Large-scale Chemical Informatics on the GPU.
I. Haque and V. S. Pande. GPU Computing Gems (2010)
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Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU.
I. Haque and V. S. Pande. Resilience (2010) SUMMARY. GPU computing has great potential, but consumer GPUs lack some key features that are present in CPUs, especially error checking RAM.…
Read moreEverything you wanted to know about Markov State Models but were afraid to ask.
V. S. Pande, K. Beauchamp, and G. R. Bowman. Methods (2010) ABSTRACT. Simulating protein folding has been a challenging problem for decades due to the long timescales involved (compared with…
Read moreProtein folded states are kinetic hubs.
G. Bowman and V. S. Pande. Proceedings of the National Academy of Sciences, USA 107 10890-10895 (2010) ABSTRACT. Understanding molecular kinetics, and particularly protein folding, is a classic grand challenge…
Read moreEnhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models.
G. Bowman and V. S. Pande. Journal of Computational and Theoretical Chemistry 6 787–794 (2010) ABSTRACT. Computer simulations can complement experiments by providing insight into molecular kinetics with atomic resolution.…
Read moreOpenMM: A Hardware Abstraction Layer for Molecular Simulations.
P. Eastman and V. S. Pande. Computing in Science and Engineering 12 34-39 (2010) SUMMARY. OpenMM is the key library which powers GPU computing in Folding@home. This paper discusses some…
Read moreCurrent Status of the AMOEBA Polarizable Force Field.
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. J. Phys. Chem. B., 114 2549-2564…
Read moreUnfolded state dynamics and structure of protein L characterized by simulation and experiment.
V. Voelz, V. Singh, W. J. Wedemeyer, L. Lapidus, and V. S. Pande. Journal of the ACS, 132 4702–4709 (2010) ABSTRACT. While several experimental techniques now exist for characterizing protein…
Read moreNetwork models for molecular kinetics and their initial applications to human health.
G. Bowman, X. Huang, and V. S. Pande. Cell Research 20 622-630 (2010) ABSTRACT. Molecular kinetics underlies all biological phenomena and, like many other biological processes, may best be understood…
Read moreWater Ordering at Membrane Interfaces Controls Fusion Dynamics
Peter M. Kasson, Erik Lindahl, and Vijay S. Pande. Journal of the American Chemical Society (2011) Epub 25 Feb. SUMMARY. Building on our previous simulations of membrane fusion, we have…
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