Simbios Talk by Vince Voelz, Stanford University, November 4, 2009

Title: Using distributing computing and GPU simulation to study protein unfolded states and folding dynamics

Accelerated molecular dynamics simulations on GPUs can now access longer time scales than ever before. I will discuss two projects in which GPU simulation, along with distributed computing via Folding@Home platform, played a key role. First, I will present work characterizing unfolded state structure and dynamics of protein L using a combination of molecular simulation and intramolecular Trp-Cys quenching experiments. Next, I will describe landmark ab initio folding simulations of a millisecond folder, NTL9(1-39). Markov State Models (MSMs) built from the larger body of simulation data yield important mechanistic insights into how this protein folds. This work opens the door for using MSM construction and adaptive resampling to achieve statistically converged descriptions of folding landscapes at longer time scales than ever before.