Collaborative Research: Advanced Methodology for Calculation of Pairwise Interactions

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Robert Skeel of Purdue University and Klaus Schulten from University of Illinois Urbana-Champain have received a collaborative award from the Theory, Models and Computational Methods. The project focuses on the creation, analysis, and implementation of methods of broad applicability for calculating pairwise interatomic interactions in atomistic computer simulations with applications in chemistry, physics, and materials science.Atomistic simulations of macromolecules, biomolecules, nano-systems, and condensed phases of atomic or molecular systems require vast amounts of computer time. Typically, the bulk of this time is spent on calculating pairwise interactions between particles. The calculation of pairwise interactions is done either directly or with standard tools like the fast multipole method or the particle-mesh Ewald sums. This proposal will investigate the advantages of a less well known O(N) algorithm, the multilevel summation method (MSM). This algorithm has the potential of becoming very useful for approaches such as molecular dynamics. The project will explore creative implementations involving mathematical techniques for improving the software and exploring implementation in emerging hardware like GPUs. It is the objective of the proposal to study the efficiency and scalability of MSM as applied to several interdisciplinary molecular dynamics problems, to analyze the implication of approximations both theoretically and experimentally, and to implement and disseminate the results.The project provides an opportunity for graduate students to engage in high-impact interdisciplinary research. Open source implementations of the algorithms as libraries of modules will be made available. The software modules will also be embedded in simulation software such as NAMD. Molecular dynamics has applications beyond chemistry, and N-body solvers have applications outside of molecular dynamics. Better methods and software in the hands of scientists will enable chemical and biomolecular simulations of much larger systems with improved accuracy, and this will result in benefits to society. The impact will be broad.