Past Event: Oden Institute Seminar

Protein Folding and the Blue Gene Project: A Retrospective

Jed Pitera,

Abstract

In late 1999, the IBM Corporation announced a five-year research program to develop a massively parallel computer architecture, Blue Gene, which would be used to simulate biomolecular processes such as protein folding. Over a decade later, Blue Gene has gone from a research vision to a real product, with Blue Gene/L and Blue Gene/P systems deployed in supercomputer centers around the world and work continuing on the next generation of Blue Gene systems. On October 7, 2009, the Blue Gene Project was awarded the U.S. National Medal of Technology and Innovation. The Blue Gene project was not just a hardware design effort, but also included a science program focused on using Blue Gene systems to study protein folding and membrane protein dynamics. In this talk, I will describe some of the protein folding research we carried out using Blue Gene systems, starting from initial implicit solvent peptide folding studies and force field tests and extending to large-scale explicit solvent simulations of folding thermodynamics and kinetics. The insights gleaned from these simulations have helped refine our view of folding from a directed reaction along a single coordinate to a stochastic process with a diversity of paths. As in any science project, there were good ideas, bad ideas, successful and unsuccessful experiments, and this presentation will emphasize the lessons we learned along the way. *Refreshments served at 2:15.