Ultra-Coarse-Grained Simulations of Biomolecular Processes at the Petascale

千万亿级生物分子过程的超粗粒度模拟

• 批准号: 1440027
• 负责人: Gregory Voth
• 金额: $ 1.59万
• 依托单位: University of Chicago
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-09-01 至 2018-02-28
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1440027&HistoricalAwards=false
• 关键词: Ultra; Coarse; Grained; Simulations; Biomolecular

The rapid growth of supercomputing power has enabled computer simulations to provide an increasingly useful complement to conventional experimental techniques. One important application of computer simulations is the study of biological systems at a molecular level of detail. Even modern supercomputers, however, struggle to simulate cell-scale processes at the molecular level.The Voth group have recently developed software for very large-scale "coarse-grained" (CG) simulations of biological processes, addressing several key technical barriers that can otherwise seriously hinder the efficient use of CG models. This software will be used to study a number of large-scale biomolecular systems of current interest in close collaboration with experimental colleagues.The software consists of a highly scalable parallel molecular dynamics engine, using sparse data structures and space filling curves to provide highly efficient CG simulations of extremely large-scale molecular systems. In particular, the MD engine efficiently "load-balances" all required calculations across large supercomputing resources - even for extremely heterogeneous particle distributions, such as "implicit solvent" CG models. These characteristics will be of great value in the study of key aspects of the HIV-1 viral lifecycle, and the behavior of the large-scale branched actin assemblies which are important for cellular function. The continued development of the CG software, and the results of the large-scale CG simulations themselves, will provide valuable leads into both advancing the state-of-the-art in computer simulations and also helping to direct experiments to further elucidate processes of great biological importance.

超级计算能力的快速增长使计算机模拟能够为传统的实验技术提供越来越有用的补充。计算机仿真的一种重要应用是对分子细节的生物系统的研究。然而，即使是现代超级计算机，也很难在分子级别模拟细胞尺度过程。该小组最近开发了用于对生物学过程的非常大规模的“粗粒”（CG）模拟的软件，这些软件可以严重地解决了几个关键的技术障碍，这些障碍可以严重阻碍CG模型的有效使用。该软件将用于研究许多与实验同事密切合作的当前感兴趣的大规模生物分子系统。该软件由高度可扩展的平行分子动力学发动机组成，使用稀疏的数据结构和空间填充曲线，以提供高效的CG模拟，用于极大的大型分子系统的高效CG模拟。特别是，MD发动机有效地“负载平衡”所有必需的计算都在大型超级计算资源上 - 即使对于极其异质的粒子分布，例如“隐式溶剂” CG模型。这些特征在研究HIV-1病毒生命周期的关键方面以及对细胞功能很重要的大型分支肌动蛋白组件的行为方面将具有很大的价值。 CG软件的持续开发以及大规模CG模拟本身的结果将为推进计算机仿真的最新技术提供宝贵的潜在客户，并帮助指导实验以进一步阐明具有极大重要性的过程。