Vijay Pande

(Last Updated on July 22, 2008, at 11:52 PM.)

EDUCATION

1988-1992 BA, Physics, Princeton University, Princeton, NJ (Thesis advisor: P. W. Anderson, Nobel Laureate)

1992-1995 PhD, Physics, Massachusetts Institute of Technology, Cambridge, MA (Thesis advisors: T. Tanaka, and A. Grosberg)

PROFESSIONAL EXPERIENCE

1990 Undergraduate research, Princeton University, (R. Austin)

1991 Undergraduate research, Princeton University, (R. Goldstein)

1991 Undergraduate research, Princeton University, (J. Taylor, Nobel Laureate)

1992 Undergraduate research, Princeton University, (P. W. Anderson, Nobel Laureate)

1995-1996 Postdoctoral fellow, Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA (T. Tanaka, A. Grosberg, M. Kardar)

1996-1998 Miller Fellow, U. C. Berkeley, Berkeley, CA (D. Rokhsar)

1998-1999 LBNL fellow in physical biosciences (D. Rokhsar)

1999-2005 Assistant Professor of Chemistry, Stanford University, Stanford, CA

2000-2005 Assistant Professor of SSRL (by courtesy), Stanford University, Stanford, CA

2000-2005 Assistant Professor of Structural Biology (by courtesy), Stanford University, Stanford, CA

2006- Associate Professor of Chemistry, Stanford University, Stanford, CA

HONORS AND AWARDS

2008 Netxplorateur of the Year 2008

2006 Irving Sigal Young Investigator Award, Protein Society

2006 Keynote Speaker, HPDC-15 Meeting, Paris

2005 Keynote Speaker, HiCOMB 2005, Denver

2004 Global Indus Technovators Award

2003 Dreyfus Teacher-Scholar Award

2002-2005 Frederick E. Terman Fellow, Stanford University

2002 Named to TR100 (MIT Tech Review top 100 young innovators of 2002)

2002 Levinthal Lecture (Keynote speaker, OpenEye CUP II)

2001 Keynote speaker, workshop on Evolvable Hardware JPL

1996-1998 Miller Fellow, Miller Institute for Basic Research, UC Berkeley

1992-1995 National Science Foundation Graduate Fellow (Physics Dept, MIT)

1992 Kawasaki Prize in experimental physics, Princeton University

1988-1992 ONR Science Fellowship

1988-1992 Westinghouse Science Talent Search Scholarship (4th place in 1998)

1988-1992 TRW Science Scholarship

TEACHING

1999- Chemistry 171: Chemical Thermodynamics (undergraduate)

1999-2003, 2006- Chemistry 275: Statistical Mechanics (graduate)

2002 Nominated for university teaching award

2003- Biochemistry 241: Biological Macromolecules (graduate, co-taught)

2003 Dreyfus Teacher-Scholar Award

COMMITTEE DUTIES

1999-2005 Computational infrastructure (Chemistry Department, chair)

2000- Admissions (Biophysics Program)

2001- Executive committee (Biophysics Program)

2001- Supercomputer (BioX, co-chair)

2002-2004 Curriculum (Chemistry Department)

2002-2004 Graduate student awards (Chemistry Department)

2002-2004, 2007 Admissions (Chemistry Department)

2002-2003, 2005- Admissions (Structural Biology Department)

2002-2004 Interdisciplinary Initiatives Program (BioX)

2002- Computational infrastructure Committee (BioX)

2005- Executive Committee (Chemistry Department)

2006- Executive Committee (Biophysics Program)

2006- Curriculum Committee (Chemistry Department, chair)

2008- University-wide committee on computational infrastructure, co-chair

REFEREE AND STUDY SECTIONS

2000- Reviewer for NSF proposals

2004 NIH BBCA study section (ad hoc)

2005 NIH Research Resource study section (ad hoc)

2006 Special NIH study section on small molecule drug design for protein aggregation related disease

2006 NIH ZRG1 computational study section (ad hoc)

2007 NIH AIDS discovery and development of therapeutics study section (ad hoc)

PUBLICATIONS

1994

1. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Non-Randomness in Protein Sequences: Evidence for a Physically Driven Stage of Evolution? Proceeding of the National Academy of Science, U.S.A., 91, 12972 (1994)

2. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Thermodynamic Procedure to Synthesize Heteropolymers that can Renature to Recognize a Given Target Molecule. Proceeding of the National Academy of Science, U.S.A., 91, 12976 (1994)

