Vijay Pande

Simulating vesicle fusion on Blue Waters

(jn9)
Sep 2016 - Aug 2017

2018

Evan N. Feinberg, Debnil Sur, Zhenqin Wu, Brooke E. Husic, Huanghao Mai, Yang Li, Saisai Sun, Jianyi Yang, Bharath Ramsundar, and Vijay S. Pande (2018): PotentialNet for Molecular Property Prediction, ACS Central Science, American Chemical Society, Vol 4, Num 11, pp1520-1530

2017

Matthew P. Harrigan, Keri A. McKiernan, Veerabahu Shanmugasundaram, Rajiah Aldrin Denny, and Vijay S. Pande (2017): Markov Modeling Reveals Novel Intracellular Modulation of the Human TREK-2 Selectivity Filter, Scientific Reports, Springer Nature, Vol 7, Num 1

2016

Sheel C. Dodani, Gert Kiss, Jackson K. B. Cahn, Ye Su, Vijay S. Pande, and Frances H. Arnold (2016): Discovery of a Regioselectivity Switch in Nitrating P450s Guided by Molecular Dynamics Simulations and Markov Models, Nature Chemistry, Nature Publishing Group, Vol 8, Num 5, pp419-425
Diwakar Shukla, Ariana Peck, and Vijay S. Pande (2016): Conformational Heterogeneity of the Calmodulin Binding Interface, Nature Communications, Nature Publishing Group, Vol 7, pp10910

2014

Kai J. Kohlhoff, Diwakar Shukla, Morgan Lawrenz, Gregory R. Bowman, David E. Konerding, Dan Belov, Russ B. Altman, and Vijay S. Pande (2014): Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways, Nature Chemistry, Springer Nature Limited, Vol 6, Num 1, pp15-21
Lee-Ping Wang, Alexey Titov, Robert McGibbon, Fang Liu, Vijay S. Pande, and Todd J. Martinez (2014): Discovering Chemistry with an Ab Initio Nanoreactor, Nature Chemistry, Nature Publishing Group, Vol 6, Num 12, pp1044-1048

2017

Vijay Pande (2017): Machine Learning Reveals Ligand-Directed Conformational Change of μ Opioid Receptor, 2017 Blue Waters Annual Report, pp230-231

2016

Vijay Pande (2016): Allosteric Selectivity and Drug Binding Pathway of µ-Opioid Receptors, 2016 Blue Waters Annual Report, pp230-231

2015

Vijay Pande (2015): Understanding P53, A Protein “Shape Shifter” Responsible for Many Cancer Tumors, 2015 Blue Waters Annual Report, pp164-165

Morgan Lawrenz: Simulating vesicle fusion on Blue Waters


Blue Waters Symposium 2014, May 14, 2014

(Cloud + super) computing = results


Oct 29, 2014

Can cloud computing replace supercomputers like Blue Waters in the future? No, says Vijay Pande, director of the biophysics program at Stanford University. He says both are critical to his study of serious diseases like Alzheimer's and cancer. Pande's lab uses cloud computing through Folding@home and Google Exacycle to run many detailed molecular dynamics (MD) simulations of protein folding independent of one another. "A lot of what we do is run the raw trajectories on Folding@home, or Google Exacycle, analyze it on Blue Waters, and spit it back out to Folding@home," says Pande.


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NSF awards time on Blue Waters to seven new projects


Oct 1, 2014

The National Science Foundation (NSF) has awarded 14 new allocations on the Blue Waters petascale supercomputer at the National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign. Seven of the awards are for new projects.


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A Heterogeneous Approach to Molecular Dynamics


May 22, 2014

As director of the biophysics program at Stanford University, Vijay Pande understands that cloud is no replacement for supercomputers like the petascale Blue Waters machine, but the scientist is having success using loosely-coupled cloudy cores for molecular dynamics research. Pande has been using the Blue Waters system at the National Center for Supercomputing Applications (NCSA) to study protein folding errors to determine which errors are correlated with diseases like Alzheimer’s, Parkinson’s, Mad Cow disease and many cancers.


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