protein Active Sites; Principles and Examples, A. Warshel, in The Enzyme Catalysis Process, ed. A. Cooper, J. Houben and L. C. Chien, NATO ASI Series, Plenum Press, 178, 305-330 (1989).

121. Electrostatic Correlation of Structure and Function in Proteins, A. Warshel and J. Åqvist, Nobel Symposium, Chemica Scripta, 29A, 75-83 (1989).

122. Dispersed Polaron Simulations of Electron Transfer in Photosynthetic Reaction Centers, A. Warshel, Z. T. Chu and W. W. Parson, Science 246, 112-116 (1989).

123. A Surface Constrained All-Atom Solvent Model for Effective Simulations of Polar Solutions, G. King and A. Warshel, J. Chem. Phys. 91, 3647-3661 (1989).

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124. Electrostatic Free Energy as the Fundamental Structure Function Correlation in Proteins. Some Perspectives from Microscopic Simulations of Protein Functions. A. Warshel, in Modeling of Molecular Structure and Properties, ed. J. L. Rivail, Studies in Physical and Theoretical Chemistry, Elsevier Science Publishers B. V. Amsterdam 71, 515-526 (1990).

125. Incorporating Electric Polarizabilities in Water-Water Interaction Potentials, S. Kuwajima and A. Warshel, J. Phys. Chem. 94, 460-466 (1990).

126. Free Energy Relationships in Metalloenzyme-Catalyzed Reactions. Calculations of the Effect of Metal Ion Substitutions in Staphylococcal Nuclease, J. Åqvist and A. Warshel, J. Am. Chem. Soc. 112, 2860-2868 (1990).

127. Quantum Corrections for Rate Constants of Diabatic and Adiabatic Reactions in Solutions, A. Warshel and Z. T. Chu, J. Chem. Phys. 93, 4003-4015 (1990).

128. Electrostatic Control of Charge Separation in Bacterial Photosynthesis, W.W. Parson, Z. T. Chu, and A. Warshel, BBA 1017, 251-272 (1990).

129. Investigation of the Free Energy Functions for Electron Transfer Reactions, G. King and A. Warshel, J. Chem. Phys. 93, 8682-8692 (1990).

130. Microscopic Simulations of Chemical Processes in Proteins and the Role of Electrostatic Free Energy, A. Warshel and J. Åqvist, in Theoretical Biochemistry and Molecular Biophysics, eds. D. L. Beveridge and R. Lavery, Adenine Press, Volume 2, p. 257-274.(1991).

131. Electrostatic Energy and Macromolecular Function. A. Warshel and J. Åqvist, Annu. Rev. Biophys. Biophys. Chem. 20, 267-298 (1991).

132. Dipoles Localized at Helix Termini of Proteins Stabilize Charges. J. Åqvist, H. Luecke, F. A. Quiocho, and A. Warshel, Proc. Natl. Acad. Sci. USA 88, 2026-2030 (1991).

133. Role of Solvent Reorganization Energies in the Catalytic Activity of Enzymes. A. Yadav, R. M. Jackson, J. J. Holbrook and A. Warshel, J. Am. Chem. Soc. 113, 4800-4805 (1991).

134. Microscopic Calculations of Solvent Effects on Absorption Spectra of Conjugated Molecules. V. Luzhkov and A. Warshel, J. Am. Chem. Soc. 113, 4491-4499 (1991).

135. Computer Simulations of Electron Transfer Reactions in Solution and Photosynthetic Reaction Centers. A. Warshel, and W. W. Parson, Annu. Rev. Phys. Chem. 42, 279-309 (1991).

136. Electrostatic Effects on the Speed and Directionality of Electron Transfer in Bacterial Reaction Centers: The Special Role of Tyrosine M-208. W. W. Parson, V. Nagarajan, D. Gaul, C. C. Schenck, Z.-T. Chu, and A. Warshel, in Reaction Centers of Photosynthetic Bacteria, ed. M.-E. Michel-Beyerle, Springer, Berlin, p. 239 (1991).

137. Microscopic Simulations of Macroscopic Dielectric Constants of Solvated Proteins. G. King, F. S. Lee, and A. Warshel, J. Chem. Phys. 95, 4366-4377 (1991).

138. Simulations of Quantum Mechanical Corrections for Rate Constants of Hydride-Transfer Reactions in Enzymes and Solutions. J.-K. Hwang, Z. T. Chu, A. Yadav, and A. Warshel, J. Phys. Chem. 95, 8445-8448 (1991).

139. The Dynamics of the Primary Event in Rhodopsins Revisited, A. Warshel, Z. T. Chu and J.-K. Hwang, Chem. Phys. 158, 303-314 (1991).

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140. Calculations of Antibody-Antigen Interactions: Microscopic and Semi-Microscopic Evaluation of the Free Energies of Binding of Phosphorylcholine Analogs to McPC603, F. S. Lee, Z. T. Chu, M. B. Bolger, and A. Warshel, Protein Eng. 5, 215-228 (1992).

141. Microscopic Models for Quantum Mechanical Calculations of Chemical Processes in Solutions: LD/AMPAC and SCAAS/AMPAC Calculations of Solvation Energies. V. Luzhkov and A. Warshel, J. Comput. Chem. 13, 199-213 (1992).

142. Quantum-mechanical Calculations of Solvation Free Energies. A Combined ab initio Pseudopotential Free-energy Perturbation Approach. N. Vaidehi, T. A. Wesolowski, and A. Warshel, J. Chem. Phys. 97, 4264-4271 (1992).

143. Computer Simulation of the Initial Proton Transfer Step in Human Carbonic Anhydrase I. J. Åqvist and A. Warshel, J. Mol. Biol. 224, 7-14 (1992).

144. Computer Simulations of Enzymatic Reactions, A. Warshel, Curr. Opin. Struc. Biol. 2, 230-236 (1992).

145. A Local Reaction Field Method for Fast Evaluation of Long-range Electrostatic Interactions in Molecular Simulations, F. S. Lee and A. Warshel, J. Chem. Phys. 97, 3100-3107 (1992).

146. Computer Simulations of Enzymatic Reactions: Examination of Linear Free-energy Relationships and Quantum-mechanical Corrections in the Initial Proton-transfer Step of Carbonic Anhydrase, A. Warshel, J.-K. Hwang, J. Åqvist, Faraday Discuss. 93, 225-238 (1992).

147. Effect of the Asn52Ile Mutation on the Redox Potent of Yeast Cytochrome C, R. Langen, G. D. Brayer, A.M. Berghuis, G. McLendon, F. Sherman and A. Warshel, J. Mol. Biol. 224, 589-600 (1992).

148. Protein Control of Iron-Sulfur Cluster Redox Potentials, R. Langen, G. M. Jensen, U. Jacob, P. J. Stephens and A. Warshel, J. Biol. Chem. 267, No. 36, 25625-25627 (1992).

149. On the Mechanism of Guanosine Triphosphate Hydrolysis in ras p21 Proteins. R. Langen, T. Schweins and A. Warshel, Biochemistry 31, 8691-8696 (1992).

150. Simulations of Proton Transfer and Hydride Transfer Reactions in Proteins, A. Warshel, in Molecular Aspects of Biotechnology Computational Models and Theories, ed. J. Bertran, Kluwer Academic Publishers, Netherlands (1992).

151. Computer Simulation of the CO2/HCO3- Interconversion Step in Human Carbonic

Anhydrase I. J. Åqvist, M. Fothergill, A. Warshel, J. Am. Chem. Soc. 115, 631-635 (1993).

152. Microscopic and Semimicroscopic Calculations of Electrostatic Energies in Proteins by the POLARIS and ENZYMIX Programs, F. S. Lee, Z. T. Chu, and A. Warshel, J. Comput. Chem. 14,161-185 (1993).

153. Simulations of Electron Transfer in Bacterial Reaction Centers, W. W. Parson and A. Warshel, in The Photosynthetic Reaction Center, 2, ed. J. Norris and J. Deisenhofer Academic Press, Inc., p. 23 (1993).

154. Molecule Recognition in the Catalytic Action of Metallo-Enzymes, J. Åqvist, and A. Warshel, in Principles of Molecular Recognition, ed. Buckingham, A. Legon and S. Robert, Blackie Academic Professional, p. 108-136 (1993).

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155. Frozen Density Functional Approach for Ab Initio Calculations of Solvated Molecules, T. A. Wesolowski and A. Warshel, J. Phys. Chem. 97, 8050-8053 (1993).

156. Simulation of Enzyme Reactions Using Valence Bond Force Fields and Other Hybrid Quantum/Classical Approaches, J. Åqvist and A. Warshel, Chem. Rev. 93, 2523-2544 (1993).

157. A Quantized Classical Path Approach for Calculations of Quantum Mechanical Rate Constants, J.-K. Hwang and A. Warshel, J. Phys. Chem. 97, 10053-10058 (1993).

158. Chemical Shifts in Proteins: A Shielding Trajectory Analysis of the Fluorine Nuclear Magnetic Resonance Spectrum of the Escherichia coli Galactose Binding Protein Using a Multipole Shielding Polarizability-Local Reaction Field-Molecular Dynamics Approach, J. G. Pearson, E. Oldfield, F. S. Lee, A. Warshel, J. Am. Chem. Soc. 115, 6851-6862 (1993).

