Vijay Pande

CURRICULUM VITAE (CV)

Also see Prof. Pande’s Wikipedia or Google Scholar pages.

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
2006-2011 Associate Professor of Chemistry, Stanford University, Stanford, CA
2008-2011 Associate Professor of Structural Biology (by courtesy), Stanford University, Stanford, CA
2008-2011 Associate Professor of Computer Science (by courtesy), Stanford University, Stanford, CA
2008- Director, Program in Biophysics, Stanford University, Stanford, CA
2011- Professor of Chemistry, and (by courtesy) of Structural Biology and of Computer Science, Stanford University
2012- Affiliated faculty, Institute for Computational and Mathematical Engineering (ICME), Stanford University
2012- Fellow, Stanford Institute for Chemical Biology (SICB), Stanford University


HONORS AND AWARDS

2013 “Best Mentoring Award,” Stanford University Postdoctoral Association
2013 Closs Lecture, University of Chicago
2013 Henry Eyring Lecture, University of Utah
2013 Keynote Speaker, Texas Protein Folding and Function Meeting
2013 Biophysical Society, Best of 2012 Papers Collection Citation
2012 Michael and Kate Bárány Award for Young Investigators, Biophysical Society
2011 Keynote, Pacific Symposium in Biocomputing
2011- Executive Committee, US Protein Folding Consortium
2010 ACS Thomas Kuhn Paradigm Shift Award
2008 Fellow, American Physical Society
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 Office of Naval Research Science Fellowship
1988 Westinghouse Science Talent Search Scholarship (4th place in 1988)
1988 TRW Science Scholarship

 

 DEPARTMENTAL VISITING COMMITTEES

2011 Johns Hopkins Biophysics Department
2011 UCSF Biophysics Program

 

 JOURNAL EDITORIAL BOARDS

2008- Associate Editor, PLoS Computational Biology
2009- Advisory Board, Journal of Chemical Theory and Computation
2010- Editorial board, Computational Science & Discovery
2013-2015 Editorial board, Journal of Chemical Physics

 

PROFESSIONAL SERVICE

2009 Organizer, Molecular Kinetics Conference 1, Berlin
2010 Organizer, Vertex Free Energy Meeting
2011 Organizer, Protein Folding Consortium
2011 Organizer, Molecular Kinetics Conference 2, Berlin
2012 Organizer, Protein Folding Consortium
2012 Site Host and Organizer, SAMPL3
2012 Organizer, Vertex Free Energy Meeting
2012 Site Host and Organizer, Folding@home Consortium Meeting
2013 Organizer, Protein Folding Consortium
2013 Organizer, Molecular Kinetics Conference 3, Berlin
2013 Site Host and Organizer, SAMPL4
2014 Organizer, Vertex Free Energy Meeting
2015 Vice Chair, Proteins Gordon Research Conference

UNIVERSITY COMMITTEE DUTIES (Active committees in bold-face)

1999-2005 Computational infrastructure (Chemistry Department, chair)
2000- Admissions (Biophysics Program)
2001- Executive committee (Biophysics Program), Chair from 2008-
2001-2008 Supercomputer (BioX, co-chair)
2002-2004,2008- 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)
2002-2008 Computational infrastructure Committee (BioX)
2005-2008 Executive Committee (Chemistry Department)
2006-2007 Curriculum Committee (Chemistry Department, chair 2006)
2008-2010 University-wide committee on postdoctoral fellows
2008- University-wide committee on computational infrastructure (SRCF), co-chair
2011- Committee on Academic Computing and Information Services (C-ACIS), Chair of C-ACIS from 2012-

CORPORATE CONSULTING AND SCIENTIFIC ADVISORY BOARDS (SAB)

2000-2004 SAB, Protein Mechanics, Mountain View, CA
2000-2001 SAB, Omnipod Distributed Computing Project, New York, NY
2002 Consultant, Hitachi Computer Corporation
2002- 2009 SAB, Acumen Pharmaceuticals
2003-2006 Consultant, Fujitsu Computer Corporation
2004-2006 SAB, Pharmix, Inc, San Francisco, CA
2005-2007 SAB, Clearspeed Inc, Los Gatos, CA
2008-2012 SAB, Numerate, Mountain View, CA
2008- SAB, Counsyl, San Francisco, CA
2008-2010 SAB, Discovery Engine, San Francisco, CA
2009-2011 Member, Board of Directors, ClusterCorp, San Francisco, CA
2012- SAB, OpenEye Scientific Software
2013- Non-executive Chairman, Board of Directors, Reanimed Pharmaceuticals, South San Francisco, CA
2013- Chairman, SAB, 1729, Palo Alto, CA
2013- SAB, Code For India (CodeForIndia.org)

 

 

GRANT PROPOSAL REFEREE, NIH 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)
2008 NIH MSFD study section (ad hoc)
2009 NIH MSFB study section (ad hoc)

 

TEACHING (Active in bold-face)

1999- 2008 Chemistry 171: Chemical Thermodynamics (undergraduate)
1999-2003, 2006-2007 Chemistry 275: Statistical Mechanics (graduate)
2003 Dreyfus Teacher-Scholar Award
2003-2008 Biochemistry 241: Biological Macromolecules (graduate, co-taught)
2010- Chemistry 135: Physical Chemistry Principles (undergraduate)
2012- Thinking Matters 001:  The Science of Mythbusters (co-taught)
2013- CS184/CME184:  Startup Software Engineering  (http://startup.stanford.edu) (co-taught)
2013- Coursera MOOC:  Startup Software Engineering (http://startup.stanford.edu) (co-taught)

 

PUBLICATIONS

Summary as of November 1, 2013:  H-index: 61, Total Citations: 13,478
Google scholar url:  http://scholar.google.com/citations?user=cWe_xpUAAAAJ