3. V. S. Pande, C. Joerg, A. Yu. Grosberg, and T. Tanaka. Enumeration of the Hamiltonian Walks on a Cubic Sublattice. Journal of Physics, A27, 6231 (1994)

4. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Phase Diagram of Imprinted Copolymers, Journal of Physics (Paris), 4, 1771 (1994)

5. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Folding Thermodynamics and Kinetics of Imprinted Renaturable Heteropolymers, Journal of Chemical Physics, 101, 8246 (1994)

6. V. S. Pande and C. Joerg, Enumeration of the Hamiltonian Walks on a Sublattice, Student Workshop on Scalable Computing, MIT/LCS/TR-622, 53 (1994)

1995

7. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Freezing Transition of Random Heteropolymers Consisting of an Arbitrary Set of Monomers. Physical Review, E51, 3381 (1995)

8. V. S. Pande, A. Yu. Grosberg, and T. Tanaka, Phase Diagram of Heteropolymers with an Imprinted Conformation. Macromolecules, 28, 2218 (1995)

9. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Freezing Transition of an Imprinted Copolymer in a Random External Field. Journal of Physics A28, 3657 (1995)

10. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. How Accurate Must Potentials Be for Successful Modeling of Protein Folding? Journal of Chemical Physics 103, 9482 (1995)

11. T. Tanaka, C-n Wang, A. English, S. Masamune, H. Gold, R. Levy, K. King, V. S. Pande, and A. Yu. Grosberg. Polymer Gels that can Recognize and Recover Molecules. Faraday Discussions, 101, 201-206 (1995)

12. V. S. Pande, A. Yu. Grosberg, C. Joerg, and T. Tanaka. How Well is Heteropolymer Freezing Described by the Random Energy Model? Physical Review Letters, 76, 3987-3990 (1995)

1996

13. V. S. Pande, A. Yu. Grosberg, M. Kardar, C. Joerg, and T. Tanaka. Polyampholyte Freezing Transition. Physical Review Letters, 77, 3565-3568 (1996)

1997

14. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. On the Theory of Folding Kinetics for Short Proteins. Folding and Design 2, 109 (1997)

15. V. S. Pande and J. Onuchic. Electron Transport in Disordered Polymeric Systems. Physical Review Letters 78, 146 (1997)

16. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. How to make Heteropolymers which can Renature to Recognize a Given Target Molecule, 107 316 Physica D (1997)

17. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Statistical Mechanics of Simple Models of Protein Folding. Biophysical Journal 73, 3192-3210 (1997)

18. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Thermodynamics of the coil to frozen globule transition in heteropolymers. Journal of Chemical Physics 107, 5118-5124 (1997)

19. M. Tanaka, A. Yu. Grosberg, V. S. Pande, and T. Tanaka. Molecular Dynamics Study of the Structural Organization of a Strongly-Coupled Chain of Charged Particles. Physical Review E 56 5798-5808 (1997)

20. A. Chakraborty, E. I. Shakhnovich, and V. S. Pande. Broken Ergodicity in Compact Random Heteropolymers with Correlated Sequence Fluctuations. Journal of Chemical Physics . 108, 1683-1687 (1997)

1998

21. R. Du, V. S. Pande, A. Yu. Grosberg, T. Tanaka, and E. I. Shakhnovich. On the Transition Coordinate for Protein Folding. Journal of Chemical Physics 108, 334-350 (1998)

22. V. S. Pande and D. S. Rokhsar. Is the Molten Globule a third Phase of Proteins? Proceedings of the National Academy of Science, USA 95, 1490-1494 (1998)

23. V. S. Pande, A. Yu. Grosberg, and T. Tanaka, D. S. Rokhsar. Protein Folding Pathways: Is a “new view” needed? Current Opinion in Structural Biology 8, 68-79 (1998)

1999

24. V. S. Pande and D. S. Rokhsar. Folding Pathway of a Lattice Model for Protein Folding. Proceedings of the National Academy of Science, USA 96, 1273-1278 (1999)

25. R. Du, V. S. Pande, A. Yu. Grosberg, T. Tanaka, and E. I. Shakhnovich. On the Role of Conformational Geometry in Protein Folding. 111, 10375-10380 Journal of Chemical Physics (1999)

