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| Vijay Pande, Stanford University |
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Prof. Pande's current research centers on the development and application of novel grid computing simulation techniques to address problems in chemical biology. In particular, he has pioneered novel distributed computing methodology to break fundamental barriers in the simulation of kinetics and thermodynamics of proteins and nucleic acids. As director of the Folding@Home project http://folding.stanford.edu, Prof. Pande has, for the first time, directly simulated protein folding dynamics with quantitative comparisons with experiment, often considered a "holy grail" of computational biology. His current research also includes novel simulation methods for high precision drug binding affinity calculations, protein design, and synthetic bio-mimetic polymers.
Prof. Pande received a BA in Physics from Princeton University in 1992. There, he was first introduced to biophysical questions, especially in his undergraduate thesis research with Prof. Philip Anderson, a Nobel Laureate in physics. In 1995, he received his PhD in physics from MIT, studying as a NSF Fellow under Profs. Toyoichi Tanaka and Alexander Grosberg. At MIT, Prof. Pande's research centered on statistical mechanical models of protein folding and design, suggesting novel ways to design protein sequences to have the desired stability and folding properties. As a Miller Fellow working with Prof. Daniel Rokhsar at UC Berkeley, Prof. Pande extended this methodology to examine atomistic protein models, laying the foundations for his later work at Stanford University.
Prof. Pande has won numerous awards, including most recently being named to MIT's TR100 (top young innovators in 2002), a Frederick E. Terman Fellowship (2002), a Henry and Camile Dreyfus Teacher-Scholar (2003), and the MIT Indus Global Technovator's Award. Prof. Pande is currently an Assistant Professor of Chemistry and (by courtesy) of Structural Biology.
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Folding@Home: Using worldwide desktop grid computing to break fundamental barriers in molecular simulation
Vijay Pande, Stanford University
Simulations of biological molecules offers a lot of promise to complement and extend current experiments in the areas of biophysics and biomedicine. However, there are some serious limitations that must be overcome before computational methods are universally accepted. For example, one must be able to examine time scales that are thousands to billions of times longer than most typical simulations. How can one surmount such fundamental computational barriers? I will discuss our solutions to this problem, which combine novel physical chemistry theory and computational paradigms. In addition, I will discuss recent applications of these methods to fundamental questions in biophysics and biomedical applications, including protein folding, protein-protein association, protein-ligand binding, and protein misfolding & aggregation.
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