  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)
  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)
  13. V. S. Pande, A. Yu. Grosberg, M. Kardar,  C. Joerg, and T. Tanaka.  Polyampholyte Freezing Transition.  Physical Review Letters, 77, 3565-3568 (1996)
  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)
  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)
  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 b-hairpin.  Proceedings of the National Academy of Science, USA  96  9062-9067  (1999)
  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)
  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)
  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 bba 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)
  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)
  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)
  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)
  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)
  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)
  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. Side-chain 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 Ab 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 & Modeling . 27: 978-982 (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 Symposium in Biocomputing 492-503 (2009)
  131. V. Voelz, P. Petrone, and V. S. Pande.  Multiscale methods for the ribosome. Pacific Symposium 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 Symposium on Parallel & Distributed Processing, 1-7 (2009) http://doi.ieeecomputersociety.org/10.1109/IPDPS.2009.5161139
  138. A. Beberg and V. S. Pande.  Folding@home:  lessons from eight years of distributed computing, IEEE International Symposium on Parallel & Distributed Processing, 1-8 (2009) http://doi.ieeecomputersociety.org/10.1109/IPDPS.2009.5160922
  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 49 197-201 (2009)
  141. I. Haque and V. S. Pande. PAPER — Accelerating Parallel Evaluations of ROCS. Journal of Computational Chemistry, 31 117-32 (2010)
  142. A.L. Beberg and V.S. Pande.  Constructing a Flexible Internet-Scale Time-Sharing System using Deterministic Checkpointing.  From Proceeding (724) Informatics  (2010)  DOI: 10.2316/P.2010.724-030
  143. G. R. Bowman and V. S. Pande. The Roles of Entropy and Kinetics in Structure Prediction.  PLoS One, 4 e5840 (2009)
  144. 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, D65 952-965 (2009)
  145. 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 77 66-80  (2009)
  146. 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)
  147. D. Ensign and V. S. Pande. Bayesian single-exponential kinetics in single-molecule experiments and simulations.  Journal of Physical Chemistry B 114 280-292 (2010)
  148. 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 31 11338-40 (2009)
  149. 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 15, 2195-2205 (2009)
  150. 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, 106, 19765-19769 (2009)
  151. P. Eastman and V. S. Pande.  Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit.  Journal of Computational Chemistry, 33 1268 – 1272 (2009)
  152. 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)
  153. 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, 131 124101 (2009)
  154. J. Izaguirre, C. Sweet, and V. S. Pande. Multiscale dynamics of macromolecules using Normal Mode Langevin.  PSB 240-251 (2010)
  155. P. Kasson and V. S. Pande.  “Cross-Graining: efficient multiscale simulation via Markov state models.  PSB 492-503 (2010)
  156. 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. Pacific Symposium on Biocomputing 15 228-239 (2010)
  157. D. Ensign and V. S. Pande. Bayesian Detection of Intensity Changes in Single Molecule and Molecular Dynamics Trajectories.  Journal of Physical Chemistry B 114 280-92 (2010)
  158. V. A. Voelz, G. R. Bowman, K. Beauchamp, V. S. Pande.  Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39), Journal of the ACS, 132 1526-1528 (2010)
  159. P. Eastman and V. S. Pande.  CCMA: A Robust, Parallelizable Constraint Method for Molecular Simulations.  Journal of Chemical Theory and Computation 6 434-437 (2010)
  160. G. Bowman, X. Huang, and V. S. Pande. Network models for molecular kinetics and their initial applications to human health.  Cell Research 20 622-630 (2010)
  161. V. Voelz, V. Singh, W. J. Wedemeyer, L. Lapidus, and V. S. Pande. Unfolded state dynamics and structure of protein L characterized by simulation and experiment, Journal of the ACS, 132 4702–4709 (2010)
  162. J. Ponder, C. Wu, V. S. Pande, I. Haque, R. A. Distasio Jr., D. Lambrecht, M. Head-Gordon, G. Clark, M. Johnson, and T. Head-Gordon.  Current Status of the AMOEBA Polarizable Force Field, J. Phys. Chem. B., 114 2549-2564 (2010)
  163. I. S. Haque, V. S. Pande, and W. P. Walters.   SIML: A Fast SIMD Algorithm for Calculating LINGO Chemical Similarities on CPUs and GPUs.  Journal of Chemical Information and Modeling 50 560-564 (2010)
  164. P. Eastman and V. S. Pande. OpenMM: A Hardware Abstraction Layer for Molecular Simulations. Computing in Science and Engineering 12 34-39 (2010)
  165. J. England and V. S. Pande.  Charge, hydrophobicity, and confined water: Putting past simulations into a simple theoretical framework.  Biochemistry and Cellular Biology 88 359-69 (2010)
  166. G. Bowman and V. S. Pande. Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models.  Journal of Computational and Theoretical Chemistry 6 787–794 (2010)
  167. T. D. Fenn, M. J. Schnieders, A. T. Brunger, and V. S. Pande.  Polarizable Atomic Multipole X-Ray Refinement: Hydration Geometry and Application to Macromolecules.  Biophysical Journal 98 12 (2010)
  168. D. Lucent, M. Stumpe, V. Pande. Chaperonins: The machines which fold proteins. Contributed Chapter to Nanomachines, ed B. Roux (2010)
  169. P. M. Kasson, E. Lindahl, and V. S. Pande.  Atomic-resolution simulations predict a transition state for vesicle fusion defined by contact of a few lipid tails.  PLoS Computational Biology 6 e1000829 (2010)
  170. I. S. Haque and V. S. Pande. SCISSORS – A Linear-Algebraical Technique to Rapidly Approximate Chemical Similarities. Journal of Chemical Information and Modeling 50 1075–1088 (2010)
  171. G. Bowman and V. S. Pande. Protein folded states are kinetic hubs.  Proceeedings of the National Academy of Sciences, USA 107 10890-10895 (2010)
  172. V. S. Pande, K. Beauchamp, and G. R. Bowman.  Everything you wanted to know about Markov State Models but were afraid to ask.  Methods 52 99-105 (2010)
  173. I. Haque and V. S. Pande. Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU.  Resilience (2010)
  174. D. Ensign and V. S. Pande. Bayesian inference for Brownian dynamics.  Physical Review E 82 (2010)
  175. I. Haque and V. S. Pande.  Large-scale Chemical Informatics on the GPU.  GPU Gems (2010)
  176. P. Eastman and V. S. Pande. Speeding development and execution speed with Just In Time GPU code development approaches.  GPU Gems (2010)
  177. V. S. Pande.  A Simple Theory of Protein Folding.  Physical Review Letters 105 198101 (2010)
  178. D. Lucent, C. Snow, and V. S. Pande.  Water structure in the ribosome tunnel. PLoS Computational Biology 6 e1000963 (2010)
  179. G. Bowman, V. Voelz, and V. S. Pande. Atomistic folding simulations of the five helix bundle protein λ6-85Journal of the American Chemical Society 133 664-667 (2011)
  180. S. Doniach, V. S. Pande, J. Spence, D. Herschlag, S. Boutet and J. Hastings.  Use of correlated x-ray scattering (CXS) to track protein motions during enzyme catalysis by means of an x-ray free-electron laser. Workshop on Evolution and Control of Complexity, Argonne National Lab (2011)
  181. T. D. Fenn, M. J. Schnieders, M. Mustyakimov , C. Wu, P. Langan, V. S. Pande, and A. T. Brunger.  Reintroducing Electrostatics into Macromolecular Crystallographic Refinement: Application to Neutron Crystallography and DNA Hydration. Structure 19 522-533 (2011)
  182. M. C. Stumpe, N. Blinov, D. Wishart, A. Kovalenko, and V. S. Pande.  Calculation of Local Water Densities in Biological Systems:  A Comparison of Molecular Dynamics Simulations and the 3D-RISM-KH Molecular Theory of Solvation.  J. Physical Chemistry B 115 319-328 (2011)
  183. G. Bowman, V. Volez, and V. S. Pande.  Taming the complexity of protein folding.  Current Opinion in Structural Biology 21 4-11 (2011)
  184. M. J. Schnieders, T. D. Fenn, and V. S. Pande.  Polarizable Atomic Multipole X-ray Refinement: Particle-Mesh Ewald Electrostatics for Macromolecular Crystals.  Journal of Computational and Theoretical Chemistry 7 1141-1156 (2011)
  185. P. Kasson and V. S. Pande.  Bundling a set of fusion mechanisms.  Proceedings of the National Academy of Sciences, USA 108 3827-3828 (2011)
