Applied and Computational Mathematics Seminar
Monday, November 10, 2008 - 13:00
1 hour (actually 50 minutes)
Solvation process is of fundamental importance to other complex biological processes, such signal transduction, gene regulation, etc. Solvation models can be roughly divided into two classes: explicit solvent models that treat the solvent in molecular or atomic detail while implicit solvent models take a multiscale approach that generally replaces the explicit solvent with a dielectric continuum. Because of their fewer degrees of freedom, implicit solvent methods have become popular for many applications in molecular simulation with applications in the calculations of biomolecular titration states, folding energies, binding affinities, mutational effects, surface properties, and many other problems in chemical and biomedical research. In this talk, we introduce a geometric flow based multiscale solvation model that marries a microscopic discrete description of biomolecules with a macroscopic continuum treatment of the solvent. The free energy functional is minimized by coupled geometric and potential flows. The geometric flow is driven not only by intrinsic forces, such as mean curvatures, but also by extrinsic potential forces, such as those from electrostatic potentials. The potential flow is driven mainly by a Poisson-Boltzmann like operator. Efficient computational methods, namely the matched interface and boundary (MIB) method, is developed for to solve the Poisson- Boltzmann equation with discontinuous interface. A Dirichlet- to-Neumann mapping (DTN) approach is developed to regularize singular charges from biomolecules.