Arieh warshel



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RESEARCH GRANTS


1973 - 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).

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).

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).
PATENTS

2014 Arieh Warshel, Spyridon Vicatos, “Production of Stable Proteins,” U.S. Patent 8855936- B2, October 7, 2014.



LIST OF PUBLICATIONS


  1. 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).




  1. 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).




  1. 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).




  1. 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).




  1. 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).




  1. 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).




  1. 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).




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




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




  1. 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).




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




  1. 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).




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




  1. 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).




  1. 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).




  1. 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).




  1. 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).




  1. 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).




  1. 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).




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




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




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




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




  1. 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).




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




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




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




  1. 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).




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




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




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




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

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




  1. 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).




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




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




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




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




  1. 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).




  1. 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).




  1. 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).




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




  1. 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).




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




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




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




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




  1. 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).




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




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




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




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




  1. 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).




  1. 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).




  1. 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).




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




  1. 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).




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




  1. 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).




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




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




  1. 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).




  1. 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).




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




  1. 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).




  1. 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).

  2. 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).




  1. 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).




  1. 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).




  1. 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).




  1. 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).




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




  1. 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).




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




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




  1. 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).




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




  1. 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).




  1. 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).




  1. 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).


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