  186. J. Wagoner and V. S. Pande.  A smoothly decoupled particle interface (SDPI): new methods for coupling explicit and implicit solvent.  Journal of Chemical Physics 134 214103 (2011)
  187. J. D. Chodera, W. C. Swope, F. Noé, J-H Prinz, M. R. Shirts, and V. S. Pande.  Dynamical Reweighting:  Improved estimates of dynamical properties from simulations at multiple temperatures.  Journal of Physical Chemistry 134 244107 (2011)
  188. J.-H. Prinz, J. D. Chodera, V. S. Pande, W. C. Swope, J. C. Smith, and Frank Noé.  Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics.  Journal of Chemical Physics 134 244108 (2011)
  189. J. Chodera and V. S. Pande. The social network (of protein conformations).  Proceedings of the National Academy of Sciences, USA 108 12969-70 (2011)
  190. K. Beauchamp, D. Ensign, R. Das, and V. S. Pande.  Quantitative comparison of villin headpiece subdomain simulations and triplet-triplet energy transfer experiments. Proceedings of the National Academy of Sciences, USA, 108 12734-9 (2011)
  1. S. Pronk, P. Larson, I. Pouya, G. Bowman, I. Haque, K. Beaucamp, B. Hess, V. S. Pande, P. M. Kasson, E. Lindahl.  Copernicus: A new paradigm for parallel adaptive molecular dynamics.  Supercomputing 2011 (2011)
  2. P. Novick, J. Rajadas, C.W. Liu, N. W. Kelley, M. Inayathullah, and V. S. Pande. Rationally designed turn promoting mutation in the amyloid β-peptide sequence to stabilize oligomers in solution.  PLoS ONE 6(7): e21776 (2011)
  3. J. Chodera and V. S. Pande.  Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments.  Physical Review Letters 107 098102 (2011)
  4. S. L. Delp, J. P. Ku, V. S. Pande, M. A. Sherman, R. B. Altman.  Simbios: An NIH National Center for Physics-Based Simulation of Biological Structures.  Journal of the American Medical Informatics Association 19 186-9 (2011).
  5. V. Voelz and V. S. Pande.  Rate Spectra.  Proteins 80 342-351 (2011)
  6. V. S. Pande.  (Compressed) Sensing and Sensibility.  PNAS 108 14713-4 (2011)
  7. I. S. Haque and V. S. Pande. Error Bounds on the SCISSORS Approximation Method. Journal of Chemical Information and Modeling, 51 2248-53 (2011).
  8. I. Haque, V. S. Pande, and W. P. Walters.  The Anatomy of High-Performance 2D Similarity Calculations.  Journal of Chemical Information and Modeling 51 2345-51 (2011)
  9. K. J. Kohlhoff, M. H. Sosnick, W. T. Hsu, V. S. Pande, and R. B. Altman.  CAMPAIGN: An open-source Library of GPU-accelerated Data Clustering Algorithms.  Bioinformatics 27 2322-3 (2011)
  10. K. Beauchamp, G. R. Bowman, T. J. Lane, L. Maibaum, I. S. Haque, and V. S. Pande.  MSMBuilder2: Modeling Conformational Dynamics at the Picosecond to Millisecond Scale. Journal of Computational and Theoretical Chemistry, 7 3412-3419 (2011).
  11. J. Weber and V. S. Pande.  Characterization and rapid sampling of protein folding Markov state model topologies.  Journal of Computational and Theoretical Chemistry, 7 3405-3411 (2011).
  12. T. J. Lane, G. Bowman, K. Beauchamp, V. Voelz, and V. S. Pande.   WW Domains Take a New Turn: Markov State Model Reveals Folding and Functional Dynamics in Ultra-Long MD Trajectories. JACS 133 18413-9 (2011)
  13. R. Brandman, Y. Brandman, and V. S. Pande.  A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome.  PLoS ONE 7 e29377 (2012)
  14. R. Brandman, Y. Brandman, and V. S. Pande.  Sequence coevolution between RNA and protein characterized by mutual information between residue triplets.  PLoS ONE, 7 e30022 (2012)
  15. P. A. Novick, D. H. Lopes, K. M. Branson, A. Esteras-Chopo, I. A. Graef, G. Bitan, and V. S. Pande.  Design of β-Amyloid Aggregation Inhibitors from a Predicted Structural Motif.  J. Med. Chem. 55 3002-3010 (2012)
  16. A. M. Levin, D. L. Bates, A. M. Ring, J. T. Lin, L. Su, C. Krieg, G. R. Bowman, P. Novick, V. S. Pande, H. E. Kohrt, O. Boyman, C. G. Fathman, K. C. Garcia.  An Interleukin-2 super-kine engineered by toggling a conformational switch.  Nature 484 529-33 (2012)
  17. A. M. Ring, J-X Lin, D. Feng, S. Mitra, M. Rickert, G. R. Bowman, V. S. Pande, P. Li, I. Moraga, R. Spolski, E. Özkan, W. J. Leonard, K. C. Garcia.  Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15.  Nature Immunology 13 1187-1195 (2012)
  18. J. K. Weber and V. S. Pande. Protein folding is mechanically robust.  Biophysical Journal 102 859-67 (2012)
  19. Y-S Lin, G. R. Bowman, K. Beauchamp, and V. S. Pande.  Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer.  Biophysical Journal 102 315-324 (2012).
  20. K. Beauchamp, R. Das, and V. S. Pande.  Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements.  Journal of Theoretical and Computational Chemistry 8 1409-1414 (2012)
  21. V. S. Pande.  Protein folding studied with molecular simulation.  Encyclopedia of Biophysics (2012)
  22. T. J. Lane and V. S. Pande.  A Simple Model Predicts Experimental Folding Rates and a Hub-Like Topology.  JPC B 116 6764-6774 (2012)
  23. C.J.B. Harvey, J. D. Puglisi, V. S. Pande,  D. E. Cane, and C. Khosla.  Precursor Directed Biosynthesis of an Orthogonally Functional Erythromycin Analogue: Selectivity in the Ribosome Macrolide Binding Pocket.  Journal of the ACS 134 12259–12265 (2012).
  24. V. A. Voelz, M. Jäger, S. Yao, Y. Chen, L. Zhu, G. R. Bowman, M. Friedrichs, O. Bakajin, L. J. Lapidus, S. Weiss, and V. S. Pande.  Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment.  Journal of the ACS 134 (30) 12565–12577 (2012)
  25. K. Beauchamp, R.T. McGibbon, Y-S. Lin, R. Das, and V. S. Pande.  Simple multi-state models reveal hidden complexity in protein folding.  PNAS 109 17807–17813 (2012)
  26. K. J. Kohlhoff, V. S. Pande, and R. B. Altman.  K-means for parallel architectures using all-prefix-sum sorting and updating steps.  IEEE Transactions on Parallel and Distributed Systems doi: 10.1109/TPDS.2012.234 (2012)
  27. Y-S Lin and V. S. Pande.  Effects of familial mutations on the monomer structure of Aß42.  Biophysical Journal 103 L47-L49 (2012)
  28. T. J. Lane, D. Shukla, K. Beauchamp, and V. S. Pande.  To Milliseconds and Beyond: Challenges in the Simulation of Protein Folding.  Current Opinion in Structural Biology 23 58-65 (2012)
  29. P. Eastman, M. S. Friedrichs, J. D. Chodera, R. J. Radmer, C. M. Bruns, J. P. Ku, K. A. Beauchamp, T. J. Lane, L.-P. Wang, D. Shukla, T. Tye, M. Houston, T. Stich, C. Klein, M. R. Shirts, and V. S. Pande.  OpenMM 4.0: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation.  Journal of Computational and Theoretical Chemistry 9 461–469 (2013).
  30. G. Kiss, V. S. Pande, and K. N. Houk.   Molecular Dynamics Simulations for the Ranking, Evaluation, and Refinement of Computationally Designed Proteins.   Methods in Enzymology 523 (2012)
  31. J. Sun, Y. Yao, X. Huang, V. S. Pande, G. Carlsson, L. J. Guibas.  A Fast Geometric Clustering Method on Conformation Space of Biomolecules.  Learning 2 (2012)
  32. T. J. Lane and V. S. Pande.  Eigenvalues of the Homogeneous Finite Linear One Step Master Equation:  Applications to Downhill Folding.  Journal of Chemical Physics 137 215106 (2012).
  33. J. Wagoner and V. S. Pande.  Reducing the effect of Metropolization on mixing times in molecular dynamics simulations.  Journal of Chemical Physics, in press (2013)
  34. B. Cronkite-Ratcliff  and V. S. Pande.  MSMExplorer: Visualizing Markov State Models for Biomolecule Folding Simulations.  Bioinformatics, in press (2013)  doi: 10.1093/bioinformatics/btt051
  35. H-W Chang, S. Bacallado, V. S. Pande, G. E. Carlsson.  Persistent Topology and Metastable State in Conformational Dynamics.  PLoS ONE, in press (2013)
  36. J. K. Weber and V. S. Pande.  Functional understanding of solvent structure in GroEL cavity through dipole field analysis.  Journal of Chemical Physics, in press (2013)
  37. J. K. Weber, R. Jack, and V. S. Pande.  Emergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics.  JACS, in press (2013)
  38. C. Schwantes and V. S. Pande.  Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.  Journal of Computational and Theoretical Chemistry, in press (2013)
  39. C. Gu, H-W Chang, L. Maibaum, V. S. Pande, G. E. Carlsson, and L. J. Guibas.  Building Markov State Models with Solvent Dynamics.  BMC Bioinformatics, in press (2013)
  40. J. C. Sweet, R. J. Nowling, T. Cickovski, C. R. Sweet, V. S. Pande, and J. A. Izaguirre.  Long Timestep Molecular Dynamics on the Graphical Processing Unit.  JCTC, in press (2013)
  41. R. T. McGibbon and V. S. Pande.  Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics.  J. Chem. Theory Comput., DOI: 10.1021/ct400132h (2013)
  42. T. J. Lane and V. S. Pande.  Inferring the Rate-Length Law of Protein Folding.  PLoS ONE (2013)
  43. T. J. Lane, C. R. Schwantes, K. A. Beauchamp, and V. S. Pande.  Probing the origins of two-state folding.  Journal of Chemical Physics 139 145104 (2013)