26. A. Golumbfskie, V. S. Pande, and A. Chakraborty. Simulation of biomimetic recognition between polymers and surfaces. Proceedings of the National Academy of Science, USA, 96, 11707-11712 (1999)

27. V. S. Pande and D. S. Rokhsar. Molecular dynamics simulation of unfolding and refolding of a β-hairpin. Proceedings of the National Academy of Science, USA 96 9062-9067 (1999)

2000

28. Z. Bryant, V. S. Pande, and D. S. Rokhsar. Mechanical unfolding of a beta hairpin using molecular dynamics. Biophysical Journal, 78, 584-589 (2000)

29. V. S. Pande, A. Yu. Grosberg, and T. Tanaka. Heteropolymer Freezing and Design: Towards Physical Models of Protein Folding. Reviews of Modern Physics 72, 259-286 (2000)

30. R. Anderson, V. S. Pande, and C. Radke. Dynamic lattice Monte Carlo simulation of a model protein at an oil-water interface. Journal of Chemical Physics, 112, 9167-9185 (2000)

31. M. R. Shirts and V. S. Pande. Screen Savers of the World, Unite! Science, 290, 1903-1904 (2000)

2001

32. S. Elmer and V. S. Pande. A new twist on the helix-coil transition: a non-biological polymer with protein-like intermediates. Journal of Physical Chemistry B, 105, 482-485 (2001)

33. M. R. Shirts and V. S. Pande. Mathematical Foundations of Ensemble Dynamics. Physical Review Letters, 86, 4983-4987 (2001)

34. B. Zagrovic, E. Sorin, and V. S. Pande. Atomistic folding simulations of a beta hairpin. Journal of Molecular Biology 313, 151-169 (2001)

2002

35. E. Sorin, M. Engelhardt, D. Herschlag, and V. S. Pande. Unfolding simulations of a GNRA tetraloop. Journal of Molecular Biology, 317, 493-506 (2002)

36. R. Russell, I. S. Millet, M. W. Tate, L. W. Kwok, B. Nakatani, S. M. Gruner, S. G. J. Mochrie, V. S. Pande, S. Doniach, D. Herschlag, and L. Pollack. Rapid Compaction During RNA Folding. Proceedings of the National Academy of Science, USA, 99, 4266-4271 (2002)

37. B. Zagrovic, C. Snow, S. Khaliq, M. Shirts, and V. S. Pande. Native-like mean structure in the unfolded ensemble of small proteins. Journal of Molecular Biology 323, 153-164 (2002)

38. C. Snow, H. Nguyen, V. S. Pande, and M. Gruebele. Folding of a ββα protein: simulation and theory. Nature, 420, 102-106 (2002)

39. B. Zagrovic, C. D. Snow, M. R. Shirts and V. S. Pande. Simulation of Folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. Journal of Molecular Biology, 323, 927-937 (2002)

40. S. M. Larson, J. England, J. DesJarlais, and V. S. Pande. Thoroughly sampling sequence space: large-scale protein design of structural ensembles. Protein Science 11 2804-2813 (2002)

41. C. Snow, B. Zagrovic, and V. S. Pande. The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations. Journal American Chemical Society, 124, 14548-14549 (2002)

2003

42. V. S. Pande, I. Baker, J. Chapman, S. P. Elmer, S. Khaliq, S. M. Larson, Y. M. Rhee, M. R. Shirts, C. Snow, E. Sorin, B. Zagrovic. Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing. Kollman Memorial Issue, Biopolymers, 68(1), 91-109 (2003)

43. Y. M. Rhee and V. S. Pande. Multiplexed Replica Exchange Molecular Dynamics Method for Protein Folding Simulation. Biophysical Journal, 84, 775–786 (2003)

44. A. I. Jewett, V. S. Pande, and K. W. Plaxco. Cooperativity, smooth energy landscapes and the origins of topology-dependent protein folding rates. Journal of Molecular Biology, 326 247-253 (2003)

45. S. M. Larson, A. Garg, J. DesJarlais, and V. S. Pande. Increased detection of structural templates using alignments of designed sequences. Proteins: Structure, Function, and Genetics 51 390-396 (2003)

46. B. Zagrovic and V. S. Pande. Solvent Viscosity Dependence of the Folding Rate of a Small Protein: a Distributed Computing Study. Journal of Computational Chemistry, 24 1432–1436 (2003)

