A fast N-body solver for the Poisson(-Boltzmann) equation
Presenter
December 11, 2008
Keywords:
- Poisson-Boltzmann equation
MSC:
- 31A30
Abstract
Descriptions of implicit solvent models like the Poisson-Boltzmann
equation express the electrostatic potential as the solution of an
elliptic PDE with delta function source terms. These equations are
particularly good fits with iterative solvers that use a fast N-body
solver as a preconditioner. Also, modern architectures favor such
algorithms due to their high ratio of floating-point operations
to memory references. Two types of N-body solvers can be distinguished:
hierarchical-clustering algorithms, such as the celebrated
fast multipole method, and kernel-splitting algorithms,
such as the popular particle--mesh Ewald method.
By formulating the problem as that of computing a matrix--vector
product, the basic structure of these algorithms is elucidated.
Additionally, evidence is presented indicating
that kernel-splitting algorithms are much to be preferred
for molecular simulations and that the virtually unknown multilevel
summation method of Brandt and Lubrecht is the best among these.
This method uses hierarchical interpolation of interaction potentials
on nested grids to calculate energies and forces in linear time
for both periodic and nonperiodic boundary conditions.
This is joint work with David Hardy. Its application to the
Poisson(-Boltzmann) equation is being pursued in a collaboration
with Stephen Bond.