 

 

 

PATENTS

  1. J. Izaguirre, C. Sweet, P. Petrone, and V. S. Pande.  Accelerated Dynamics of Proteins and Other Macromolecules.  University of Notre Dame and Stanford University (2009)
  1. I. Haque and V. S. Pande.   Fast methods for construction of vector embeddings of molecules for similarity search.  Stanford University, provisional patent (2010)

 

 

SELECTED INVITED TALKS

  1. Boston University, Polymer Physics Seminar, October 1995
  2. University of California, Berkeley, Condensed Matter Physics Seminar, November 1995
  3. University of California, San Diego, Condensed Matter Theory Seminar, November 1995
  4. Harvard University, Polymer Chemistry Seminar, December 1995
  5. Lawrence Berkeley National Laboratory, LBNL Biophysics Meeting, September 1996
  6. Rutgers University, Statistical Mechanics Meeting, December 1996
  7. University of California, Berkeley, Condensed Matter Physics Seminar, October 1997
  8. Stanford University, Physical Chemistry Seminar, January 25, 1998
  9. University of California, Berkeley, Chemical Engineering Seminar, February 12, 1998
  10. Lawrence Berkeley National Laboratory, NERSC Seminar, February 20, 1998
  11. Massachusetts Institute of Technology, Chemical Engineering Seminar, March 9, 1998
  12. University of California, Berkeley, Molecular and Cell Biology Seminar, March 30, 1998
  13. Los Alamos National Laboratory, Third International Symposium on Biological Physics, September 20, 1998
  14. National Institutes of Health, Laboratory of Chemical Physics, March 17, 1999
  15. National Centre for Biological Sciences (NCBS), Banglore, India; Frontiers in Structural Biology, August 25-27, 1999
  16. UC Berkeley, Statistical Mechanics Meeting, January 2000
  17. La Jolla Interfaces in Science (LJIS), Quantitative Challenges in the Post Genomic Sequence Era, January 11-12, 2000
  18. International School of Physics, Enrico Fermi, Varenna, Lake Como Italy, July 11, 2000
  19. Columbia University, Chemistry Dept Seminar, December 2000
  20. IBM Watson Research center, Blue Gene seminar, December 2000
  21. Jet Propulsion Lab, Pasadena, CA, Seminar, February 2001
  22. UCSD, Blue Gene Conference, March 2001
  23. ACS meeting, symposium on folding and energy landscapes, March 2001
  24. National Museum of Natural History, Supercomputing Symposium, 2001
  25. Rockefeller University, Chemistry Dept Seminar, 2001
  26. Kyoto University, Fourth International Symposium on Biological Physics, July 2001
  27. Chicago ACS meeting, September 2001
  28. IBM Almaden research center, San Jose, October 2001
  29. Polarizable Forcefields Workshop, University of Utah, December 2001
  30. ICAM/LANL conference on self organizing systems, Santa Fe, January 2002
  31. Protein Folding Gordon Conference, January 2002
  32. UCSF, Kollman Memorial Symposium, February 2002
  33. UCSD, Chemistry Dept Student Invited Seminar, February 2002
  34. OpenEye conference, keynote speaker, February 2002
  35. Stanford University, Materials Science Departmental Seminar, February 2002
  36. Stanford University, Mechanical Engineering Departmental Seminar, April 2002
  37. UIUC, Theoretical Biophysics Seminar, April 15, 2002
  38. Stanford University, CPIMA Forum, August 9, 2002
  39. Caltech, Biophysics Seminar, October 24, 2002
  40. Aspen Meeting on Single Molecule Experiments, January 2003
  41. UC Davis, Physics Colloquium, January 27, 2003
  42. University of Pennsylvania, Chemistry Department Seminar, February 20, 2003
  43. Princeton University, Chemical Engineering Department Seminar, February 21, 2003
  44. Association for Lab Automation (ALA), Session on bioinformatic applications to proteomics, Palm Springs, February 2003
  45. International Symposium on Simulation Science, March 6, 2003
  46. American Physical Society Meeting, March 3, 2003
  47. Chemistry Symposium, Seoul National University, March 13, 2003
  48. Cambridge Health Tech Conference, Strategic Biocomputing: Implementations, Applications and Results.  March 18, 2003
  49. Johns Hopkins, “Coolfont” Protein Folding Meeting, March 22-25, 2003
  50. University of Maryland, Statistical Physics/Biophysics Seminar, March 26, 2003
  51. Biomedical Engineering Society (BMES).  Understanding the Role of Protein Unfolded States in Folding, Function, Evolution and Disease, April 11, 2003
  52. SD Forum, Sun Microcomputers, “Build A Bioinformatics Supercomputer Using Grid Technology,” June 17, 2003
  53. Telluride 2003 workshop on “Energy Landscapes and Dynamics,” July 2003
  54. ACS Meeting, Session on Protein Folding Kinetics, September 2003
  55. ACS Meeting, Session on Protein Design, September 2003
  56. Keynote address, 16th annual workshop on Languages and Compilers for Parallel Computing (LCPC). (declined), October 2-4, 2003
  57. CECAM Meeting, October 2003, declined
  58. Biophysics seminary, Cornell University, October 29, 2003
  59. NIH BISTI conference, declined, November 2003
  60. Science at the Interface Seminar, Michigan State University, November 14, 2003
  61. DGRIDS 2003, Phoenix, November 17, 2003
  62. ALA meeting, February 2004
  63. U. Minnesota, February 10, 2004
  64. Biophysical society, February 2004
  65. Xerox PARC, February 19, 2004
  66. Isaac Newton Workshop, March 15-19 2004, declined
  67. Keystone Meeting on Structural Biology. April, 2004
  68. NSF Workshop on Cyber infrastructure.  April 20, 2004
  69. CECAM Meeting on Free Energy Methods.  May, 2004
  70. Protein Society.  August, 2004
  71. “Algorithms for Macromolecular Modeling” Leicester, UK,  August 19-21, 2004
  72. ACS Meeting.  Session on High Performance Supercomputing in Drug Design.  August, 2004
  73. Washington University, St Louis.  December, 2004
  74. Chemistry Department, New York University, January, 2005
  75. Chemistry Department, Northwestern University, February, 2005
  76. Chemistry Department, University of Wisconsin, February, 2005
  77. Chemistry Department, MIT, February, 2005
  78. American Physical Society, March 2005
  79. HiComb Meeting, Keynote Address, April 2005
  80. GA Tech, Frontiers in Molecular Simulation, May 2005
  81. US-Japan Meeting on Protein Folding (Saven and Gai, organizers), May 2005
  82. Biomolecular Simulation: From physical principles to biological function, May 2005
  83. CECAM, June 2005
  84. NAS, German-American Frontiers of Science (GAFOS) Symposium, May 2005
  85. Proteins Gordon Conference, June 2005
  86. ACT, July 2005
  87. Merck, West Point Office, July 2005
  88. IPAM, UCLA, Multiscale Modeling in Soft Matter and Bio-Physics, September 2005
  89. UCSF, Dept of Pharmaceutical Chemistry, October 2005