47. E. Sorin, Y. M. Rhee, B. Nakatani, and V. S. Pande. Insights into nucleic acid hairpin conformational dynamics from massively parallel stochastic simulations. Biophysical Journal, 85 790-803 (2003)

48. M. R. Shirts, J. W. Pitera, W. C. Swope, and V. S. Pande. Extremely Precise Free Energy Calculations of Amino Acid Side Chain Analogs: Comparison of Common Molecular Mechanics Force Fields for Proteins. Journal of Chemical Physics, 119 5740-5761 (2003)

49. S. M. Larson and V. S. Pande. Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein. Journal of Molecular Biology, 332 275-286 (2003)

50. S. M. Larson, C. Snow, V. S. Pande. Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology. Modern Methods in Computational Biology, R. Grant, ed, Horizon Press (2003)

51. M. R. Shirts, E. Bair, G. Hooker, and V. S. Pande. Equilibrium free energies from nonequilibrium measurements using maximum likelihood methods. Physical Review Letters, 91 (2003)

52. B. Zagrovic and V. S. Pande. How Can Proteins be Unfolded and yet Have Native-like Properties: Structural Correspondence between the Alpha Helix and the Random-Flight Chain. Nature Structural Biology, 10 955-961 (2003)

53. V. S. Pande. Meeting half way on the bridge between protein folding theory and experiment. Proceedings of the National Academy of Sciences, USA, 100 3555-3556 (2003)

54. P. Lenz, B. Zagrovic, J. Shapiro, and V. S. Pande. Folding probabilities: a novel approach to folding transitions. Journal of Chemical Physics, 120 6769-6778 (2003)

55. E. Sorin, B. Nakatani, Y. M. Rhee, G. Jayachandran, V. Vishal, and V. S. Pande. Does Native State Topology Determine the RNA Folding Mechanism? Journal of Molecular Biology 337 789-797 (2003)

2004

56. Y. M. Rhee, E. J. Sorin, G. Jayachandran, E. Lindahl, V. S. Pande. Simulations of the role of water in the protein folding mechanism. Proceedings of the National Academy of Science, USA 101 6456-6461 (2004)

57. C. D. Snow, L. Qiu, D. Du, F. Gai, S. J. Hagen, and V. S. Pande. Tryptophan Zipper Folding Kinetics via Molecular Dynamics and Temperature Jump Spectroscopy. Proceedings of the National Academy of Sciences, USA, 101 4077-4082 (2004)

58. P. Kasson and V. S. Pande. Molecular Dynamics Simulation of Lipid Reorientation at Bilayer Edges. Biophysical Journal, 86 3744-3749 (2004)

59. N. Singhal, C. Snow, and V. S. Pande. Path sampling to build better roadmaps: predicting the folding rate and mechanism of a Trp Zipper beta hairpin. Journal of Chemical Physics 121 415-425 (2004)

60. B. Zagrovic and V. S. Pande. How Does Averaging Affect Protein Structure Comparison on the Ensemble Level? Biophysical Journal 87 2240-6 (2004)

61. J. E. Kohn, I. S. Millett, J. Jacob, B. Zagrovic, T. M. Dillon, N. Cingel, R. S. Dothager, S. Seifert, P. Thiyagarajan, T. R. Sosnick, M. Z. Hasan, V. S. Pande, I. Ruczinski, S. Doniach and K. W. Plaxco. Do the dimensions of chemically unfolded proteins differ significantly from the expectations of a random-coil model? Proceedings of the National Academy of Sciences, USA, 101 12491-6 (2004)

62. S. Elmer and V. S. Pande. Foldamer simulations: Novel computational methods and applications to poly-phenylacetylene oligomers. Journal of Chemical Physics 121 12760-12771 (2004)

63. V. S. Pande. Protein Aggregation and Disease: A universal TANGO? Nature Biotechnology 22, 1240-1241 (2004)

64. L. T. Chong, C. D. Snow, Y. M. Rhee, and V. S. Pande. Dimerization of the p53 oligomerization domain: Identification of a folding nucleus by molecular dynamics simulations. Journal of Molecular Biology 345 869-78 (2004)

2005

65. C. D. Snow, E. J. Sorin, Y. M. Rhee, and V. S. Pande. How well can simulation predict protein folding kinetics and thermodynamics? Annual Reviews of Biophysics 34 43-69 (2005)

66. S. Elmer and V. S. Pande. Length Dependent Folding Kinetics of poly-Phenylacetylene Oligomers: Structural Characterization of a Kinetic Trap, Journal of Chemical Physics 122 124908 (2005)

