David A. Case
Dept. of Molecular Biology
The Scripps Research Institute
La Jolla, California

Monday, November 11, 2002
3:00 pm (CT)
3269 Beckman Institute

Abstract

It is often useful in computer simulations to use a simple description of solvation effects, instead of explicitly representing the individual solvent molecules. Continuum dielectric models often work well in describing the thermodynamic aspects of aqueous solvation, and approximations to such models that avoid the need to solve the Poisson-Boltzmann equation are attractive because of their computational efficiency. I will discuss on approach, the generalized Born model, which is simple and fast enough to be used for molecular dynamics simulations of proteins and nucleic acids. Strengths and weaknesses will be discussed, both for fidelity to the underlying continuum model, and for the ability to replace explicit consideration of solvent molecules in macromolecular simulations. The focus will be on versions of the generalized Born model that have a pairwise analytical form, and therefore fit most naturally into conventional molecular mechanics calculations. I will discuss both static energetic analysis and molecular dynamics simulations using the new methods.

Tea and coffee will be served in R3151 Beckman Institute at 2:15pm.