159. On the Energetics of the Primary Electron-Transfer Process in Bacterial Reaction Centers, A. Warshel, Z. T. Chu, and W. W. Parson, J. Photoch. Photobio. A 82, 123-128 (1994).

160. Theoretical Analyses of Electron-Transfer Reactions, W. W. Parson and A. Warshel, in Anoxygenic Photosynthetic Bacteria, ed. R. E. Blankenship, M. T. Madigan, and C. E. Bauer, Kluyer Academic Publishers (1994).

161. Why Have Mutagenesis Studies Not Located the General Base in ras p21, T. Schweins, R. Langen and A. Warshel, Nat. Struct. Biol. 1, 476-484 (1994).

162. Effective Methods for Estimation of Binding Energies in Computer-Aided Drug Design, A. Warshel, H. Tao, M. Fothergill and Z-T. Chu, Isr. J. Chem. 34, 253-256 (1994).

163. Calculation of the Redox Potentials of Iron-Sulfur Proteins: the 2-/3-- Couple of [Fe4S4*Cys4] Clusters in Peptococcus aerogenes Ferredoxin, Azotobacter vinelandii Ferredoxin I, and Chromatium vinosum High-Potential Iron Protein, G. M. Jensen, A. Warshel and P. J. Stephens, Biochemistry 33, 10911-10924 (1994).

164. Ab Initio Free Energy Perturbation Calculations of Solvation Free Energy Using the Frozen Density Functional Approach, T. Wesolowski and A. Warshel, J. Phys. Chem. 98, 5183-5187 (1994).

165. Linear Free Energy Relationships in Enzymes. Theoretical Analysis of the Reaction of Tyrosyl-tRNA Synthetase, A. Warshel, T. Schweins and M. Fothergill, J. Am. Chem. Soc. 116, 8437-8442 (1994).

166. Calculations of Solvation Free Energies in Chemistry and Biology, A. Warshel and Z. T. Chu, in ACS Symposium Series: Structure and Reactivity in Aqueous Solution: Characterization of Chemical and Biological Systems, ed. C. J. Cramer and D. G. Truhlar, 568, p. 71-94 (1994).

167. Linear Free Energy Relationships with Quantum Mechanical Corrections: Classical and Quantum Mechanical Rate Constants for Hydride Transfer Between NAD+ Analogues in Solutions, Y. Kong and A. Warshel, J. Am. Chem. Soc. 117, 6234-6242 (1995).

168. Substrate-Assisted Catalysis as a Mechanism for GTP Hydrolysis of p21ras and Other GTP-binding Proteins, T. Schweins, M. Geyer, K. Scheffzek, A. Warshel, H. R. Kalbitzer and A. Wittinghofer, Nat. Struct. Biol. 2, 36-44 (1995).

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169. On Low-Barrier Hydrogen Bonds and Enzyme Catalysis, A. Warshel, A. Papazyan and P. A. Kollman, Science 269, 102-104 (1995).

170. Structure-Energy Analysis of the Role of Metal Ions in Phosphodiester Bond Hydrolysis by DNA Polymerase I, M. Fothergill, M. F. Goodman, J. Petruska and A. Warshel, J. Am. Chem. Soc. 117, No.47, 11619-11627 (1995).

171. Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution, R. P. Muller and A. Warshel, J. Phys. Chem. 99, 17516-17524 (1995).

172. Calculations of Electrostatic Energies in Photosynthetic Reaction Centers, R. G. Alden, W. W. Parson, Z. T. Chu and A. Warshel, J. Am. Chem. Soc. 117, 12284-12298 (1995).

173. Ab Initio Calculations of Free Energy Barriers for Chemical Reactions in Solution: Proton Transfer in [FHF]-, R. P. Muller and A. Warshel, Pacific Symposium for Biocomputing. L. Hunter and T. E. Klein, eds. World Scientific Press, Singapore (1996).

174. Macroscopic and Microscopic Estimates of the Energetics of Charge Separation in Bacterial Reaction Centers, R. G. Alden, W. W. Parson, Z. T. Chu and A. Warshel, in Reaction Centers of Photosynthetic Bacteria, Structure and Dynamics, ed. M. E. Michel-Beyerly, Springer-Verlag, Berlin (1996).

175. Electrostatic Control of GTP and GDP Binding in the Oncoprotein p21ras, I. Muegge, T. Schweins, R. Langen and A. Warshel, Structure 4, 475-489 (1996).

176. Calculations of the Electrostatic Free Energy Contributions to the Binding Free Energy of Sulfonamides to Carbonic Anhydrase, J. D. Madura, Y. Nakajima, R. M. Hamilton, A. Wierzbicki and A. Warshel, Struct. Chem. 7, 131-138 (1996).

177. Energy Considerations Show that Low-Barrier Hydrogen Bonds Do Not Offer A Catalytic Advantage Over Ordinary Hydrogen Bonds, A. Warshel and A. Papazyan, Proc. Natl. Acad. Sci. USA 93, 13665-13670 (1996).

178. Mechanistic Analysis of the Observed Linear Free Energy Relationships in p21ras and Related System, T. Schweins and A. Warshel, Biochemistry 35, 14232-14243 (1996).

179. Linear Free Energy Relationships in the Intrinsic and GTPase Activating Protein-Stimulated Guanosine 5'-Triphosphate Hydrolysis of p21ras, T. Schweins, M. Geyer, H. R. Kalbitzer, A. Wittinghofer and A. Warshel, Biochemistry 35, 14225-14231 (1996).

180. Protein Control of Redox Potentials of Iron-Sulfur Proteins, P. J. Stephens, D. R. Jollie and A. Warshel, Chem. Rev. 96, 2491-2513 (1996).

181. How Important Are Quantum Mechanical Nuclear Motions in Enzyme Catalysis? J.-K. Hwang and A. Warshel, J. Am. Chem. Soc. 118, 11745-11751 (1996).

182. Orientation of the OH Dipole of Tyrosine (M)210 and Its Effect on Electrostatic Energies in Photosynthetic Bacterial Reaction Centers, R. G. Alden, W. W. Parson, Z. T. Chu and A. Warshel, J. Phys. Chem. 100, 16761-16770 (1996).

183. Ab Initio Frozen Density Functional Calculations of Proton Transfer Reactions in Solution, T. Wesolowski, R. P. Muller and A. Warshel, J. Phys. Chem. 100, 15444-15449 (1996).

184. Calculations of Chemical Processes in Solution by Density Functional and Other Quantum Mechanical Techniques, R. P. Muller, T. Wesolowski and A. Warshel, in Density Functional

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Methods: Applications in Chemistry and Materials Science, ed. M. Springborg, John Wiley and Sons: p.189-206 (1997).

185. Two-Dimensional Free Energy Surfaces for Primary Electron Transfer in a Photosynthetic Reaction Center, A. Warshel, Z. T. Chu and W. W. Parson, Chem. Phys. Lett. 265, 293-296 (1997).

186. Microscopic and Semimacroscopic Redox Calculations: What Can and Cannot be Learned from Continuum Models, A. Warshel, A. Papazyan and I. Muegge, Int. J. Bioinorg. Chem. 2, 143-152 (1997).

187. Electrostatic Basis of Enzyme Catalysis, G. Naray-Szabo, M. Fuxreiter and A. Warshel, in Computational Approaches to Biochemical Reactivity, eds. A. Warshel and G. Naray-Szabo, Kluwer Academic Publishers: p. 237-293 (1997).

188. Consistent Calculations of pKa's of Ionizable Residues in Proteins: Semi-Microscopic and Macroscopic Approaches, Y. Y. Sham, Z. T. Chu and A. Warshel, J. Phys. Chem. B 101, 4458-4472 (1997).

189. A Fundamental Assumption About OH- Attack in Phosphate Hydrolysis is Not Fully Justified, J. Flórian and A. Warshel, J. Am. Chem. Soc. 119, 5473-5474 (1997).

190. Langevin Dipoles Model for Ab Initio Calculations of Chemical Processes in Solution: Parameterization and Application to Hydration Free Energies of Neutral and Ionic Solutes and Conformational Analysis in Aqueous Solution, J. Flórian and A. Warshel, J. Phys. Chem. 101, 5583-5595 (1997).

191. On the Relationship Between the Dispersed Polaron and Spin-Boson Models, J.-K. Hwang and A. Warshel, Chem. Phys. Lett. 271, 223-225 (1997).

192. The Reorganization Energy of Cytochrome c Revisited, I. Muegge, P. X. Qi, J. Wand, Z. T. Chu and A. Warshel, J. Phys. Chem. B 101, 825-836 (1997).

193. Computer Simulations of the Action of Metalloenzymes, A. Warshel in Molecular Modeling and Dynamics of Bioinorganic Systems, eds. L. Banci and P. Comba, NATO: ASI Series, Kluwer Academic Publishers: p. 343-359 (1997).

194. A Stringent Test of the Cavity Concept in Continuum Dielectrics, A. Papazyan and A. Warshel, J. Chem. Phys. 107, 7975-7978 (1997).

195. Semiempirical and Ab Initio Modeling of Chemical Processes: From Aqueous Solution to Enzymes, R. P. Muller, J. Florian, A. Warshel in Biomolecular Structure and Dynamics, eds. G. Vergoten and T. Theophanides, NATO: ASI Series, Kluwer Academic Press: p. 47-77 (1997).

