Validation of the PyGBe code for Poisson-Boltzmann equation with boundary element methods

2013-01-30T19:44:29Z (GMT) by Christopher Cooper Lorena A. Barba
<p>The PyGBe code solves the linearized Poisson-Boltzmann equation using a boundary-integral formulation. We use a boundary element method with a collocation approach, and solve it via a Krylov-subspace method. To do this efficiently, the matrix-vector multiplications in the Krylov iterations are accelerated with a treecode, achieving O(N log N) complexity. The code presents a Python environment for the user, while being efficient and fast. The core computational kernels are implemented in Cuda and interface with the user-visible code with PyCuda, for maximum ease-of-use combined with high performance on GPU hardware. This document provides background on the model and formulation of the numerical method, evidence of a validation exercise with well-known benchmarks---a spherical shell with a centered charge and one with an off-center charge--- and a demonstration with a realistic biological geometry (lysozyme molecule)</p> <p> </p> <p><strong>Acknowledgement</strong></p> <p>This research is made possible by support from the Office of Naval Research, Applied Computational Analysis Program. LAB also acknowledges support from NSF CAREER award OCI-1149784.</p> <p> </p>