This proposal centers on the creation, analysis, and implementation of methods of broad applicability and unsurpassed effectiveness for calculating pairwise interactions arising in time-consuming simulations in chemistry, particularly molecular dynamics.
Molecular simulations of scientific interest require vast amounts of computer time, and the bulk of this time is typically spent on calculating pairwise interactions between particles. It is currently not feasible to do simulations of the duration or scale needed for many scientific investigations. Additionally, current models are often compromised based on the features and strengths of existing N-body solvers. In particular, the lack of an efficient solver for nonperiodic boundaries discourages the use of solvent boundary potentials as well as the use of implicit solvent models based on the Poisson equation. These shortcomings of current N-body technology will be addressed by the developments described below.
Typically, the calculation of pairwise interactions
is done either directly or with standard tools like the
fast Fourier transform (or the fast multipole method). For many of these
problems there exists a less well known O(
Last updated 2014-6-22