196. Continuum and Dipole-Lattice Models of Solvation, A. Papazyan and A. Warshel, J. Phys. Chem. B 101, 11254-11264 (1997).

197. A Fast Estimate of Electrostatic Group Contributions to the Free Energy of Protein-Inhibitor Binding, I. Muegge, H. Tao and A. Warshel, Protein Eng. 10, 1363-1372 (1997).

198. Oscillations of the Energy Gap for the Initial Electron-Transfer Step in Bacterial Reaction Centers, W. W. Parson, Z. T. Chu and A. Warshel, Photosynth. Res. 55, 147-152, (1998).

199. Origin of the Catalytic Power of Acetylcholinesterase: Computer Simulation Studies, M. Fuxreiter and A. Warshel, J. Am. Chem. Soc. 120, 183-194 (1998).

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200. Electrostatic Contributions to Protein-Protein Binding Affinities: Application to Rap/Raf Interaction, I. Muegge, T. Schweins and A. Warshel, Proteins 30, 407-423 (1998).

201. Phosphate Ester Hydrolysis in Aqueous Solution: Associative Versus Dissociative Mechanisms, J. Flórian and A. Warshel, J. Phys. Chem. B 102, 719-734 (1998).

202. Hybrid ab initio Quantum Mechanics/Molecular Mechanics Calculations of Free Energy Surfaces for Enzymatic Reactions: The Nucleophilic Attack in Subtilisin, J. Bentzien, R. P. Muller, J. Florián and A. Warshel, J. Phys. Chem. B 102, 2293-2301 (1998).

203. Reorganization Energy of the Initial Electron-Transfer Step in Photosynthetic Bacterial Reaction Centers, W. W. Parson, Z. T. Chu, and A. Warshel, Biophys. J. 74, 182-191 (1998).

204. Electrostatic Effects in Macromolecules: Fundamental Concepts and Practical Modeling, A. Warshel and A. Papazyan, Curr. Opin. in Struc. Biol. 8, 211-217 (1998).

205. The Effect of Protein Relaxation on Charge-Charge Interactions and Dielectric Constants of Proteins, Y. Y. Sham, I. Muegge and A. Warshel, Biophys. J. 74, 1744-1753 (1998).

206. Computer Simulations of Enzyme Catalysis. Finding Out What Has Been Optimized by Evolution, A. Warshel and J. Florián, Proc. Natl. Acad. Sci. USA 95, 5950-5955 (1998).

207. Quantum Mechanical - Molecular Mechanical Approaches for Studying Chemical Reactions in Proteins and Solution, J. Bentzien, J. Florián, T. M. Glennon and A. Warshel in: Combined Quantum Mechanical & Molecular Mechanical Methods, ACS Symposium Series, 712, J. Gao and M. A. Thompson, eds., pp. 16-34 (1998).

208. Conformational Flexibility of Phosphates, Phosphonate and Phosphorothiate Methyl Esters in Aqueous Solution, J. Florián and M. Strajbl and A. Warshel, J. Am. Chem. Soc. 120, 7959-7966 (1998).

209. On the Reactivity of Phosphate Monoester Dianions in Aqueous Solution: Bronsted Linear Free-Energy Relationships Do Not Have a Unique Mechanistic Interpretation, J. Florián, J. Åqvist and A. Warshel, J. Am. Chem. Soc. 120, 11524-11525 (1998).

210. Electrostatic Origin of the Catalytic Power of Enzymes and the Role of Preorganized Active Sites, A. Warshel, Mini Review, J. Biol. Chem. 273, 27035-27038 (1998).

211. Energetics of the Catalytic Reaction of Ribonuclease A: A Computational Study of Alternative Mechanisms, T. M. Glennon and A. Warshel, J. Am. Chem. Soc. 120, 10234-10247 (1998).

212. Energetics of Cation Radical Formation at the Proximal Active Site Tryptophan of Cytochrome c Peroxidase and Ascorbate Peroxidase, G. M. Jensen, S. W. Bunte, A. Warshel and D. B. Goodin, J. Phys. Chem. B 102, 8221-8228 (1998).

213. The Surface Constraint All Atom Model Provides Size Independent Results in Calculations of Hydration Free Energies, Y. Y. Sham and A. Warshel, J. Chem. Phys. 109, 7940-7944 (1998).

214. Free Energy Functions for Charge Separation in Wild-type and Mutant Bacterial Reaction Centers, W. W. Parson, Z. T. Chu, A. Warshel, in Photosynthesis: Mechanism and Effects. G. Garab, ed., (Kluwer Acad. Publ., Dordrecht) 2, 703-706 (1998).

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215. Effect of Solvent Discreteness on Solvation, A. Papazyan and A. Warshel, J. Phys. Chem. B 102, 5348-5357 (1998).

216. Thermodynamic Parameters for Stacking and Hydrogen Bonding of Nucleic Acid Bases in Aqueous Solution. Ab Initio/Langevin Dipoles Study, J. Florián, J. Sponer and A. Warshel, J. Phys. Chem. B 103, 884-892 (1999).

217. Mechanistic Alternatives in Phosphate Monoester Hydrolysis: What Conclusions Can be Drawn from Available Experimental Data?, J. Åqvist, K. Kolmodin, J. Florián and A. Warshel, Chem. Biol. 6, R71-R80 (1999).

218. Catalytic Hydrolysis of Adenosine 2',3'-Cyclic Monophosphate by Cu(II) Terpyridine, L. A. Jenkins, J. K. Bashkin, J. D. Pennock, J. Florian and A. Warshel, Inorg. Chem. 38, 3215-3222 (1999).

219. Role of Active Site Residues in the Glycosylase Step of T4 Endonuclease V. Computer Simulation Studies on Ionization States, M. Fuxreiter, A. Warshel and R. Osman, Biochemistry 38, 9577-9589 (1999).

220. Simulating Proton Translocations in Proteins: Probing Proton Transfer Pathways in the Rhodobacter sphaeroides Reaction Center, Y. Y. Sham, I. Muegge and A. Warshel, Proteins 36, 484-500 (1999).

221. Calculations of Hydration Entropies of Hydrophobic, Polar, and Ionic Solutes in the Framework of the Lnagevin Dipoles Solvation Model, J. Florian and A. Warshel, J. Phys. Chem. B 103, 10282-10288 (1999).

222. Energetics and Dynamics of Transition States of Reactions in Enzymes and Solutions, A. Warshel and J. Bentzien, in "Transition State Modeling for Catlysis", ed. D. G. Truhlar and K. Morokuma, ACS Symposium Series 725, 489-499 (1999).

223. Quantum Catalysis: The Modeling of Catalytic Transition States, M. B. Hall, P. Margl, G. Naray-Szabo, V. L. Schramm, D. G. Truhlar, R. A. van Santen, A. Warshel and J. L. Whitten, in "Transition State Modeling for Catalysis", ed. D. G. Truhlar and K. Morokuma, ACS Symposium Series 721, 2-17 (1999).

224. Using Simplified Protein Representation as a Reference Potential for All-Atom Calculations of Folding Free Energy, Z.Z. Fan, J.-K. Hwang and A. Warshel, Theor. Chem. Acc. 103, 77-80 (1999).

225. Quantum-Chemical Insights into Mechanisms of the Nonenzymatic Hydrolysis of Phosphate Monoesters, J. Florian and A. Warshel, Phosphorus Sulfur 144-146, 525-528 (1999).

226. Microscopic Based Density Matrix Treatments of Electron-Transfer Reactions in Condensed Phases, C.F. Jen and A. Warshel, J. Phys. Chem. 103, 11378-11386 (1999).

227. Computer Simulation of Biological Molecules, A. Warshel, Encyclopedia of Molecular Biology, Ed. T.E. Creighton, John Wiley & Sons, Inc., 555 (1999).

228. Free Energy Calculations, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 939 (1999).

229. Molecular Mechanics, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 1526 (1999).

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230. Potential Functions (Force Fields), A. Warshel, Encyclopedia of Molecular Biology Ed., T. E. Creighton, John Wiley & Sons, Inc., 1937 (1999).

231. Monte Carlo Calculations, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 1537 (1999).

232. Neural Networks and Genetic Algorithms, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 1589 (1999).

233. Molecular Dynamics, A. Warshel, Encyclopedia of Molecular Biology, Ed. T. E. Creighton, John Wiley & Sons, Inc., 1527 (1999).

234. Perspective on "The Energetics of Enzymatic Reactions”, A. Warshel, Proc. Natl. Acad. Sci. USA, 75, 5250 (1978)," Theor. Chem. Acc. 103, 337-339, (2000).

235. What is the Relationship Between Dynamical Effects and Biological Functions? A. Warshel, in Simplicity and Complexity in Proteins and Nucleic Acids, eds. H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, Dahlem University Press, 199-211(2000).

236. Group Report: How Does Complexity Lead to an Apparently Simple Function? K. Moffat, J.-P. Changeux, D. M. Crother, H. Grubmuller, G. U. Nienhaus, M. U. Palma, F. G. Parak, K. Schulten, and A. Warshel, in Simplicity and Complexity in Proteins and Nucleic Acids, eds. H. Frauenfelder, J. Deisenhofer, and P. G. Wolynes, Dahlem University Press, 255-280(2000).

237. Ab Initio/LD Studies of Chemical Reactions in Solution: Reference Free-Energy Surfaces for Acylation Reactions Occurring in Serine and Cysteine Proteases, M. Strajbl, J. Florian and A. Warshel, Int. J. Quantum Chem. 77, 44-53(2000).

