Structural Insight into RNA Hairpin Folding Intermediates
Gregory R. Bowman, Xuhui Huang, Yuan Yao, Jian Sun, Gunnar Carlsson, Leonidas J. Guibas, and Vijay S. Pande J. Am. Chem. Soc., 130 (30), 9676–9678, 2008 ABSTRACT. Hairpins are a…
Read moreAuthor: Viktor
Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment.
Xuhui Huang,Gregory R. Bowman,and Vijay S. Pande J Chem Phys. 2008 May 28;128(20):205106. ABSTRACT.We have implemented the serial replica exchange method (SREM) and simulated tempering (ST) enhanced sampling algorithms in…
Read moreCalculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics
Nina Singhal Heinrichs and Vijay S. Pande. Journal of Chemical Physics (2007) SUMMARY. This paper lays out how one can revamp FAH calculations to make them considerably more efficient, perhaps…
Read moreHeterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece
D. Ensign, P. M. Kasson, and V. S. Pande. Journal of Molecular Biology (2007) SUMMARY: This paper describes the first set of results generated using the SMP clients. The main…
Read moreControl of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics.
P. M. Kasson and V. S. Pande. PLoS Computational Biology (2007) SUMMARY: Here, we use molecular molecular-dynamics simulations of lipid vesicle fusion under different lipid compositions to generate a more…
Read morePersistent voids: a new structural metric for membrane fusion.
P. M. Kasson, A. Zomorodian, S. Park, N. Singhal, L. J. Guibas, and V. S. Pande. Bioinformatics (2007) SUMMARY: One challenge in analyzing membrane fusion pathways is simply characterizing the…
Read moreProtein folding under confinement: a role for solvent.
D. Lucent, V. Vishal, V. S. Pande. Proceedings of the National Academy of Sciences (2007) Local PDF SUMMARY: When proteins fold inside a cell, they are frequently subjected to various…
Read moreAutomatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics.
J. Chodera, N. Singhal, V. S. Pande, K. Dill, and W. Swope. Journal of Chemical Physics, (2007) SUMMARY: In order to break up calculations to run on Folding@home and then…
Read moreStorage@home: Petascale Distributed Storage
Adam L Beberg and Vijay S. Pande. IPDPS (2007) SUMMARY: Storage@home is a distributed storage infrastructure developed to solve the problem of backing up and sharing petabytes of scientific results…
Read moreN-Body simulation on GPUs
Erich Elsen, Mike Houston, V. Vishal, Eric Darve, Pat Hanrahan, and Vijay Pande. Proceedings of the 2006 ACM/IEEE conference on Supercomputing (2006). SUMMARY. This paper details our first efforts with…
Read more