Category: Papers

P. M. Kasson, E. Lindahl, and V. S. Pande. PLoS Computational Biology 6(6): e1000829 (2010). SUMMARY. Membrane fusion is a common underlying process critical to neurotransmitter release, cellular trafficking, and…

Voelz VA, Bowman GR, Beauchamp K, Pande VS. Journal of the American Chemical Society (2010) SUMMARY. Simulating protein folding on the millisecond timescale has been a major challenge for many…

S. Bacallado, J. Chodera, and V. Pande. Journal of Chemical Physics 131, 045106 (2009). SUMMARY. Markov State Models (MSMs) are one of the most common ways to analyze Folding@Home simulations.…

P. M. Kasson, D. L. Ensign, and V. S. Pande. Journal of the American Chemical Society (2009). Published online 2009 July 28. SUMMARY. The influenza virus infects people and animals…

G. R. Bowman and V. S. Pande. PLoS ONE 4(6): e5840 (2009) ABSTRACT. Here we continue our efforts to use methods developed in the folding mechanism community to both better…

G. R. Bowman, X. Huang, and V. S. Pande. Methods 49(2): 197-201 (2009) ABSTRACT Part of understanding a molecule’s conformational dynamics is mapping out the dominant metastable, or long lived,…

A. Beberg and V. S. Pande. ipdps, pp.1-8, IEEE International Symposium on Parallel & Distributed Processing (2009) ABSTRACT Accurate simulation of biophysical processes requires vast computing resources. Folding@home is a…

V. A. Voelz, E. Luttmann, G. R. Bowman, and V.S. Pande. International Journal of Molecular Sciences 10(3): 1013 (2009) ABSTRACT Recently a temperature-jump FTIR study of a designed three-stranded sheet…

Vincent A. Voelz, Paula Petrone and Vijay S. Pande. Pacific Symposium on Biocomputing, 14:340-352 (2009) ABSTRACT We present a new multiscale method that combines all-atom molecular dy- namics with coarse-grained…

D. L. Ensign and V. S. Pande. Biophysical Journal 96 L53-55 (2009) ABSTRACT. We describe molecular dynamics simulations resulting in the folding the Fip35 Hpin1 WW domain. The simulations were…