238. Examining Methods for Calculations of Binding Free Energies: LRA, LIE, PDLD-LRA and PDLD/S-LRA Calculations of Ligands Binding to an HIV Protease, Y.Y. Sham, Z.T. Chu, H. Tao and A. Warshel, Proteins 39, 393-407 (2000).

239. Ab Initio Evaluation of the Potential Surface for General Base Catalyzed Methanolysis of Formamide: A Reference Solution Reaction for Studies of Serine Proteases, M. Strajbl, J. Florian and A. Warshel, J. Am. Chem. Soc. 122, 5354-5366 (2000).

240. An Effective Way of Modeling Chemical Catalysis: An Empirical Valence Bond Picture of the Role of Solvent and Catalyst in Alkylation Reactions, J. Villà, J. Bentzien, A. Gonzalez-Lafont, J.M. Lluch, J. Bertran and A. Warshel, J. Comput. Chem. 21, 607-625(2000).

241. Computer Simulation Studies of the Catalytic Mechanism of Human Aldose Reductase, P. Varnai, A. Warshel, J. Am. Chem. Soc. 122, 3849-3860 (2000).

242. Calculations of Activation Entropies of Chemical Reactions in Solution, M. Strajbl, Y. Sham, J. Villa, Z. T. Chu, A. Warshel, J. Phys. Chem. B 104, 4578-4584 (2000).

243. How Does GAP Catalyze the GTPase Reaction of Ras? A Computer Simulation Study, T. M. Glennon, J.Villà and A. Warshel, Biochemistry 39, 9641-9651 (2000).

244. How Important are Entropic Contributions to Enzyme Catalysis?, J. Villa, M. Strajbl, T. M. Glennon, Y. Y. Sham, Z. T. Chu and A. Warshel, Proc. Natl. Acad. Sci. USA 97, 11899-11904 (2000).

245. Free-Energy Perturbation Calculations of DNA Destabilization by Base Substitutions: The Effect of Neutral Guanine-Thymine, Adenine-Cytosine and Adenine-Difluorotoluene

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Mismatches, J. Florian, M. F. Goodman and A. Warshel, J. Phys. Chem. B 104, 10092-10099 (2000).

246. Remarkable Rate Enhancement of Orotidine 5’-Monophosphate Decarboxylase is Due to Transition-State Stabilization Rather than to Ground-State Destabilization, A. Warshel, M. Strajbl, J. Villa, J. Florian, Biochemistry 39, 14728-14738 (2000).

247. Q-Chem 2.0: A High-Performance Ab Initio Electronic Structure Program Package: J. Kong, C. A. White, A. I. Krylov, D. Sherrill, R. D. Adamson, T. R. Furlani, M. S. Lee, A. M. Lee, S. R. Gwaltney, T.R. Adams, C. Ochsenfeld, A. T. B. Gilbert, G.S. Kedziora, V. A. Rassolov, D. R. Maurice, N. Nair, Y. Shao, N. A. Besley, P. E. Maslen, J. P. Dombroski, H. Daschel, W. Zhang, P. P. Korambath, J. Baker, E.F. C. Byrd, T. Van Voorhis, M. Oumi, S. Hirata, C-P. Hsu, N. Ishikawa, J. Florian, A. Warshel, B. G. Johnson, P. M. W. Gill, M. Head-Gordon and J. A. Pople, J. Comput. Chem. 21, 1532-1548 (2000).

248. Constraining the Electron Densities in DFT Methods as an Effective Way for Ab Initio Studies of Metal-Catalyzed Reactions. G. Hong, M. Strajbel, T. Wesolowski and A. Warshel, J. Comput.Chem. 21, 1554-1561(2000).

249. Comment on “A Fast and Simple Method to Calculate Protonation States in Proteins”, E. L. Mehler and A. Warshel, Proteins 40, 1-3 (2000).

250. Dynamics of Biochemical and Biophysical Reactions: Insight from Computer Simulations, A. Warshel and W. W. Parson, Q. Rev. Biophys.34, 563-679 (2001).

251. Circe Effect versus Enzyme Preorganization: What Can Be Learned from the Structure of the Most Proficient Enzyme?, A. Warshel, J. Florian, M. Strajbl, J. Villa, ChemBiochem 2, 109-111 (2001).

252. Ab Initio Evaluation of the Free Energy Surfaces for the General Base/Acid Catalyzed Thiolysis of Formamide and the Hydrolysis of Methyl Thioformate: A Reference Solution Reaction for Studies of Cysteine Proteases, M. Strajbl, J. Florian, A. Warshel, J. Phys. Chem. B 105, 4471-4484 (2001).

253. What are the Dielectric “Constants” of Proteins and How to Validate Electrostatic Models?, C. N. Schutz and A. Warshel, (Invited Review), Proteins 44, 400-417 (2001).

254. Energetics and Dynamics of Enzymatic Reactions, J. Villa and A. Warshel, J. Phys. Chem. B 105, 7887-7907 (2001).

255. Nature of the Surface Crossing Process in Bacteriorhodopsin: Computer Simulations of the Quantum Dynamics of the Primary Photochemical Event, A. Warshel and Z. T. Chu, J. Phys. Chem. B 105, 9857-9871 (2001).

256. Simulations of Ion Current Realistic Models of Ion Channels: The KcsA Potassium Channel, A. Burykin, C. N. Schutz, J. Villa, and A. Warshel, Proteins 47, 265-280(2002).

257. Modeling and Analyzing Biocatalysis, J. Villa and A. Warshel, Encyclopedia of Catalysis, Wiley (2002).

258. Molecular Dynamics Simulations of Biological Reactions, A. Warshel, Accounts Chem. Res. 35, 385-395 (2002).

259. Theoretical Investigation of the Binding Free Energies and Key Substrate-Recognition Components of DNA Polymerase β Fidelity, J. Florian, M. F. Goodman, and A. Warshel, J. Phys. Chem. B 106, 5739-5753 (2002).

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260. Molecular Dynamics Free Energy Simulations of the Binding Contribution to the Fidelity of DNA Polymerase T7, J. Florian, A. Warshel, and M. F. Goodman, J. Phys. Chem. B 106, 5754-5760 (2002).

261. How Much Do Enzymes Really Gain by Restraining Their Reacting Fragments?, A. Shurki, M. Strajbl, J. Villa, and A. Warshel, J. Am. Chem. Soc. 124, 4097-4107 (2002).

262. Ab-initio QM/MM Simulation with Proper Sampling: “First Principle” Calculations of the Free Energy of the Auto-dissociation of Water in Aqueous Solution, M. Strajbl, G. Hong, and A. Warshel, J. Phys. Chem. B 106,13333-13343 (2002).

263. Computer Simulations of Enzyme Catalysis: Methods, Progress and Insights, A. Warshel, Annual Review of Biophysics and Biomolecular Structure 32, 425-443 (2003).

264. Frozen Density Functional Free Energy Simulations of Redox Proteins: Computational Studies of the Reduction Potential of Plastocyanin and Rusticyanin, M.H. Olsson, G. Hong and A. Warshel, J. Am. Chem. Soc. 125, 5025-5039 (2003).

265. On the Generation of Catalytic Antibodies by Transition State Analogues, M. Barbany, H. Gutierrez-de-Teran, F. Sanz, J. Villa and A. Warshel, ChemBiochem 4, 277-285 (2003).

266. Computer Simulation Studies of the Fidelity of DNA Polymerases, J. Florian, M. Goodman, and A. Warshel, Biopolymers 68, 286-299 (2003).

267. Structure/Function Correlations of Enzymes using MM, QM/MM and Related Approaches; Methods, Concepts, Pitfalls and Current Progress, A. Shurki and A. Warshel., Advances in Protein Chemistry 66, 249-313 (2003).

268. Computer Simulation of the Chemical Catalysis of DNA Polymerases: Discriminating Between Alternative Nucleotide Insertion Mechanisms for T7 DNA Polymerase, J. Florian, M. F. Goodman and A. Warshel, J. Am. Chem. Soc. 125, 8163-8177 (2003).

269. Apparent NAC Effect in Chorismate Mutase Reflects Electrostatic Transition State Stabilization, M. Strajbl, A. Shurki, M. Kato and A. Warshel, J. Am. Chem. Soc. 125, 10228-10237 (2003).

270. Comment on “Effect of Active Site Mutation Phe93Trp in the Horse Liver Alcohol Dehydrogenase Enzyme on Catalysis: A Molecular Dynamics Study”, A. Warshel and J. Villà-Freixa, J. Phys. Chem. B 107, 12370-12371 (2003).

271. Exploring the Origin of the Ion Selectivity of the KcsA Potassium Channel, A. Burykin, M. Kato and A. Warshel, Proteins 52, 412-426 (2003).

272. What Really Prevents Proton Transport Through Aquaporin? Charge Self-Energy vs. Proton Wire Proposals, A. Burykin and A. Warshel, Biophys. J. 85, 3696-3706(2003).

273. Converting Conformational Changes to Electrostatic Energy in Molecular Motors: The Energetics of ATP Synthase m, M. Strajbl, A. Shurki and A. Warshel, Proc. Natl. Acad. Sci. USA 100, 14834-14839 (2003).