67. V. S. Pande. Atomistic models of protein folding. Encyclopedia of Materials Research (2005)

68. E. Sorin and V. S. Pande. Exploring the helix-coil transition via all-atom equilibrium ensemble simulations. Biophysical Journal 88 2472-93 (2005)

69. E. Sorin, Y. M. Rhee, and V. S. Pande. Does water play a structural role in the folding of small nucleic acids? Biophysical Journal 88 2516-24 (2005)

70. Y. M. Rhee and V. S. Pande. One-Dimensional Reaction Coordinate and the Corresponding Potential of Mean Force from Commitment Probability Distribution. Journal of Physical Chemistry B 109 6780-6786 (2005)

71. E. Sorin and V. S. Pande. Empirical force Field Assessment: the Interplay between van der Waals Scaling and Backbone Torsions. Journal of Computational Chemistry 26 682-690 (2005)

72. M. R. Shirts and V. S. Pande. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration. Journal of Chemical Physics 122 144107 (2005)

73. M. R. Shirts and V. S. Pande. Solvation free energies of amino acid side chains for common molecular mechanics water models. Journal of Chemical Physics 122 134508 (2005)

74. S. Park, R. Radmer, T. Klein, V. S. Pande. New parameters for collagen simulation. Journal of Computational Chemistry, 26 1612-6 (2005)

75. S. Elmer, S. Park, and V. S. Pande. PPA simulations in explicit solvent: 1. studying the role of solvaphobicity on foldamers assembly. Journal of Chemical Physics 123 114902 (2005)

76. S. Elmer, S. Park, and V. S. Pande. Foldamer dynamics expressed via Markov State Models: 2. Explicit solvent molecular dynamics simulations in acetonitrile, chloroform, methanol, and water. Journal of Chemical Physics 122 124908 (2005)

77. B. Zagrovic, J. Lipfert, E. J. Sorin, I. S. Millett, W. F. van Gunsteren, S. Doniach and V. S. Pande. Unusual compactness of a polyproline type II structure. Proceedings of the National Academy of Science, USA, 102 11698-703 (2005)

78. H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. Snow, M. R. Shirts, E. Sorin, and V. S. Pande. Direct calculation of the binding free energies of FKBP ligands using the Fujitsu BioServer massively parallel computer. Journal of Computational Physics, 123 084108 (2005)

79. N. Singhal and V. S. Pande. Error Analysis in Markovian State Models for protein folding. Journal of Chemical Physics, 123 204909 (2005)

80. B. Zagrovic, G. Jayachandran, I. S. Millett, S. Doniach and V. S. Pande. How large is alpha-helix in solution? Studies of the radii of gyration of helical peptides by SAXS and MD. Journal of Molecular Biology, 353 232-41 (2005)

2006

81. Y. M. Rhee and V. S. Pande. On the role of chemical detail in simulating protein folding kinetics. Chemical Physics, 323 66–77 (2006)

82. E. Elsen, M. Houston, V. Vishal, E. Darve, P. Hanrahan, and V. S. Pande. N-Body simulation on GPUs. Proceedings of the 2006 ACM/IEEE conference on Supercomputing, 188 (2006)

83. P. Petrone and V. S. Pande. Can conformational change be described by only a few normal modes? Biophysical Journal, 90 1583-93 (2006)

84. E. J. Sorin, Y. M. Rhee, M. R. Shirts, and V. S. Pande. The solvation interface is a determining factor in protein conformational preferences. Journal of Molecular Biology, 356 248-56 (2006)

85. S. Park and V. S. Pande. How to validate Markovian Models. Journal of Chemical Physics 124 54118 (2006)

86. L.T. Chong, W. C. Swope, J. W. Pitera, and V. S. Pande. Kinetic Computational Alanine Scanning: Application to p53 Oligomerization. Journal of Molecular Biology, 357 1039-1049 (2006)

87. G. Jayachandran, V. Vishal, and V. S. Pande. Folding Simulations of the Villin Headpiece in All-Atom Detail. Journal of Chemical Physics, 124 164902 (2006)

88. C. Snow and V. S. Pande. Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates. Biophysical Journal, 91 14-24 (2006)

89. E. Sorin and V. S. Pande. Nanotube confinement denatures proteins in confined spaces. JACS, 128 6316-7 (2006)

90. I. Suydam, C. D. Snow, V. S. Pande and S. G. Boxer. Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory. Science, 313 200-4 (2006)

