Joint Biochemistry / Chemical Physics Seminar

David E. Shaw

D. E. Shaw Research and 

Center for Computational Biology and Bioinformatics, Columbia University

Molecular dynamics (MD) simulation has long been recognized as a potentially powerful tool for understanding the structural, dynamic, and functional characteristics of proteins at an atomic level of detail. Many biologically important phenomena, however, occur over timescales that have previously fallen far outside the reach of MD technology. We have constructed a specialized, massively parallel machine, called Anton, that is capable of performing all-atom simulations of proteins in an explicitly represented solvent environment at a speed roughly two orders of magnitude beyond that of the previous state of the art. Using novel algorithms developed within our lab, the machine has now simulated the behavior of a number of proteins for periods as long as two milliseconds -- approximately 200 times the length of the longest such simulation previously published. Such simulations have allowed us to observe and analyze key characteristics of the dynamics of proteins (including central elements of the process of protein folding) that were previously inaccessible to both computational and experimental study.