  90. National Parkinson’s Foundation meeting, November 2005
  91. Biomolecular Modeling Symposium, Rice, December 2005
  92. Interfacial Phenomena at Different Length and Timescales, PacficChem, December 2005
  93. Protein Folding Gordon Conference, January 2006
  94. Chemistry Department, University of Pittsburgh, January 2006
  95. Chemistry Department, UCLA, January 2006
  96. University of Michigan, February 2006
  97. Sanibel Quantum Meeting, February 2006
  98. Computational/Experimental Approaches to Protein Defects in Human Disease, Rutgers, April 2006
  99. EMBO Workshop, May 2006
  100. HPDC-15, Keynote address, June 2006
  101. FOMMS 2006, July 2006
  102. Protein Society meeting, Irving Sigal Young Investigator Award Presentation, August 2006
  103. ACS Conference, San Francisco, August 2006
  104. Chemistry Department, MIT, September 2006
  105. CECAM meeting on protein folding, September 2006
  106. UCSF conference on free energy calculation, October 2006
  107. Berkeley Statistical Mechanics Conference, January 2007
  108. Sanibel Conference, February 2007
  109. Open Eye CUP, February 2007
  110. APS March Meeting, Denver, March 2007
  111. ACS Meeting, Chicago, March 2007
  112. PCGRID2007, Long Beach, March 2007
  113. European Protein Society Meeting, May 2007
  114. Biophysics seminar, Yale University, September 2007
  115. Protein Folding Gordon Conference, January 2008
  116. Metastability and Rare Events in Complex Systems, Vienna, 2008
  117. Monterey ASC PI Meeting, February 2008
  118. Open Eye CUP, March 2008
  119. New Orleans ACS, April 2008
  120. Mathematical and Numerical Methods for Free Energy Calculations in Molecular Systems (at BIRS), June 2008
  121. Algorithmic Development on Enhanced Sampling, Telluride, July 2008
  122. Philadelphia ACS, August, 2008
  123. QB3 Structural Biology Seminar, UC Berkeley, February 2009
  124. Joint Chemistry Biology Seminar, UC Davis, February 2009
  125. IPAM Workshop, UC Los Angeles, February 2009
  126. ACS Meeting, Salt Lake City, March 2009
  127. Molecular Kinetics 2009, Berlin, May 2009
  128. Canadian Society of Biochemistry, Molecular and Cellular Biology (CSBMCB), Ontario, June 2009
  129. ACS Meeting, Protein Misfolding and Disease.  Washington D.C., August 2009
  130. ACS Meeting, Protein Dynamics and Function.  Washington D.C., August 2009
  131. Beckman conference in honor of Klaus Schulten.  UIUC, September 2009
  132. AM^3 meeting.  Austin, November 2009
  133. NIH IMAG, December 2009
  134. Protein Folding GRS, Keynote Talk, January 2010
  135. Protein Folding GRC, January 2010
  136. NIH Structural Biology Special Interest Group, February 2010
  137. Biophysical Society, February 2010
  138. NNIN Meeting, February 2010
  139. SIAM, Seattle, February 2010
  140. ACS Meeting, San Francisco, CA, March 2010
  141. Nanomedicine Meeting, April 2010
  142. Cold Spring Harbor, May 2010
  143. Protein Folding Meeting, ASU, May 2010
  144. Vertex Free Energy Conference, May 2010
  145. Telluride Free Energy Conference, June 2010
  146. Telluride Protein Folding Conference, June 2010
  147. Single Molecule Approaches to Biology GRC, June 2010
  148. Multiscale Simulation, Edinburgh, Scotland, July 2010
  149. Protein Folding In the Cell, FASEB, Saxtons River, Vermont, July 2010
  150. ACS Meeting, Symposium Honoring Bruce Berne, Boston, August 2010
  151. ACS Meeting GPU session, Boston, August 2010
  152. ACS Meeting, CINF, Boston, August 2010
  153. Joint Stanford-Institute Pasteur Conference, Paris, 2010
  154. CECAM Meeting on Protein Folding, Switzerland, October 2010
  155. PacificChem 2010, December 2010
  156. PSB 2011, Keynote, January 2011
  157. Chemical Engineering Department, UCSB, January 2011
  158. Chemistry Department, UCLA, January 2011
  159. Joint Chemistry & Physics Seminar, Boston University, February 2011
  160. Chemistry Department, Harvard University, February 2011
  161. MIT, February 2011
  162. Biophysics Seminar, Brandeis University, February 2011
  163. Physics Department, Princeton University, February 2011
  164. US-Mexico Folding Meeting, March 2011
  165. Texas Folding Meeting, Keynote, March 2011
  166. CUP, Santa Fe, March 2011
  167. UCLA IPAM, April 2011
  168. Johns Hopkins Biophysics Department, April 2011
  169. Chemistry Department, U. Pittsburgh, April 2011
  170. Proteins Gordon Conference, June 2011
  171. ACS Meeting, Denver, 2012
  172. Biophysical Society, San Diego 2012.  Baranay Young Investigator Award Lecture.
  173. CUP, Santa Fe, March 2012
  174. ACS Meeting, San Diego, 2012
  175. CHARMM+AMBER joint meeting, Bethesda, 2012
  176. Vertex Pharmaceuticals, Boston, 2012
  177. ACS, Philadelpha, 2012 (four talks)
  178. CECAM on protein folding, Zurich, 2012
  179. BioIT World, San Francisco, 2012
  180. CCG Meeting, Montreal, 2012
  181. NCBC Meeting, NIH, Bethesda, November 10, 2012
  182. Berkeley Mini Stat Mech Meeting, January 2013
  183. Physical Chemistry Seminar, UC Berkeley, February 2013
  184. NVIDIA GTC, Santa Clara, CA, March 2013
  185. Texas Folders Meeting, Keynote, Houston, TX, March 2013
  186. Genetech, South San Francisco, April 2013
  187. Henry Eyring Lecture, University of Utah, April 2013
  188. ACS Meeting, New Orleans, LA, April 2013
  189. WMEN Meeting, San Jose de Cabo San Lucas, Mexico, May 2013
  190. Special Physical Chemistry Seminar, MIT, Cambridge, MA, May 2013
  191. Computational Drug Discovery Seminar, Novartis, Cambridge, MA, May 2013
  192. Proteins GRC, June 2013
  193. CCG Meeting, Montreal, Canada, June 2013
  194. Computer Aided Drug Design GRC, July 2013
  195. Molecular Kinetics Meeting, Berlin, September 2013
  196. ACS Meeting, Indianapolis, IN, September 2013
  197. Seminar, Vertex Pharmaceuticals, San Diego, September 2013
  198. Computer Aided Drug Design CECAM Workshop, Lausanne, October 2013
  199. Theoretical Chemistry Seminar, University of California, Berkeley, October 2013
  200. Keynote, PICS opening seminar, University of Pennsylvania, October 2013
  201. Biophysics seminar, University of Chicago, October 2013
  202. Chemistry Seminar, University of Pennsylvania, October 2013
  203. AiChE Meeting, San Francisco, November 2013
  204. Biochemistry Seminar, University of Notre Dame, November 2013
  205. Protein Folding GRC, January, 2014
  206. Biophysical Society, February, 2014
  207. ACS Meeting, Dallas, March 2014
  208. Student hosted seminar, Chemistry Dept, University of Chicago, April 2014
  209. Royal Society of Chemistry Faraday Discussions, May 2014
  210. Japanese Protein Society, July 2014

