Collaborative Research: Advanced Methodology for Calculation of Pairwise Interactions

普渡大学的罗伯特·斯基尔和伊利诺伊大学厄巴纳-香槟分校的克劳斯·舒尔滕获得了理论、模型和计算方法合作奖。该项目致力于在原子计算机模拟中创建、分析和实现广泛适用的计算原子间相互作用的方法，这些方法在化学、物理和材料科学中的应用。对大分子、生物分子、纳米系统和原子或分子系统的凝聚相的原子模拟需要大量的计算机时间。通常，大部分时间花在计算粒子之间的成对相互作用上。成对相互作用的计算要么直接完成，要么使用标准工具，如快速多极子方法或粒子网格Ewald和。该提案将研究一种不太为人所知的O(N)算法--多级求和法(MSM)的优点。这种算法有可能成为非常有用的方法，如分子动力学。该项目将探索创造性的实现，涉及改进软件的数学技术，并探索在新兴硬件(如GPU)中的实现。该计划的目的是研究MSM应用于几个跨学科分子动力学问题的效率和可扩展性，从理论和实验两个方面分析近似的含义，并实施和传播结果。该项目为研究生提供了一个从事高影响力跨学科研究的机会。将提供作为模板库的算法的开源实现。软件模块还将嵌入到NAMD等仿真软件中。分子动力学有化学以外的应用，N体解算器也有分子动力学以外的应用。科学家手中掌握的更好的方法和软件将能够以更高的精度对更大的系统进行化学和生物分子模拟，这将给社会带来好处。其影响将是广泛的。

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.