Collaborative Research: Advanced Methodology for Calculation of Pairwise Interactions

普渡大学的Robert Skeel和伊利诺伊大学厄巴纳-香槟分校的Klaus Schulten获得了《理论、模型和计算方法》的合作奖。该项目侧重于创建、分析和实现广泛适用于计算原子计算机模拟中的成对原子相互作用的方法，并将其应用于化学、物理和材料科学。大分子、生物分子、纳米系统和原子或分子系统的缩合相的原子模拟需要大量的计算机时间。通常，大部分时间都花在计算粒子之间的成对相互作用上。对相互作用的计算可以直接进行，也可以使用快速多极法或粒子网格埃瓦尔德和等标准工具进行。本提案将研究一种不太为人所知的O(N)算法，即多层求和法（MSM）的优点。这种算法有潜力成为非常有用的方法，如分子动力学。该项目将探索涉及数学技术的创造性实现，以改进软件，并探索在新兴硬件（如gpu）中的实现。本文的目标是研究MSM在多个跨学科分子动力学问题中的效率和可扩展性，分析近似的理论和实验意义，并实现和传播结果。该项目为研究生提供了从事高影响力跨学科研究的机会。将提供作为模块库的算法的开源实现。软件模块也将嵌入到模拟软件中，如NAMD。分子动力学应用于化学之外，n体解算器应用于分子动力学之外。科学家手中更好的方法和软件将使更大系统的化学和生物分子模拟具有更高的准确性，这将给社会带来好处。影响将是广泛的。

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.