High performance computing for the application of molecular theories to biological systems

Abstract

In this paper we summarize our work to bring modern numerical methods to bear in computations for density functional theories (DFTs) of inhomogeneous fluid systems. We present the general mathematical structure of the problem, and briefly discuss different strategies for solving the problems. Finally, we present a few recent results from calculations on complex peptide assemblies in lipid bilayers to demonstrate the application of the methods in one complex 3-dimensional system. We find that while solver strategies developed and optimized for partial differential equations (PDEs) can be applied to these systems of equations, they do not provide optimal solutions with respect to speed, memory use, or parallel partitioning. © 2006 IOP Publishing Ltd.