91. G. Jayachandran, M. R. Shirts, S. Park, and V. S. Pande. Parallelized Over Parts Computation of Absolute Binding Free Energy with Docking and FEP. Journal of Chemical Physics, 125 084901 (2006)

92. P. Kasson, N. Kelley, N. Singhal, M. Vrjlic, A. Brunger, and V. S. Pande. Sub-millisecond kinetics and intermediates of membrane fusion from molecular dynamics. Proceedings of the National Academy of Sciences, USA, 103 11916-21 (2006)

93. Christophe Chipot, Vijay S. Pande, Alan E. Mark, and Thomas Simonson. “Significant applications of free energy calculations tochemistry and biology.” Ed., C. Chipot (2006)

94. Vijay S. Pande, Eric J. Sorin, Christopher D. Snow, & Young Min Rhee. Protein “Folding Simulation.” Chapter to be published by the Royal Society, Ed. Victor Munoz (2006).

95. B. Zagrovic, and V. S. Pande. Simulated unfolded-state ensemble and the experimental NMR structures of villin headpiece yield similar wide angle solution X-ray scattering profiles. J. Am. Chem. Soc., 128 (36), 11742 -11743 (2006)

96. G. Jayachandran, V. Vishal, A. E. García, and V. S. Pande. Local Structure Formation in Simulations of Two Small Proteins. Special "Advances in Molecular Dynamics Simulations" issue of the Journal of Structural Biology, (2006).

97. S. Park, D. Ensign, and V. S. Pande. A Bayesian Update Method for Adaptive Weighted Sampling. Physical Review E, 74 066703 (2006)

2007

98. P. Kasson and V. S. Pande. Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide. Pacific Symposium on Biocomputing 12:40-50 (2007)

99. A. Beberg and V. S. Pande, Storage@home: Petascale Distributed Storage. IEEE International Parallel and Distributed Processing Symposium 1-6 (2007)

100. J. Chodera, N. Singhal, V. S. Pande, K. Dill, and W. Swope. Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics. Journal of Chemical Physics, 126 155101 (2007)

101. P. Kasson, A. Zomorodian, S. Park, N. Singhal, L. Guibas, and V. S. Pande. Persistent voids: a new structural metric for membrane fusion. Bioinformatics 23 1753-9 (2007)

102. D. Lucent, V. Vishal, and V. S. Pande. Protein folding under confinement: A new role for solvent. Proceedings of the National Academy of Sciences, USA 104 10430-10434 (2007)

103. N. Singhal-Heinrichs and V. S. Pande. Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics. Journal of Chemical Physics, 126 244101 (2007)

104. S. Park, T. Klein, and V. S. Pande. Simulations of collagen protein folding. Biophysical Journal, 93(12) 4108-15 (2007)

105. S. Park and V. S. Pande. How to Choose Weights for Simulated Tempering. Physical Review E, 76 016703 (2007)

106. P. Kasson and V. S. Pande. Ensemble molecular dynamics simulation predicts membrane fusion mechanism controlled by lipid composition. PloS Computational Biology, 3 e220 (2007)

107. D. Ensign, P. Kasson, and V. S. Pande. Heterogeneity Even at the Speed Limit of Folding: Large-Scale Molecular Dynamics Study of a Fast-Folding Variant of the Villin Headpiece. Journal of Molecular Biology, 374 806-16 (2007)

108. M. R. Shirts, D. Mobley, J. Chodera, and V. S. Pande. Accurately and efficiently correcting for missing dispersion due to cutoffs in molecular simulations. J. Phys. Chem. B., 111 13052-63 (2007)

2008

109. A. Robertson, E. Luttmann, and V. S. Pande. Effects of Long-Range Electrostatic Forces on Simulated Protein Folding Kinetics, J. Comp. Chem., 15 694-700 (2008)

110. D. Rother, G. Sapiro, and V. S. Pande. Statistical Characterization of Protein Ensembles. IEEE/ACM Transactions on Computational Biology and Bioinformatics 5 42-55 (2008)

111. J. England, S. Park, and V. S. Pande. Theory for an order-driven disruption of the liquid state in water. Journal of Chemical Physics, 28 044503 (2008)

112. Y. M. Rhee and V. S. Pande. Solvent Viscosity Dependence of the Protein Folding Dynamics. Journal of Physical Chemistry B, 112 6221-7 (2008)

