Latino Studies at New York University

Kenneth Ho

Computational Biology Program
New York University

May 1, 2012

Doctoral Dissertation Public Defense

Fast direct methods for molecular electrostatics

Electrostatic interactions are vital for many aspects of biomolecular structure and function. In this talk, we describe a fast direct solver for the boundary integral formulation of the linearized Poisson-Boltzmann equation for the electrostatic potential of a solvated macromolecule. Unlike most current methods, our scheme directly constructs the solution operator and so can be far more efficient when the same system must be solved with multiple right-hand sides. We demonstrate an application to protein pKa calculations and outline several more in charge optimization, structure prediction, and docking. Our solver is general and applies to many non-oscillatory integral kernels such as those for the Laplace, low-frequency Helmholtz, and Stokes equations.