274. A Density Matrix Model of Photosynthetic Electron Transfer with Microscopically Based Estimated Vibrational Relaxation Times, W. W. Parson and A. Warshel, Chem. Phys. 296, 201-216 (2004).

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275. Simulating Large Nuclear Quantum Mechanical Corrections in Hydrogen Atom Transfer Reactions in Metalloenzymes, M. H. M. Olssen, P. E. M Siegbahn and A. Warshel, J. Biol. Inorg. Chem. 9, 96-99 (2004).

276. Analyzing Linear Free Energy Relationship for Proton Translocations in Enzymes; Carbonic Anhydrase Revisited, C. N. Schutz and A. Warshel, J. Phys. Chem. B 108, 2066-2075 (2004).

277. Electrostatic Basis for Bioenergetics. Shurki, M. Strajbl, C. N. Schutz and A. Warshel. Method Enzymol. 380, 52-84 (2004).

278. Why does the Ras Switch “Break” By Oncogenic Mutations?, A. Shurki, A. Warshel, Proteins 55, 1-10 (2004).

279. Simulations of the Large Kinetic Isotope Effect and the Temperature Dependence of the Hydrogen Transfer in Lipoxygenase, M. H. M. Olsson, P. E. M Siegbahn and A. Warshel, J. Am. Chem. Soc. 126, 2820-2828 (2004).

280. The Low Barrier Hydrogen Bond (LBHB) Proposal Revisited: The Case of the Asp…His Pair in Serine Proteases, C. N. Schutz and A. Warshel, Proteins 55, 711-723 (2004).

281. Dependence of Photosynthetic Electron-Transfer Kinetics on Temperature and Energy in a Density-Matrix Model, W. W. Parson and A. Warshe, J. Phys. Chem. B. 108, 10474-10483 (2004).

282. On the Origin of the Electrostatic Barrier for Proton Transport in Aquaporin, A. Burykin and A. Warshel, FEBS Lett. 570, 41-46 (2004).

283. Solute Solvent Dynamics and Energetics in Enzyme Catalysis: The SN2 Reaction of Dehalogenase as a General Benchmark, M. H. M. Olsson and A. Warshel, J. Am. Chem. Soc. 126, 15167-15179 (2004).

284. Studies of Proton Translocations in Biological Systems: Simulating Proton Transport in Carbonic Anhydrase by EVB Based Models, S. Braun-Sand, M. Strajbl, and A. Warshel. Biophys. J. 87, 2221-2239 (2004).

285. The Empirical Valence Bond, A. Warshel and J. Florian, The Encyclopedia of Computational Chemistry (2004).

286. Realistic Simulations of Proton Transport Along the Gramicidin Channel: Demonstrating the Importance of Solvation Effects, S. Braun-Sand, A. Burykin, and A. Warshel, J. Phys. Chem. B. 109, 583-592 (2005).

287. Inverting the Selectivity of Aquaporin 6: Gating versus Direct Electrostatic Interaction, A. Warshel, Proc. Natl. Acad. Sci. USA 102, 1813-1814 (2005).

288. Electrostatics of Proteins: Principles, Models and Applications S. Braun-Sand and A. Warshel in Protein Folding Handbook. Part I. Edited by J. Buchner and T. Kiefhaber 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim, p. 163-200 (2005).

289. Simulating Redox Coupled Proton Transfer in Cytochrome c Oxidase; Looking for the Proton Bottleneck, M. H. M. Olsson, P. K. Sharma and A. Warshel, FEBS Lett. 579, 2026-2034 (2005).

290. Computer Simulations of Protein Functions: Searching for the Molecular Origin of the Replication Fidelity of DNA Polymerases. J. Florián, M. F. Goodman and A. Warshel, Proc. Natl. Acad. Sci. USA 102, 6819-6824 (2005).

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291. What are the Roles of Substrate-Assisted Catalysis and Proximity Effects in Peptide Bond Formation by the Ribosome?, P. K. Sharma, Y. Xiang, M. Kato, and A. Warshel, Biochemistry 44, 11307-11314 (2005).

292. On Possible Pitfalls in Ab Initio Quantum Mechanics/Molecular Mechanics Minimization Approaches for Studies of Enzymatic Reactions, M. Klahn, S. Braun-Sand, E. Rosta, and A. Warshel, J. Phys. Chem. B 109,15645-15650 (2005)

293. Through the Channel and Around the Channel: Validating and Comparing Microscopic Approaches for the Evaluation of Free Energy Profiles for Ion Penetration through Ion Channels, M. Kato and A. Warshel. J. Phys. Chem. B. 109, 19516-19522 (2005)

294. Computer Modeling of Enzyme Catalysis and its Relationship to Concepts in Physical Organic Chemistry, S. Braun-Sand, M.H.M. Olsson, A. Warshel in Advances in Physical Organic Chemistry, ed. J.P. Richard,Vol. 40, 201-245 (2005).

295. Computer Simulations of Isotope Effects in Enzyme Catalysis, A. Warshel, M. H. M. Olsson, and J. Villà-Freixa, in Isotope Effects In Chemistry and Biology, ed. A. Kohen and H-H Limbach, CRC press, pp. 621-644 (2005).

296. Towards Accurate Ab Initio QM/MM Calculations of Free-Energy Profiles of Enzymatic Reactions; E. Rosta, M. Klahn, and A Warshel, J. Phys. Chem. B 110, 2934-2941 (2006).

297. Dynamical Contributions to Enzyme Catalysis: Critical Tests of a Popular Hypothesis; M. H. M. Olsson, W. W. Parson and A. Warshel, Chem. Rev. 106, 1737-1756 (2006).

298. Using a Charging Coordinate in Studies of Ionization Induced Partial Unfolding; M. Kato and A Warshel, J. Phys. Chem. B 110, 11566-11570 (2006).

299. Monte Carlo Simulations of Proton Pumps: On the Working Principles of the Biological Valve that Controls Proton Pumping in Cytochrome c Oxidase; M. H. M. Olsson and A. Warshel, Proc. Natl. Acad. Sci. USA 103, 6500-6505 (2006).

300. Membranes Assembled from Narrow Carbon Nanotubes Block Proton Transport and Can Form Effective Nano Filtration Devices; A Burykin and A Warshel, Journal of Computational Theoretical Nanoscience, 3, 237-242 (2006).

301. Transition State Theory Can be Used in Studies of Enzyme Catalysis: Lessons from Simulations of Tunnelling and Dynamical Effects in Lipoxygenase and Other Systems; M. H. M. Olsson, J. Mavri and A. Warshel, Philos. T. R. Soc. London B – Biol. Sci. 361, 1417-1432 (2006).

302. The Barrier for Proton Transport in Aquaporins as a Challenge for Electrostatic Models: The Role of Protein Relaxation in Mutational Calculations M. Kato, A. V. Pisliakov, and A. Warshel. Proteins 64, 829-844 (2006).

303. Simulating the Effect of DNA Polymerase Mutations on Transition-State Energetics and Fidelity: Evaluating Amino Acid Group Contribution and Allosteric Coupling for Ionized Residues in Human Pol beta; Y. Xiang, P. Oelschlaeger, J. Florian, M. F. Goodman, A. Warshel, Biochemistry 45, 7036-7048 (2006)

304. Electrostatic Basis for Enzyme Catalysis; A. Warshel, P. K. Sharma, M. Kato, Y. Xiang, H. Liu, and M. H. M. Olsson, Chem. Rev. 106, 3210-3235 (2006).

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305. Modeling Electrostatic Effects in Proteins; A. Warshel, P. K. Sharma, M. Kato and W. W. Parson, BBA-Proteins Proteom. 1764, 1647-1676 (2006).

306. Using the Constrained DFT Approach in Generating Diabatic Surfaces and Off Diagonal Empirical Valence Bond Terms for Modeling Reactions in Condensed Phases, G. Hong, E. Rosta and A. Warshel, J. Phys. Chem. B.110, 19570-19574 (2006).

307. On the Mechanism of Hydrolysis of Phosphate Monoesters Dianions in Solutions and Proteins; M. Klahn, E. Rosta and A. Warshel, J. Am. Chem. Soc. 128, 15310-15323 (2006).

308. Modifying the beta, gamma Leaving-Group Bridging Oxygen Alters Nucleotide Incorporation Efficiency, Fidelity, and the Catalytic Mechanism of DNA Polymerase beta; C. Sucato, T. G. Upton, B. A. Kashemirov, V. K. Batra, V. Martinek, Y. Xiang, W. A. Beard, L. C. Petersen, S. H. Wilson, C. E. McKenna, J. Florian, A. Warshel, M. F. Goodman, Biochemistry 46, 461-471 (2007).

309. Magnesium-Cationic Dummy Atom Molecules Enhanced Representation of DNA Polymerase β in Molecular Dynamics Simulations: Improved Accuracy in Studies of Structural Features and Mutational Effects; P. Oelschlaeger, M. Klahn, W. A. Beard, S. H. Wilson and Arieh Warshel, J. Mol. Biol. 366, 687-701 (2007).

310. DNA Polymerase β Catalytic Efficiency Mirrors the Asn279–dCTP H-Bonding Strength, V. Martınek, U. Bren, M. F. Goodman, A. Warshel and J. Florian, FEBS Lett. 581,775-780 (2007).

311. Exploring Pathways and Barriers for Coupled ET/PT in Cytochrome c Oxidase: A General Framework for Examining Energetics and Mechanistic Alternatives. M. H. M. Olsson, P. E. M. Siegbahn, M. R. A. Blomberg, and A. Warshel, BBA-Bioenergetics 1767, 244-260 (2007).