113. C. Sweet, P. Petrone, V. S. Pande, and J. Izaguirre. Normal mode partitioning of Langevin dynamics for biomolecules. Journal of Chemical Physics, 128 145101 (2008)

114. A. Nicholls*, D. L. Mobley*, J. P. Guthrie, J. D. Chodera, C. I. Bayly, M. D. Cooper and V. S. Pande. Predicting small-molecule solvation free energies: a blind challenge test for computational chemistry, J. Med. Chem., 51 769-779 (2008)

115. X. Huang, G. R. Bowman, and V. S. Pande. Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment. J. Chem. Phys., 128 205106 (2008)

116. J. England, D. Lucent, and V. S. Pande. Rattling the cage: computational models of chaperonin-mediated protein folding. Current Opinion in Structural Biology, 18 163-9 (2008)

117. J. P. Schmidt, S. L. Delp, M. A. Sherman, C. A. Taylor, V. S. Pande, and Russ B. Altman. The Simbios National Center: Systems Biology in Motion. Proceedings of the IEEE, 96 1266-1280 (2008)

118. E. Luttmann, D. L. Ensign, V. Vishal, M. Houston, N. Rimon, J. Øland, G. Jayachandran, M. Friedrichs, and Vijay S. Pande. Accelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3. Journal of Computational Chemistry, 30 268-74 (2008)

119. L. Monticelli, E. J. Sorin, D. P. Tieleman, V. S. Pande, and Giorgio Colombo. Molecular Simulation of Multistate Peptide Dynamics: A Comparison Between Microsecond Timescale Sampling and Multiple Shorter Trajectories. Journal of Computational Chemistry. 29 1740-52 (2008).

120. G. R. Bowman, X. Huang, Y. Yao, J. Sun, G. Carlsson, L. J. Guibas and V. S. Pande. Structural Insight into RNA Hairpin Folding Intermediates, JACS 130 9676-8 (2008)

121. G. Bowman and V. S. Pande. Simulated Tempering yields insight into the low-resolution Rosetta scoring functions. Proteins, 74 777-88 (2008)

122. J. England and V. S. Pande. Potential for modulation of the hydrophobic effect inside chaperonins. Biophysical Journal, 95 3391-9 (2008)

123. P. M. Kasson and V. S. Pande. Structural basis for influence of viral glycans on ligand binding by influenza hemagglutinin, Biophysical Journal, 95 L48-50 (2008)

124. J. L. England, D. Lucent, and V. S. Pande. A Role for Confined Water in Chaperonin Function. JACS, 130 11838-9 (2008)

125. Y. Bai, V. B. Chu, J. Lipfert, V. S. Pande, D. Herschlag, and S. Doniach. Critical assessment of nucleic acid electrostatics via experimental and computational investigation of an unfolded state ensemble. Journal of the American Chemical Society, 130 12334-41 (2008)

126. J. England, V. S. Pande, and G. Haran. Chemical Denaturants Inhibit the Onset of Dewetting. Journal of the American Chemical Society, 130 11854-5 (2008)

127. P. Petrone, C. D. Snow, D. Lucent, and V. S. Pande. Protein recognition and gating in the ribosome exit tunnel, PNAS, 105 16549-54 (2008)

128. N. W. Kelley, V. Vishal, R. Jaykumar, C. Liu, T. Pray, G. Krafft, and V. S. Pande. Simulation of the rate of formation and structure of Aβ oligomers. Journal of Chemical Physics, 129 214707 (2008)

129. L. T. Chong, J. W. Pitera, W. C. Swope, and V. S. Pande. Comparison of computational approaches for predicting the effects of missense mutations on p53 function. Journal of Molecular Graphics & Modelling (2008)

2009

130. P. M. Kasson and V. S. Pande. Combining mutual information with structural analysis to screen for functionally important residues in influenza hemagglutinin. Pacific Sympsoium in Biocomputing 492-503 (2009)

131. V. Voelz, P. Petrone, and V. S. Pande. Multiscale methods for the ribosome. Pacific Sympsoium in Biocomputing 340-52 (2009)

132. M. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. LeGrand, A. Beberg, D. Ensign, C. Bruns, and V. S. Pande. Accelerating Molecular Dynamic Simulation on Graphics Processing Units. Journal of Computational Chemistry, 30 864-72 (2009)

