Title: Numerical Methods for Coarse-Grained Molecular Systems Speaker: Eric Cyr, University of Illinois, Urbana Champaign Date/Time: Wednesday, July 23, 2008, 9:30 AM Location: CSRI Building, Room 90 (Sandia NM) Brief Abstract: We present algorithms for two distinct, but related, forms of coarse grained molecular systems. The first form reduces a fully explicit solvent-solute system to an explicit solute in an implicitly represented solvent environment. The critical step in this reduction is to solve a PDE known as the Poisson-Boltzmann equation. Our approach is to develop algorithms that accurately compute the solvation free energy by using goal-oriented refinement in this context are presented. The second form of coarse graining computes the Potential of Mean Force (PMF) along a prescribed reaction coordinate. We described algorithm to calculate the PMF based on both solving a simple differential equation and applying techniques in density estimation. Using empirical results, the error and convergence properties of these methods are compared.CSRI POC: Ray Tuminaro, (925) 294-2564 |