312. Electrostatic Contributions to Binding of Transition State Analogues Can Be Very Different from the Corresponding Contributions to Catalysis: Phenolates Binding to the Oxyanion Hole of Ketosteroid Isomerase, A. Warshel, P. K. Sharma, Z. T. Chu and J. Aqvist, Biochemistry 46, 1466-1476 (2007).

313. Electrostatic Contributions to Protein Stability and Folding Energy; M. Roca, B. Messer and A. Warshel, FEBS Lett. 581, 2065-2071(2007).

314. The Catalytic Effect of Dihydrofolate Reductase and its Mutants is Determined by Reorganization Energies, H. Liu and A. Warshel, Biochemistry 46, 6011-6025 (2007).

315. Origin of the Temperature Dependence of Isotope Effects in Enzymatic Reactions: The Case of Dihydrofolate Reductase, H. Liu and A. Warshel, J. Phys. Chem. B 111, 7852-7861 (2007).

316. A New Paradigm for Electrostatic Catalysis of Radical Reactions in Vitamin B-12 Enzymes, P. K. Sharma, Z. T. Chu, M. H. M. Olsson and A. Warshel, Proc. Natl. Acad. Sci. USA 104, 9661-9666 (2007).

317. Polarizable Force Fields: History, Test Cases, and Prospects, A. Warshel, M. Kato, and A.V. Pisliakov, J. Chem. Theory Comput. 3, 2034-2045 (2007).

318. On the Relationship Between Thermal Stability and Catalytic Power of Enzymes, M. Roca, H. Liu, B. Messer, and A. Warshel, Biochemistry 46, 15076-15088 (2007)

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319. Computer simulations of Proton transfer in proteins and Solutions, S, Braun-Sand, M. H. M. Olsson, J. Mavri and A. Warshel in Hydrogen –Transfer Reactions. Ed J. T. Hynes, J. P. Klinmann, H. H. Limbach and R. L. Schowen WILEY-VCH Verlag GmbH&Co KGaA, Weinheim, 1171- 1205 (2007)

320. Challenges and Progresses in Calculations of Binding Free Energies – What Does it Take to Quantify Electrostatic Contributions to Protein–Ligand Interactions? M. Kato, S. Braun-Sand and A. Warshel, in Computational and Structural Approaches to Drug Discovery, Ed by R. M. Stroud and J. Finer–Moore, RSC Publishing, 268-292 (2008).

321. Prediction of Drug Resistance Mutation of HIV Protease, H. Ishikita and A. Warshel, Angew. Chem. Int. Ed., 47, 697-700 (2008).

322. Exploring the Role of Large Conformational Changes in the Fidelity of DNA Polymerase β; Y. Xiang, M. F. Goodman, W. A. Beard, S. H. Wilson and A. Warshel, Proteins 70, 231-247 (2008).

323. DNA Polymerase β Fidelity: Halomethylene-Modified Leaving Groups in Pre-Steady-State Kinetic Analysis Reveal Differences at the Chemical Transition State, C. A. Sucato, T. G. Upton, B. A. Kashemirov, J. Osuna, K. Oertell, W. A. Beard, .S. H. Wilson, J. Florian, A. Warshel, C. E. McKenna, and M. F. Goodman, Biochemistry 47, 870-879 (2008)

324. Calculations of Electrostatic Energies in Proteins: Using Microscopic, Semimicroscopic and Macroscopic Models and Free Energy Perturbation Approaches, W. W. Parson and A. Warshel, in Biophysical Techniques in Photosystem II, Ed. J. Aartmas and J. Matysik, Springer, The Netherlands, 401-420 (2008).

325. Mechanism of Charge Separation in Purple Bacterial Reaction Centers, W.W. Parson and A. Warshel, in the Purple Photosynthetic Bacteria ed. N. Hunter, F. Daldal, M. C. Thurnauer and J.T. Beatty. Springer (2008).

326. Quantifying Free Energy Profiles of Proton Transfer Reactions in Solution and in Proteins by Using a Diabatic FDFT Mapping, Y. Xiang and A. Warshel, J. Phys. Chem. B 112, 1007-1015 (2008).

327. Simulation of Tunneling in Enzyme Catalysis by Combining a Biased Propagation Approach and the Quantum Classical Path Method: Application to Lipoxygenase, J. Mavri, H. Liu, M.H.M. Olsson and A. Warshel, J. Phys. Chem. B 112, 5950-5954 (2008).

328. On the Interpretation of the Observed Linear Free Energy Relationship in Phosphate Hydrolysis: A Thorough Computational Study of Phosphate Diester Hydrolysis in Solution, E. Rosta, S. C. L. Kamerlin and A. Warshel, Biochemistry 47, 3725–3735 (2008).

329. The Energetics of the Primary Proton Transfer in Bacteriorhodopsin Revisited: It is a Sequential Light-Induced Charge Separation After All, S. Braun-Sand, P. K. Sharma, Z. T. Chu, A. V. Pisliakov, A. Warshel, BBA-Bioenergetics 1777, 441–452 (2008).

330. Electrostatic Basis for the Unidirectionality of the Primary Proton Transfer in Cytochrome Oxidase, A.V. Pisliakov, P. K. Sharma, Z. T. Chu, M. Haranczyk, and A. Warshel, Proc. Natl. Acad. Sci. USA 105, 7726-7731 (2008).

331. Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies, S. C. L. Kamerlin, J. Florian, and A. Warshel, ChemPhysChem 9, 1767-1773 (2008).

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332. Accelerating QM/MM Free Energy Calculations: Representing the Surroundings by an Updated Mean Charge Distribution, E. Rosta, M, Haranczyk, Z. T. Chu and A. Warshel, J. Phys. Chem. B 112, 5680-5692 (2008).

333. Solvation Free Energies of Molecules. The Most Stable Anionic Tautomers of Uracil M. Haranczyk, M. Gutowski and A. Warshel, Phys. Chem. Chem. Phys. 10, 4442–4448 (2008).

334. On the Relationship Between Folding and Chemical Landscapes in Enzyme Catalysis, M. Roca, B. Messer, D. Hilvert and A. Warshel, Proc. Natl. Acad. Sci. USA 105, 13877-13882 (2008)

335. Dineopentyl Phosphate Hydrolysis: Evidence for Stepwise Water Attack, S. C. L. Kamerlin, N. H. Williams and A. Warshel, J. Org. Chem. FEATURE ARTICLE 73, 6960-6969 (2008).

336. Progresses in Ab Initio QM/MM Free Energy Simulations of Electrostatic Energies in Proteins: Accelerated QM/MM Studies of pKa, Redox Reactions and Solvation Free Energies, S. C. L. Kamerlin, M. Haranczyk and A. Warshel, J. Phys. Chem. B, Centennial Feature Article 113, 1253-1272 (2009).

337. Tunneling Does Not Contribute Significantly to Enzyme Catalysis, But Studying Temperature Dependence of Isotope Effects is Useful, H. Liu and A. Warshel, RSC Biomolecular Sciences, Quantum Tunneling in Enzyme-Catalyzed Reactions, Ed. by R. K. Allemann and N. S. Scrutton, Royal Society of Chemistry, 242-267 (2009).

338. Toward Accurate Screening in Computer-Aided Enzyme Design, M. Roca, A. Vardi-Kilshtain and A. Warshel, Biochemistry 48, 3046-3056 (2009).

339. The Empirical Valence Bond as an Effective Strategy for Computer-Aided Enzyme Design, A. Vardi-Kilshtain, M. Roca and A. Warshel, Biotechnol. J. 4, 495-500 (2009).

340. Toward Accurate Microscopic Calculation of Solvation Entropies: Extending the Restraint Release Approach to Studies of Solvation Effects, N. Singh and A. Warshel, J. Phys. Chem. B 113, 7372-7382 (2009).

341. Simulating the Electrostatic Guidance of the Vectorial Translocations in Hexameric Helicases and Translocases, H. Liu, Y. Shi, X. S. Chen, and A. Warshel, Proc. Natl. Acad. Sci. USA 106, 7449-7454 (2009).

342. Are Mixed Explicit/Implicit Solvation Models Reliable for Studying Phosphate Hydrolysis? A Comparative Study of Continuum, Explicit and Mixed Solvation Models, S. C. L. Kamerlin, M. Haranczyk and A. Warshel, ChemPhysChem 10, 1125-1134 (2009).

343. A Computational Study of the Hydrolysis of dGTP Analogues with Halomethylene-Modified Leaving Groups in Solution: Implications for the Mechanism of DNA Polymerases, S. C. L. Kamerlin, C. E. McKenna, M. F. Goodman and A. Warshel, Biochemistry 48, 5963-5971 (2009).

344. On Unjustifiably Misrepresenting the EVB Approach While Simultaneously Adopting It, S. C. L. Kamerlin, J Cao, E. Rosta and A Warshel, J. Phys. Chem. B 113, 10905-10915 (2009).

345. Enzyme Millisecond Conformational Dynamics Do Not Catalyze the Chemical Step, A. V. Pisliakov J. Cao, S. C. L. Kamerlin and A. Warshel, Proc. Natl. Acad. Sci. USA 106, 17359-17364 (2009).

