TY - JOUR
T1 - Efficient solution of poisson-boltzmann equation for electrostatics of large molecules
JF - High-Performance Computing Symposium (April 2004)
Y1 - 2004
A1 - Hao,X.
A1 - Varshney, Amitabh
AB - Development of fast computational methods to solve thePoisson-Boltzmann equation (PBE) for molecular elec- trostatics is important because of the central role played by electrostatic interactions in many biological processes. The accuracy and stability of the solution to the PBE is quite sensitive to the boundary layer between the sol- vent and the solute which defines the solvent-accessible surface. In this paper, we propose a new interface- layer-focused PBE solver for efficiently computing the electrostatic potential for large molecules. Our method analytically constructs the solvent-accessible surface of molecules and then builds nested iso-surface layers out- wards and inwards from the surface using the distance field around the surface. We then develop a volume sim- plification algorithm to adaptively adjust the density of the irregular grid based on the importance to the PBE solution. We also generalize finite difference methods on our irregular grids using Taylor series expansions. Our algorithm achieves about three times speedup in the iter- ative solution process of PBE, with more accurate results on an analytical solvable testing case, compared with the popular optimized DelPhi program. Our approach can also be applied directly to solve partial differential equa- tions arising in other application domains.
ER -