We present a solver for the Poisson-Boltzmann equation and demonstrate its applicability for biomolecular electrostatics computation. The solver uses a level set framework to represent sharp, complex interfaces in a simple and robust manner. It also uses non-graded, adaptive octree grids which, in comparison to uniform grids, drastically decrease memory usage and runtime without sacrificing accuracy. The ba- sic solver was introduced in earlier works [16, 27], and here is extended to address biomolecular systems. First, a novel approach of calculating the solvent excluded and the solvent accessible surfaces is explained; this allows to accurately represent the loca- tion of the molecule's surface. Next, a hybrid finite difference/finite volume approach is presented for discretizing the nonlinear Poisson-Boltzmann equation and enforcing the jump boundary conditions at the interface. Since the interface is implicitly repre- sented by a level set function, imposing the jump boundary conditions is straightfor- ward and efficient.

Adaptive, finite difference solver for the nonlinear Poisson-Boltzmann equation with applications to biomolecular computations

248th National Meeting (2014)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.