 

 

 

STUDENTS AND POSTDOCTORAL FELLOWS MENTORED

 

Graduate Students (current and former)

Sergio Bacallado           2008- present, Structural Biology.  Currently, a lecturer in Statistics, Stanford University.

Kyle Beauchamp         2009-2013, Biophysics.  Currently a postdoc at MSKCC.

Adam Beberg               2005- 2011, Computer Science.  Currently at Google.

Greg Bowman              2007- 2010, Biophysics.  Currently, a Miller Fellow, UC Berkeley.

Relly Brandman           2002-2009, PhD in Molecular Pharmacology.  Currently at Coursera.

Kevin Dalton               2011-present.  Biophysics, joint with Judith Frydman.

Sidney Elmer               1999-2004, PhD in Chemistry.  Currently at LANL.

Mark Engelhardt          2004-2006 (co-advisor); PhD in Biochemistry, 2006; currently postdoc at University of Toronto

Jeremy England           2005-2009, Hertz Fellow, PhD in Physics.  Currently an Assistant Professor of Physics, MIT

Dan Ensign                  2005-2010, SGF Fellow, PhD in Chemistry

Imran Haque                2007-2012, NSF & SGF Fellow.  Currently at Counsyl.

Matthew Harrigan       2013-present, Chemistry.

Guha Jayachandran     2002-2008, DOD Fellow; PhD in Computer Science

Nick Kelley                 2001-2009, PhD in Biophysics.

Stefan Larson               2000-2004, PhD in Biophysics.  SGF Fellow.  Currently at McKinsey.

Steven Kearnes            2011-present, Structural Biology

Thomas J (“TJ”) Lane 2010-present, Chemistry.  NSF Fellow.

Del Lucent                   2004-2010, PhD in Biophysics.  Currently an Assistant Professor at Wilkes University

Robert McGibbon       2011-present, Chemistry.

Paul Novick                 2009-present, Chemistry.  CMAD Fellow.

Angelica Parente          2011-present.  Biophysics.  Joint with Zev Bryant.

Paula Petrone               2003-2008, PhD in Biophysics, BISTI Fellow.  Currently at Novartis.

