Speaker: Dr. Nathan Baker
From: Departments of Biochemistry & Molecular Biophysics, Washington University - St. Louis
Date / Time / Room: Thursday, April 27, 2006 / 4:00 PM / 140 DeBartolo Hall
Tea: 3:30 PM

Title:Computational Molecular Biophysics at Broad Range of Ttime Scales

Abstract: One of the long standing problems in computer simulations of biochemical function is of time scales. Straightforward molecular dynamics approaches are restricted to time scales which are below microseconds, far shorter than the time scale of many interesting biophysical processes. I shall discuss path finding approaches that provide unique view into atomically detailed mechanisms of biological function at extended timescales. These approaches are based on boundary value, action formulation of classical mechanics and they make it possible to take very large integration steps. The large integration step provides approximate trajectories and hierarchy of approximations which are not possible using straightforward Molecular Dynamics. This technique is especially useful to study mechanisms when the two end states are known, regardless of the time scale of the process. I will present the following concrete examples: (i) ion transport in the gramicidin channel (hundreds of nanoseconds), and (ii) the folding of the proteins: protein A and cytochrome c (milliseconds)