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346. On the Energetics of ATP Hydrolysis in Solution, S. C. L. Kamerlin and A. Warshel, J. Phys. Chem. B 113, 15692-15698 (2009).

347. On the Origin of the Catalytic Power of Carboxypeptidase A and Other Metalloenzymes, A. V. Kilshtain and A. Warshel, Proteins 77, 536-550 (2009).

348. Effective Approach for Calculations of Absolute Stability of Proteins Using Focused Dielectric Constants, S. Vicatos, M. Roca and A. Warshel, Proteins 77, 670-684 (2009).

349. A Binding Free Energy Decomposition Approach for Accurate Calculations of the Fidelity of DNA Polymerases, R. Rucker, P. Oelschlaeger and A. Warshel, Proteins 78, 671-680 (2010).

350. Multiscale Simulations of Protein Landscapes: Using Coarse-Grained Models as Reference Potentials to Full Explicit Models, B. M. Messer, M. Roca, Z. T. Chu, S. Vicatos, A. V. Kilshtain and A. Warshel, Proteins 78, 1212-1227 (2010).

351. At the Dawn of the 21st Century: Is dynamics the Missing Link for Understanding Enzyme Catalysis? S. C. L. Kamerlin and A. Warshel, Proteins (INVITED REVIEW) 78, 1339-1375 (2010).

352. Absolute Binding Free Energy Calculations: On the Accuracy of Computational Scoring of Protein-Ligand Interactions, N. Singh and A. Warshel, Proteins 78, 1705-1723 (2010).

353. A Comprehensive Examination of the Contributions to the Binding Entropy of Protein-Ligand Complexes, N. Singh and A. Warshel, Proteins 78, 1724-1735 (2010).

354. Ketosteroid Isomerase Provides Further Support for the Idea that Enzymes Work byElectrostatic Preorganization, S. C.L. Kamerlin, P. K. Sharma, Z. T. Chu and A. Warshel, Proc. Natl. Acad. Sci. USA 107, 4075-4080 (2010)

355. Reply to Karplus: Conformational Dynamics Have no Role in The Chemical Step, S. C. L. Kamerlin and A. Warshel, Proc. Natl. Acad. Sci. USA 107, E72 (2010).

356. Examining the Case for the Effect of Barrier Compression on Tunneling, Vibrationally Enhanced Catalysis, Catalytic Entropy and Related Issues (Review), S.C.L. Kamerlin, J. Mavri and A. Warshel, FEBS Lett. 584, 2759-2766 (2010).

357. Exploring Challenges in Rational Enzyme Design by Simulating the Catalysis in Artificial Kemp Eliminase, M. P. Frushicheva, J. Cao, Z. T. Chu and A. Warshel, Proc. Natl. Acad. Sci. USA 107, 16869-16874 (2010).

358. An Analysis of All the Relevant Facts and Arguments Indicates that Enzyme Catalysis Does Not Involve Large Contributions from Nuclear Tunneling, S. C. L. Kamerlin and A. Warshel, J. Phys. Org. Chem. 23, 677-684 (2010).

359. Renormalizing SMD: The Renormalization Approach and Its Use in Long Time Simulations and Accelerated PMF Calculations of Macromolecules, A. Dryga and A. Warshel, J. Phys. Chem. B 114, 12720-12728 (2010).

360. On the Energetics of Translocon Assisted Insertion of Charged Transmembrane Helices into Membranes, A. Rychkova, S. Vicatos, and A. Warshel, Proc. Natl. Acad. Sci. USA 107, 17598-17603 (2010).

361. On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models, S. C. L. Kamerlin, Z. T. Chu and A. Warshel, J. Org. Chem. 75, 6391-6401 (2010).

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362. The EVB as a Quantitative Tool for Formulating Simulations and Analyzing Biological and Chemical Reactions, S. C. L. Kamerlin and A. Warshel, Faraday Discuss. 145, 71-106 (2010).

363. Phosphate Ester Analogues as Probes for Understanding Enzyme Catalyzed Phosphoryl Transfer, A. Alkherraz, S. C. L. Kamerlin, G. Feng, Q. I. Sheikh, A. Warshel and N. H. Williams, Faraday Discuss. 145, 281-299 (2010).

364. Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems, S. C. L. Kamerlin, S. Vicatos, A. Dryga and A. Warshel, Annu. Rev. Phys. Chem. 62, 41-64 (2011).

365. Exploration of the Cytochrome c Oxidase Pathway Puzzle and Examination of the Origin of Elusive Mutational Effects, S. Chakrabarty, I. Namslauer, P. Brzezinski and A. Warshel, BBA-Bioenergetics 1807, 413-426 (2011).

366. The Empirical Valence Bond Model: Theory and Applications S. C. L. Kamerlin and A. Warshel, Wiley Interdisciplinary Reviews: Computational Molecular Sciences 1, 30-45 (2011).

367. Challenges and Advances in Validating Enzyme Design Proposals: The Case of the Kemp Eliminase Catalysis, M. P. Frushicheva, J. Cao and A. Warshel, Biochemistry 50, 3849-3858 (2011).

368. Proton-Transport Mechanisms in Cytochrome c Oxidase Revealed by Studies of Kinetic Isotope Effects, A.L. Johansson, S. Chakrabarty, C. B. Siöberg, M. Högbom, A. Warshel and P. Brzezinski, BBA-Bioenergetics 1807, 1083-1094 (2011).

369. Converting Structural Information into an Allosteric-Energy-Based Picture for Elongation Factor to Activation by the Ribosome, A. J. Adamczyk and A. Warshel, Proc. Natl. Acad. Sci. USA 108, 9827-9832 (2011).

370. Paradynamics: An Effective and Reliable Model for Ab Initio QM/MM Free-Energy Calculations and Related Tasks, N. V. Plotnikov, S. C. L. Kamerlin and A. Warshel, J. Phys. Chem. B 115, 7950-7962 (2011).

371. Multiscale Modeling of Biological Functions, S. C. L. Kamerlin and A. Warshel, Phys. Chem. Chem. Phys. 13, 10401-10411 (2011).

372. Catalysis by Dihydrofolate Reductase and Other Enzymes Arises from Electrostatic Preorganization, Not Conformational Motions, A. J. Adamczyk, J. Cao, S. C. L. Kamerlin and A. Warshel, Proc. Natl. Acad. Sci. USA 108, 14115-14120 (2011).

373. Prechemistry versus Preorganization in DNA Replication Fidelity, R. B. Prasad and A. Warshel. Proteins 79, 2900-2919, (2011).

374. Electrostatic Origin of the Mechanochemical Rotary Mechanism and The Catalytic Dwell of F1-ATPase, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 108, 20550-20555 (2011).

375. Simulating Electrostatic Energies in Proteins: Perspectives and Some Recent Studies of pK(a)s, Redox, and Other Crucial Functional Properties, A. Warshel and A. Dryga, Proteins 79, 3469-3484 (2011).

376. Coarse Grained Model for Exploring Voltage Dependent Ion Channels, A. Dryga, S. Chakrabarty, S. Vicatos, A. Warshel, BBA-Biomembranes 1818, 303-317 (2012).

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377. Realistic Simulation of the Activation of Voltage-Gated Ion Channels, A. Dryga, S. Chakrabarty, S. Vicatos and A. Warshel, Proc. Natl. Acad. Sci. USA 109, 3335-3340 (2012).

378. Towards Quantitative Computer-Aided Studies of Enzymatic Enantioselectivity: The Case of Candida antarctica Lipase A, M. Frushicheva and A. Warshel, ChemBiochem 13, 215-223 (2012).

379. Validating the Vitality Strategy for Fighting Drug Resistance, N. Singh, M. P. Frushicheva and A. Warshel, Proteins 80, 1110-1122 (2012).

380. Realistic Simulations of the Coupling Between the Protomotive Force and the Mechanical Rotation of the F0-ATPase, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 109, 14876-14881 (2012).

381. Exploring, Refining, and Validating the Paradynamics QM/MM Sampling, N.V. Plotnikov and A. Warshel, J. Phys. Chem. B 116, 10342-10356 (2012).

382. Origin of Linear Free Energy Relationships: Exploring the Nature of the Off-Diagonal Coupling Elements in SN2 Reactions, E. Rosta and A. Warshel. J. Chem. Theory Comput. 8, 3574-3585 (2012).

383. Catalytic Effects of Mutations of Distant Protein Residues in Human DNA Polymerase β: Theory and Experiment, M. Klvana, D. L. Murphy, P. Jerabek, M.F. Goodman, A. Warshel, B. Sweasy, and J. Florian, Biochemistry 51, 8829-8843 (2012).

384. Electrostatic Origin of the Catalytic Effect of a Supramolecular Host Catalyst, M. P. Frushicheva, S. Mukherjee and A. Warshel, J. Phys. Chem. B 116, 13353-13360 (2012).

385. Prechemistry Barriers and Checkpoints Do Not Contribute to Fidelity and Catalysis, as Long as They Are Not Rate Limiting, B. R. Prasad, S. C. L. Kamerlin, J. Floria´n and A. Warshel, Theor. Chem. Acc. 131, 1288-1302 (2012).

386. Studying Catalysis by QM/MM Approaches Should Not be a Black Box Process B. R. Prasad, S. C. L. Kamerlin, N. V. Plotnikov and A. Warshel, J. Thermodyn. Catal. 3, 2-4 (2012).