Young Min Rhee         2001-2005, PhD in Chemistry.  Currently an assistant professor at POSTECH, Korea, Department of Chemistry

Steven Ryckbosch       2012-present.  Chemistry.  Joint with Paul Wender.

Christian Schwantes    2010-present.  Chemistry.

Jade Shi                        2012-present.  Chemistry.

Michael Shirts             2000-2004, PhD in Chemistry.  Hertz Fellow, SGF Fellow.  Currently an assistant professor at the University of Virginia, Department of Chemical Engineering

Nina Singhal                 2001-2007, PhD in Computer Science, SGF Fellow.  Currently an assistant professor at University of Chicago

Chris Snow                  2000-2006.  PhD in Biophysics.  Currently an Assitant Professor at University of Colorado.

Eric Sorin                     2001-2007, Chemistry, PhD., DOE CGSF Fellow.  Currently an assistant professor at Cal State Long Beach

Mohammad Sultan      2012-present.  Chemistry.

Vishal Vaidyananthan  2001-2007, PhD in Chemistry.  Currently at Goldman Sachs.

Dan Vannetta               2009-present, Chemistry

Jason Wagoner             2006-2013, NSF Fellow Chemistry.  Currently at Fellow at the Lauffer Center, Stony Brook.

Jeffery Weber              2010-present, Chemistry.  Hertz Fellow.

Bojan Zagrovic            2000-2004, PhD in Biophysics,  HHMI Fellow.  Currently a postdoctoral fellow at ETH, with Prof. Wilfred van Gunsteren.  Currently a professor at Univ. Vienna.

 

Postdoctoral Associates (current and former)

Kim Branson               2006-2009. Currently at Vertex Pharmaceuticals.

John Chodera               2006-2009. Currently an Assitant Professor at Sloan Kettering

Lillian Chong               2002-2006.  Currently Assistant Professor at Chemistry Department, University of Pittsburgh

Xuhui Huang               2006-2009  (joint w/Prof. Michael Levitt).  Currently an Assistant Professor in Hong Kong

Peter Kasson               2006-2010.  Currently an Assistant Professor at the University of Virginia

Gert Kiss                     2011-present.  Simbios Distinguished Fellow.

Kai Kohlhoff               2009-2011 (joint w/Prof. Russ Altman).  Currently at Google.

Morgan Lawrenz         2011-present.

Sung Joo Lee                2003-2006.  Group leader at LG Pharmaceuticals, Korea

Yu-Shan Lin                 2009-2012.  Currently an Assistant Professor at Tufts University

Edgar Luttmann           2005-2008.  Currently a lecturer in Germany.

Lutz Maibaum             2009-2011.  Currently an Assistant Professor and U. Washington, Seattle

Sanghuyn Park             2004-2007.  Currently a fellow at Argonne National Labs.

Lili Peng                       2013-present (joint w/Prof. Russ Altman)

Mike Schnieders          2007-2010 (joint w/Prof. Axel Brunger).  Currently an Assistant Professor at University of Iowa

Diwakar Shukla           2011-present.  Simbios Distinguished Fellow

Martin Stumpe            2009-2010.  Currently at NASA.

Veena Thomas             2010-present

Vincent Voelz              2007-2011.  Currently an Assistant Professor at Temple University.

Lee-Ping Wang             2011-present (joint w/Prof. Todd Martinez).  Simbios Distinguished Fellow

 

Masters Students

Siraj Khaliq                  Masters in Computer Science, 2002.  Currently at Google

Bradley Nakatani         Masters in Chemistry, 2003.

Abhay Sukumaran       Masters in Computer Science, 2006

 

Undergraduate Students

Ian Baker                     B.A. Chemistry, 2001.

Bryce Cronkite-Ratcliff   2010.  Currently at Stanford

Amit Garg                   B.A. Computer Science, 2002.  Currently at Google.

Jeremy Lai                  2010.  Currently at Stanford

Alex Robertson           B.A. Chemistry, 2008

 

 

 

FUNDED GRANT PROPOSALS

 

COMPLETED

1.  NSF MRSEC CPIMA (Curt Frank, PI)                                    2000-2002

Simulations of branched molecules

This is a seed grant from the NSF MRSEC CPIMA center.

Role:  PI

 

2.  ARO (Michael Levitt, PI)                                                            2000-2003

Large-Scale Structure Prediction and Folding of Proteins from Sequence

This is an instrumentation grant for computer hardware to study protein dynamics and structure prediction.

Role:  Co-PI

 

3.  ACS PRF                                                                                      2000-2002

Nucleation or a topological search:  relative contributions to the folding barrier

Here, we proposed tests of the hypothesis that topology defines the folding pathway.

Role:  PI

 

4.  Intel, Inc                                                                                       2000-2001

Folding@Home

This gift from Intel helped pay for the initial computational infrastructure for Folding@Home.

Role:  PI

 

5.  Stanford Bio-X Core Facilities (Michael Levitt, PI)               2002-2003

High performance computer cluster

This grant paid for the Dell cluster now serving the biological community at Stanford.

Role:  Co-PI

 

6.  NIH 2 RO1 GM062868                                                                2002-2006      

Topology, Nucleation, and the Protein Folding Barrier

We examine the mechanisms for how proteins fold by examining protein folding using distributed computing and implicit solvent coupled to experiments (done by Kevin Plaxco, co-PI)

Role:  PI

 

7.   NIH BISTI Planning grant (Russ Altman, PI)                                    2002-2005

This proposal gave a small amount of funds for the planning of the BISTI roadmap center.  These funds helped to fund some early infrastructure aspects of Folding@Home.

Role:  co-Investigator

Role:  PI

 

8.  Stanford Internet 2                                                                     2002-2003

Folding@home 2.0: Harnessing the Internet2 for worldwide distributed computing”

This grant funded a second generation Folding@Home software infrastructure, with an emphasis on taking advantage of the Internet2 backbone.

Role:  PI

 

9.  Stanford OTL                                                                              2002-2003

Folding@Home 3: calculating ligand binding affinity with distributed computing

This small grant funded initial work to use Folding@Home to calculate protein-ligand binding free energies.

Role:  PI

 

10.  ACS PRF                                                                                    2002-2004

Comparing the accuracy of atomistic potentials in the prediction of the rate and mechanism of protein folding

Here, we tested different force fields for their ability to quantitatively predict protein folding kinetics.  This test could not be done without Folding@Home and lends insight into the relative predictive quality of force fields commonly used in computational biology.

Role:  PI

 

11.  Google, Inc                                                                                 2002-2003

Folding@Home

This gift from Google helped pay for the initial computational infrastructure for Folding@Home.

Role:  PI

 

12.  Stanford Terman Fellowship                                                   2002-2005

This work helped fund second generation  Folding@Home infrastructure and the related scientific calculations.

Role:  PI

 

13.  NSF MRSEC CPIMA III (Curt Frank, PI)                             2002-2006

As part of CPIMA, our work has centered on new methods for long timescale simulation, especially to simulate lipid vesicle fusion.

