分野別セミナー

Electrostatic effects play an important role in determining protein structure and function. Here we present a treecode-accelerated boundary integral (TABI) solver for the electrostatic potential of a solvated protein described by the linear Poisson-Boltzmann equation. In this model the solvent is a continuum dielectric material with ionic screening. The treecode reduces the computational cost from $O(N^2)$ to $O(N\log N)$, where $N$ is the number of faces in the triangulated molecular surface. We compare TABI results to those obtained using the grid-based APBS code. The TABI solver exhibits good serial and parallel performance, with relatively simple implementation, efficient memory usage, and geometric adaptability. This is joint work with Weihua Geng (Southern Methodist University).