Multiscale methods for biomolecular electrostatics and diffusion

Nathan Baker
Washington University in St. Louis
Department of Biochemistry and Molecular Biophysics

Solvent plays an important role in nearly every aspect of biomolecular structure, function, and dynamics. However, the accurate treatment of solvation in molecular simulation is a particularly daunting theoretical and algorithmic challenge. While all-atom explicit representations potentially offer the most accurate solvation model, they are limited by the computational expense of adequate sampling over the thousands of solvent degrees of freedom. Continuum models of solvation, particularly those described by the Poisson and Poisson-Boltzmann equations, provide appealing alternatives to the requirements of explicit solvent simulations. We have developed several methods for quickly solving these equations and providing polar solvation energies and forces for molecular simulation. I will describe some of the details of these methods and their application to coarse-grained diffusion modeling of bimolecular association. Additionally, I will present preliminary work on the critical comparison of polar and nonpolar implicit solvent models to mean forces obtained from explicit solvent simulations. This comparison demonstrates some of the strengths and weaknesses of implicit solvent approaches and suggests possible ways to improve these coarse-grained models.

Presentation (PowerPoint File)

Back to Workshop I: Multiscale Modeling in Soft Matter and Bio-Physics