Role:  Co-PI

 

14.  Stanford Bio-X (Scott Delp, PI)                                               2003-2006

How Myosin V Walks: 3D Simulation Brings Life to Atomic Structures of Motor Proteins

Here, we proposed to combine methods from computational biology and mechanical engineering to study the motion of myosin.

Role:  Co-PI

 

15.  Stanford Bio-X  (Seb Doniach, PI)                                          2003-2006

Counterion-Induced Forces in the Folding of RNA

We propose to combine novel experimental and computational methods to study the nature of the counterion atmosphere around nucleic acids.

Role:  Co-PI

 

16.  NSF MCB-0317072                                                                   09/01/03 – 08/31/08

Studying the Role of Water Dynamics on the Protein Folding Mechanism Using Worldwide Distributed Computing         

The goal of this project is to use massively explicit solvation simulation to study the role of water in protein folding.  In particular, does water play a structural role in the transition state for protein folding?

Role:  PI

 

17.  The Camille and Henry Dreyfus Foundation, Inc.               06/01/03 – 05/31/08               

New Methods for the Simulation of the Kinetics and Thermodynamics of Biological Molecules

The goal of this project is centered on new applications of distributed computing, including novel ways to use distributed molecular dynamics for long timescale simulation.

Role:  PI

 

18.  NIH 5 PO1 GM066275 (Daniel Herschlag, PI)                      06/06/03 – 05/31/08   

Folding of the Tetrahymena Group 1 Ribozyme

The goal of this project is to address the mechanism by which the RNA folds to active and inactive structures using a battery of physical approaches.  Dr. Pande is one of many investigators in this Program Project Grant (PPG).

Role:  Other Investigator

 

19.  NIH 5 RO1 AR051582 (Teri Klein, PI)                                   08/05/04 – 06/30/08    

Linking Collagen Genotypes to Molecular Phenotypes

The goal of this project is to link genotypes for patients with collagen-related diseases to molecular phenotypes, such as the nature of how collagen self-assembles or its final structure.

Role:  Co-PI

 

20.  Acumen Pharmaceuticals                                                         02/01/05 – 03/30/07               

The Molecular Dynamics of Formation and the Structure of Soluble Amyloid Beta 1-42 Oligomers

The goal of this project is to simulate the formation kinetics and structure of Abeta oligomers, to predict interesting small molecules to slow or break the formation of oligomers, and compare these results to experiment.

Role:  PI

 

21.  Loveless Fund (Stanford)                                                         2006-2007

Combining Xray crystallography and novel computational methods for the discovery small molecule inhibitors of cytokine signaling

We propose novel methods to design inhibitors of protein-protein interactions relevant for asthma and then to assay these molecules experimentally to test our methods.

Role:  PI

 

22.  BioX IIP (Stanford)                                                                   2006-2008

Mapping the functional surface of the ribosome exit tunnel with novel antibiotics: a combined approach using computational design, chemo-biosynthesis, and experimental characterization

This proposal combines novel synthesis, computational, and experimental characterization methods to discover new small molecule antibiotics.

Role:  PI

 

23.  NSF MURI Instrumentation (Michael Levitt, PI)                 2006-2009

MURI: Hybrid Shared-Memory/Massively-Parallel Commodity Cluster for Cost-Effective Super-Computing  (Co-PI)

This is an instrumentation proposal to bring a next generation supercomputer to Stanford.

Role:  Co-PI

 

24.  NIH 2 RO1 GM062868                                                              07/01/06 – 06/30/10   

Oligomerization, confinement and the folding barrier

This grant continues previous work on studying protein folding with implicit solvent models and distributed computing by including simple models for confinement and studies of oligomerization concurrent with folding.

Role:  PI

 

25.  NSF  CHE-0535616                                                                   08/15/05 – 07/31/10   

Collaborative Research:  Cyberinfrastructure for Next Generation Biomolecular Modeling

The goal of this project is to devise better force fields for free energy calculation, centered around the AMOEBA polarizable force field.

Role:  Co-PI

 

26.  CPIMA IV (Stanford)                                                                2002-2006

This is an NSF MRSEC to study polymers at interfaces.  This grant supports our work on lipid membranes

Role: Co-PI

 

27.  NIH Nanomedicine Center (Judith Frydman, PI)                 09/30/05 – 09/29/11

Center for Protein Folding Machinery           

The goal of this project is to support our work on studying chaperones in all-atom detail.

Role:  Other Investigator

 

29.  NSF FIBR EF-0623664                                                              2006-2011

How do proteins fold into their native and functional structures in-vitro and in the physiological milieu of the living cell?

This is a large, multi-group proposal combining single molecule fluorescence, biological expertise in ribosomes and mitochondrial channels, and computational methods to study protein folding in vivo.

Role:  Co-PI (Primary Stanford PI)

 

 

 

ACTIVE

29.  NIH  U54 GM072970 (Russ Altman, PI)                                  06/06/03 – 10/31/14

Physics-Based Simulation of Biological Structures

The goal of this project is to establish and lead the National Center for Physics-Based Simulation of Biological Structures (SimBioS).  This grant will fund work on normal mode langevin dynamics with applications to Myosin dynamics and RNA folding.

Role:  Other Investigator

 

30.  NSF DMS-0900700                                                                   2009-2013

Qualitative Analysis of Molecular Dynamical Systems

This proposal centers on mathematical methods for the analysis of protein folding trajectories.

Role:  PI

 

31.  NIH 2 RO1 GM062868                                                              04/01/11 – 03/31/15   

Oligomerization, confinement and the folding barrier

This grant continues previous work on studying protein folding with implicit solvent models and distributed computing by including simple models for confinement and studies of oligomerization concurrent with folding.

Role:  PI

 

32.  NSF MCB 0954714                                                                   02/01/10 – 01/31/15   

Development and application of a multi-scale markov model for simulating protein folding

Role: PI, Stanford

This project seeks to develop a novel scheme for Markov State Models (MSMs), applying ideas from multiscale simulation. Specifically, we will develop MSMs which can combine results from multiple models in order to gain significantly in computational efficiency without any loss in accuracy; also, when applied to a given application area, these methods can also give us direct insight into which chemical details are important as well as which simulation methods are most applicable. The aims of this proposal are to develop multi-scale MSM creation methodology, test the methodology, and then apply it to the thermodynamics and kinetics of folding in vitro in order to understand which chemical details are important for this process in vitro.

 

33.  NIH 1R01GM097463-01A1 (Sebastian Doniach, PI)             2012-2016

Tracking conformational states in enzyme catalysts using correlated x-ray scatter

 

34.  NIH 1R01GM101935-01            (Jesus Izaguirre, PI)                         2012-2016

Enabling long timestep molecular dynamics on parallel CPU and GPU environments

 

 

 

 

Last updated on Sunday, November 17, 2013