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

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。计算机模拟的一个重要应用是在分子水平上研究生物系统的细节。然而，即使是现代的超级计算机，也很难在分子水平上模拟细胞尺度的过程。Voth小组最近开发了用于非常大规模的生物过程“粗粒度”（CG）模拟的软件，解决了几个可能严重阻碍CG模型有效使用的关键技术障碍。该软件将与实验同事密切合作，用于研究当前感兴趣的一些大规模生物分子系统。该软件由一个高度可扩展的并行分子动力学引擎组成，使用稀疏数据结构和空间填充曲线，为超大规模分子系统提供高效的CG模拟。特别是，MD引擎可以有效地在大型超级计算资源中“负载平衡”所有所需的计算-即使是对于极不均匀的颗粒分布，例如“隐式溶剂”CG模型。这些特征将在研究HIV-1病毒生命周期的关键方面以及对细胞功能重要的大规模分支肌动蛋白组装体的行为方面具有重要价值。CG软件的持续发展，以及大规模CG模拟本身的结果，将为推进计算机模拟的最新技术提供有价值的线索，并有助于指导实验，以进一步阐明具有重要生物学意义的过程。

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.