387. Capturing the Energetics of Water Insertion in Biological Systems: The Water Flooding Approach, S. Chakrabarty and A. Warshel, Proteins 81, 93-106 (2013).

388. Why Nature Really Chose Phosphate, S.C.L. Kamerlin., P.B. Sharma, R.B. Prasad and A. Warshel, Q. Rev. Biophys. 46, 1-132 (2013).

389. Addressing Open Questions about Phosphate Hydrolysis Pathways by Careful Free Energy Mapping, B. R. Prasad, N. V. Plotnikov, and A. Warshel, J. Phys. Chem. B 117, 153-163 (2013).

390. Exploring the Nature of the Translocon-Assisted Protein Insertion, A. Rychkova and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 495-500 (2013).

391. Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant Ab Initio QM/MM Free Energy Surfaces, N. V. Plotnikov, R. B. Prasad, S. Chakrabarty, Z. T. Chu and A. Warshel, J. Phys. Chem. B 117, 12807-12819 (2013).

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392. Simulating the Pulling of Stalled Elongated Peptide from the Ribosome by the Translocon, A. Rychkova, S. Mukherjee, R. P. Bora, and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 10195-10200 (2013).

393. How do Enzymes Really Work? The Dawn of Simulating Biological Functions (1974-5) in “Memories and Consequences: Visiting scientists at the MRC Laboratory of Molecular Biology, Cambridge, Published by the MRC, ed. Hugh Huxley, 271-281, (2013).

394. Electrostatic Origin of the Unidirectionality of Walking Myosin V Motors, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 17326-17331 (2013).

395. Quantitative Exploration of the Molecular Origin of the Activation of GTPase, R. B. Prasad, N. V. Plotnikov, J. Lameira and A. Warshel, Proc. Natl. Acad. Sci. USA 110, 20509-20514 (2013).

396. On the Nature of the Apparent Free Energy of Inserting Amino Acids into Membrane through the Translocon, A. Rychkova and A. Warshel, J. Phys. Chem. B 117, 13748-13754 (2013).

397. Coarse-Grained Simulation of the Gating Current in the Voltage-Activation Kv1.2 Channel, I. Kim and A. Warshel, Proc. Natl. Acad. Sci. USA 111, 2128-2133 (2013).

398. Response to Vilfan: Constructing Structure-Based Free Energy Surfaces is the Key to Understand Myosin V Unidirectionality, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 111, 2077 (2014).

399. An Effective Coarse-Grained Model for Biological Simulations: Recent Refinements and Validations, S. Vicatos, A. Rychkova, S. Mukherjee and A. Warshel, Proteins 82, 1168-1185 (2014).

400. Validating Computer Simulations of Enantioselective Catalysis; Reproducing the Large Steric and Entropic Contributions in Candida Antarctica Lipase B, P. Schopf and A. Warshel, Proteins 82, 1387-1399 (2014).

401. Modeling Gating Charge and Voltage Changes in Response to Charge Separation in Membrane Proteins, I. Kim, S. Chakrabarty, P. Brzezinski, and A. Warshel, Proc. Natl. Acad. Sci. USA 111, 11353-11358 (2014).

402. Computer Aided Enzyme Design and Catalytic Concepts, M.P. Frushicheva, M.J.L. Mills, P. Schopf, M.K. Singh, R.B. Prasad, and A. Warshel, Curr. Opin. Chem. Biol. 21, 56-62 (2014).

403. Multiscale Modeling of Biological Functions: From Enzymes to Molecular Machines (Nobel Lecture), A. Warshel, Angew. Chem. Int. Ed., 53, 10020-10031 (2014).

404. Simulating the Catalytic Effect of a Designed Mononuclear Zinc Metalloenzyme that Catalyzes the Hydrolysis of Phosphate Triesters, M.K. Singh, Z.T. Chu, and A. Warshel, J. Phys. Chem. B, 118, 12146-12152 (2014).

405. Methyltransferases do not work by compression, cratic, or desolvation effects, but by electrostatic preorganization, Lameira J, B RP, Chu ZT, Warshel A, Proteins 83, 318-330 (2014).

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406. Dissecting the role of the γ-subunit in the rotary– chemical coupling and torque generation of F1-ATPase, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 112, 2746-2751

(2015).

407. The entropic contributions in vitamin B12 enzymes still reflect the electrostatic paradigm, P. Schopf, M. J. L. Mills and A. Warshel, Proc. Natl. Acad. Sci. USA,112, 4328-4333 (2015).

408. On the Challenge in Exploring the Evolutionary Trajectory from Phosphotriesterase to Arylesterase Using Computer Simulations, R. B. Prasad, M. J. L. Mills, M. P. Frushicheva,

and A. Warshel, J. Phys. Chem. B, 119, 3434-3445, (2015).

409. Torque, chemistry and efficiency in molecular motors: a study of the rotary–chemical coupling in F1-ATPase, S. Mukherjee, R. B. Prasad and A. Warshel, QRB, Discovery, 48, 395–403 (2015).

410. Simulating the function of sodium/proton antiporters, R. Alhadeff and A. Warshel, Proc. Natl. Acad. Sci. USA,112, 12378–12383 (2015).

411. Brønsted slopes based on single-molecule imaging data help to unveil the chemically coupled rotation in F1-ATPase, S. Mukherjee and A. Warshel, Proc. Natl. Acad. Sci. USA 112,14121–14122 (2015).

412. Equilibrium fluctuation relations for voltage coupling in membrane proteins, I. Kim, and A. Warshel, Biochimica et Biophysica Acta, 1848, 2985–2997 (2015).

413. Refining the treatment of membrane proteins by coarse-grained models, I. Vorobyov, I. Kim, Z. T. Chu, and A. Warshel, PROTEINS, 84, 92–117 (2016).

414. A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD, I. Kim and A. Warshel, JPC B, 120, 418-32 (2016).

415. Perspective: Defining and quantifying the role of dynamics in enzyme catalysis, Arieh Warshel and R. B. Prasad, J. Chem. Phys.144, 180901-17 (2016).

416. The Physics and Physical Chemistry of Molecular Machines, R.D. Astumian,S. Mukherjee and A. Warshel, Chemphyschem 17, 1719-1741 (2016).

417. Exploring the dependence of QM/MM calculations of enzyme catalysis on the size of the QM region. G. Jindal G and A. Warshel, J Phys Chem B 120: 9913-21 (2016).

418. Simulating the function of the MjNhaP1 transporter, R. Alhadeff and A. Warshel J. Phys. Chem. B, 120, 10951-58 (2016).

419. Enhancing Paradynamics for QM/MM Sampling of Enzymatic Reactions, J. Lameira ,I. Kupchencko and A. Warshel, J. Phys. Chem B, 120, 2155-64 (2016).

420. The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase, H. Yoon and A. Warshel, Proteins, 84, 1616-24 (2016).

421. Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase β, R. A. Matute, H. Yoon, and Arieh Warshel, Proteins, 84, 1644-57 (2016).

422. A personal perspective on calculations of binding free energies, H. Yoon and A. Warshel, Chemistry, Molecular Sciences and Chemical Engineering, online (2016).

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423. Perspective on computer modeling of enzymatic reactions, A. Warshel and R. P. Bora., In: Inaki Tunon, Vicent Moliner, editors. Simulating Enzyme Reactivity: Computational Methods in Enzyme Catalysis, Cambridge: RSC, 1-30 (2017).

424. Simulating the Dynamics of The Mechanochemical Cycle of Myosin-V, S. Mukherjee, R. Alhadeff, and A. Warshel, Proc. Natl. Acad. Sci. USA, 114, 2259-64 (2017).

425. Exploring the Design of Kemp Eliminase and the nature of two directed evolution paths, G. Jindal, B. Ramachandran, R. Prasad and A. Warshel, ACS Catalysis, 7, 3301-05 (2017).

426. On the origin of non-Arrhenius behavior of the rates of enzymatic reactions, S. Roy, P. Schopf and A, Warshel, JPC B, 121, 6520-26 (2017).

427. Exploring the drug resistance of HCV Protease, G. Jindal, D. Mondal and A. Warshel, JPC B, 121, 6831-40 (2017).

428. Simulating the Fidelity and The Three Mg Mechanism of Pol and clarifying the validity of transition state theory in enzyme catalysis, Hanwool Yoon and A. Warshel, Proteins, 85, 1446-53(2017).

BOOKS1991 Computer Simulation of Chemical Reactions in Enzymes and Solutions, A. Warshel, John

Wiley &Sons, (1991).

1997 Computational Approaches to Biochemical Reactivity, G. Naray-Szabo and A. Warshel, eds., Kluwer, Academic Publishers, (1997).

COMPUTER PROGRAMSQCFF/PI: A Program for the Consistent Force Field Evaluation of Equilibrium Geometries and

Vibrational Frequencies of Molecules, A. Warshel and M. Levitt, QCPE 247, Quantum Chemistry Program Exchange, Indiana University (1974).

MCA: Molecular Crystals Analysis, E. Huler and A. Warshel, QCPE 325, Quantum Chemistry Program Exchange, Indiana University (1976).

MOLARIS: A General Program Package for Simulations of Macromolecules (1989).

POLARIS: A Program for PDLD Calculations of Electrostatic Energies in Solution and Proteins (1989).

ENZYMIX: A General for Simulations of Chemical Processes in Enzymes and Solutions (1989).

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