Simbios Talk by Patrice Koehl, Dept. of Computer Science and Genome Center, UC Davis, February 20, 2008

Title: Understanding Electrostatics: Beyond the Poisson-Boltzmann view

Electrostatics plays an important role in stabilizing a molecule. In implicit solvent models, the electric field generated by a molecule is obtained as a solution of the Poisson-Boltzmann equation (PBE), a second order elliptic equation solved over the whole space within and around the molecule. Analytical solutions of this equation are not available for large molecules. Numerical solutions are usually obtained using finite difference methods on regular meshes. In the first part of the talk, I will describe a new PBE solver, Aqua.
In the second part of the talk, I will describe a new way to calculate the electrostatics properties of macromolecules that goes beyond the classical PBE. The solvent region is no longer modeled as an homogeneous dielectric media but rather as an assembly of self-orienting dipoles of variable density. This new model unifies the Poisson-centric view and the Langevin dipole model, yielding a Generalized Poisson-Boltzmann Langevin (GPBL) equation.