133. D. Lucent, J. England, V. S. Pande. Inside the Chaperonin toolbox: Theoretical and computational models for chaperonin mechanism, Physical Biology 6 015003 (2009)

134. D. L. Ensign and V. S. Pande. The Fip35 WW Domain Folds with Structural and Mechanistic Heterogeneity in Molecular Dynamics Simulations. Biophysical Journal 96 L53-55 (2009)

135. V. A. Voelz, E. Luttmann, G. R. Bowman, and V.S. Pande. Probing the nanosecond dynamics of a designed three-stranded beta-sheet with massively parallel molecular dynamics simulation. International Journal of Molecular Sciences, 10 1013-30 (2009)

136. Y. Yao, J. Sun, X. Huang, G. Bowman, G. Singh, M. Lesnick, L. J. Guibas, V. S. Pande, and G. Carlsson. Topological Methods for Exploring Low-density States in Biomolecular Folding Pathways. Journal of Chemical Physics,130 144115 (2009)

137. A. Beberg and V. S. Pande. Thalweg: A framework for programming 1,000 Machines With 1,000 Cores. IEEE International Parallel and Distributed Processing Symposium, in press (2009)

138. A. Beberg and V. S. Pande. Folding@home: lessons from eight years of distributed computing, IEEE International Parallel and Distributed Processing Symposium, in press (2009)

139. N. W. Kelley, X. Huang, S. Tamm, C. Spies, J. Frydman, and V. S. Pande. The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation, Journal of Molecular Biology, 388 919-927. (2009)

140. G. R. Bowman, X. Huang, and V. S. Pande. Using generalized ensemble simulations and Markov state models to identify conformational states. Methods, in press (2009)

141. I. Haque and V. S. Pande. PAPER -- Accelerating Parallel Evaluations of ROCS. Journal of Computational Chemistry, in press (2009)

142. G. R. Bowman and V. S. Pande. The Roles of Entropy and Kinetics in Structure Prediction. PLoS One, 4 e5840 (2009)

143. M. J. Schnieders, T. D. Fenn, V. S. Pande, and A. T. Brunger. Polarizable Atomic Multipole X-Ray Refinement: Application to Peptide Crystals. Acta Crysollographica, in press (2009)

144. J. MacCallum, L. Hua, M. J. Schnieders, V. S. Pande, M. P. Jacobson, and K. A. Dill. Assessment of the protein-structure refinement category in CASP8. Proteins, in press (2009)

145. S. Bacallado, J. D. Chodera, and V. S. Pande. Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint. Journal of Chemical Physics, 131 045106 (2009)

146. D. Ensign and V. S. Pande. Bayesian single-exponential kinetics in single-molecule experiments and simulations. Journal of Physical Chemistry B, in press (2009)

147. P. M. Kasson, D. L. Ensign, and V. S. Pande. Combining molecular dynamics with Bayesian analysis to predict and evaluate ligand-binding mutations in influenza hemagglutinin. JACS, in press (2009)

148. V. B. Chu, J. Lipfert, Y. Bai, V. S. Pande, S. Doniach, and D. Herschlag. Do Conformational Biases Arising From the Simple Junctions That Join Helices Influence Folding Specficity in RNA? RNA, in press (2009)

149. X. Huang, G. R. Bowman, S. Bacallado, and V. S. Pande. Adaptive Seeding Method: Rapid Equilibrium Sampling Initiated from Non-equilibrium Data. Proceedings of the National Academy of Sciences, USA, in press (2009)

150. P. Eastman and V. S. Pande. Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit. Journal of Computational Chemistry, in press (2009)

151. I. Haque and V. S. Pande. Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU. Supercomputing 2009 poster (2009)

152. G. Bowman, K. A. Beauchamp, G. Boxer, and V. S. Pande. Progress and Challenges in the Automated Construction of Markov State Models for Full Protein Systems. Journal of Chemical Physics, in press (2009)

153. J. Izaguirre, C. Sweet, and V. S. Pande. Multiscale dynamics of macromolecules using Normal Mode Langevin. PSB, in press (2009)

154. P. Kasson and V. S. Pande. “Cross-Graining: efficient multiscale simulation via Markov state models. PSB, in press (2009)

155. X. Huang, Y. Yao, G. R. Bowman, J. Sun, L. Guibas, G. Carlsson, and V. S. Pande. Constructing Multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms. PSB, in press (2009)