Vijay S. Pande

Scott L. Delp, Joy P. Ku, Vijay S. Pande, Michael A. Sherman, Russ B. Altman: Simbios: an NIH national center for physics-based simulation of biological structures. JAMIA 19(2): 186-189 (2012)

Kai J. Kohlhoff, Marc H. Sosnick, William T. Hsu, Vijay S. Pande, Russ B. Altman: CAMPAIGN: an open-source library of GPU-accelerated data clustering algorithms. Bioinformatics 27(16): 2321-2322 (2011)

Sander Pronk, Per Larsson, Iman Pouya, Gregory R. Bowman, Imran S. Haque, Kyle Beauchamp, Berk Hess, Vijay S. Pande, Peter M. Kasson, Erik Lindahl: Copernicus: a new paradigm for parallel adaptive molecular dynamics. SC 2011: 60

Peter Eastman, Vijay S. Pande: OpenMM: A Hardware-Independent Framework for Molecular Simulations. Computing in Science and Engineering 12(4): 34-39 (2010)

Imran S. Haque, Vijay S. Pande: PAPER - Accelerating parallel evaluations of ROCS. Journal of Computational Chemistry 31(1): 117-132 (2010)

Peter Eastman, Vijay S. Pande: Efficient nonbonded interactions for molecular dynamics on a graphics processing unit. Journal of Computational Chemistry 31(6): 1268-1272 (2010)

Peter M. Kasson, Erik Lindahl, Vijay S. Pande: Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails. PLoS Computational Biology 6(6) (2010)

Del Lucent, Christopher D. Snow, Colin Echeverría Aitken, Vijay S. Pande: Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel. PLoS Computational Biology 6(10) (2010)

Imran S. Haque, Vijay S. Pande: Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU. CCGRID 2010: 691-696

Xuhui Huang, Yuan Yao, Gregory R. Bowman, Jian Sun, Leonidas J. Guibas, Gunnar Carlsson, Vijay S. Pande: Constructing Multi-Resolution Markov State Models (MSMs) to Elucidate RNA Hairpin Folding Mechanisms. Pacific Symposium on Biocomputing 2010: 228-239

Jesús A. Izaguirre, Christopher R. Sweet, Vijay S. Pande: Multiscale Dynamics of Macromolecules Using Normal Mode Langevin. Pacific Symposium on Biocomputing 2010: 240-251

Peter M. Kasson, Vijay S. Pande: Cross-Graining: Efficient Multi-Scale Simulation via Markov State Models. Pacific Symposium on Biocomputing 2010: 260-268

Edgar Luttmann, Daniel L. Ensign, Vaidyanathan Vishal, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark S. Friedrichs, Vijay S. Pande: Accelerating molecular dynamic simulation on the cell processor and Playstation 3. Journal of Computational Chemistry 30(2): 268-274 (2009)

Mark S. Friedrichs, Peter Eastman, Vaidyanathan Vishal, Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande: Accelerating molecular dynamic simulation on graphics processing units. Journal of Computational Chemistry 30(6): 864-872 (2009)

Adam L. Beberg, Daniel L. Ensign, Guha Jayachandran, Siraj Khaliq, Vijay S. Pande: Folding@home: Lessons from eight years of volunteer distributed computing. IPDPS 2009: 1-8

Adam L. Beberg, Vijay S. Pande: Thalweg: A framework for programming 1, 000 machines with 1, 000 cores. IPDPS 2009: 1-7

Vincent A. Voelz, P. Petrone, Vijay S. Pande: A Multiscale Approach to Sampling Nascent Peptide Chains in the Ribosomal Exit Tunnel. Pacific Symposium on Biocomputing 2009: 340-352

Peter M. Kasson, Vijay S. Pande: Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin. Pacific Symposium on Biocomputing 2009: 492-503

Imran S. Haque, Vijay S. Pande: Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU. CoRR abs/0910.0505 (2009)

Alex Robertson, Edgar Luttmann, Vijay S. Pande: Effects of long-range electrostatic forces on simulated protein folding kinetics. Journal of Computational Chemistry 29(5): 694-700 (2008)

Luca Monticelli, Eric J. Sorin, D. Peter Tieleman, Vijay S. Pande, Giorgio Colombo: Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories. Journal of Computational Chemistry 29(11): 1740-1752 (2008)

Peter M. Kasson, Afra Zomorodian, Sanghyun Park, Nina Singhal, Leonidas J. Guibas, Vijay S. Pande: Persistent voids: a new structural metric for membrane fusion. Bioinformatics 23(14): 1753-1759 (2007)

Peter M. Kasson, Vijay S. Pande: Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics. PLoS Computational Biology 3(11) (2007)

Adam L. Beberg, Vijay S. Pande: Storage@home: Petascale Distributed Storage. IPDPS 2007: 1-6

Peter M. Kasson, Vijay S. Pande: Predicting Structure and Dynamics of Loosely-Ordered Protein Complexes: Influenza Hemagglutinin Fusion Peptide. Pacific Symposium on Biocomputing 2007: 40-50

Erich Elsen, Vaidyanathan Vishal, Mike Houston, Vijay S. Pande, Pat Hanrahan, Eric Darve: N-Body Simulations on GPUs. CoRR abs/0706.3060 (2007)

Erich Elsen, Mike Houston, Vaidyanathan Vishal, Eric Darve, Pat Hanrahan, Vijay S. Pande: Poster reception - N-Body simulation on GPUs. SC 2006: 188

Eric J. Sorin, Vijay S. Pande: Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling. Journal of Computational Chemistry 26(7): 682-690 (2005)

Sanghyun Park, Randall J. Radmer, Teri E. Klein, Vijay S. Pande: A new set of molecular mechanics parameters for hydroxyproline and its use in molecular dynamics simulations of collagen-like peptides. Journal of Computational Chemistry 26(15): 1612-1616 (2005)

Peter M. Kasson, Vijay S. Pande: Computational Simulation of Lipid Bilayer Reorientation at Gaps. CSB 2003: 464-467