MSPA-MCS: Data-Driven Parallelization of Time in Molecular Dynamics Simulations

传统的并行化策略在需要模拟长时间跨度而不是大状态空间的情况下不能很好地扩展。分子动力学模拟构成了一类重要的应用，而这被证明是一个瓶颈。研究人员开发了一种新的分子动力学并行化方法，该方法基于这样的观察，即模拟通常发生在来自其他相关模拟的丰富数据的环境中。他们使用这些数据来并行化时域，从而产生更可扩展的算法。这种方法是基于这样的观察，即在多时间尺度的模拟中经常遇到长时间跨度。finscales负责大量的计算工作。然而，精细尺度的重要贡献往往在于它们对粗尺度的影响。研究人员使用简化的有序模型来识别重要的粗尺度效应。他们使用聚类和机器学习来动态地确定正在执行的模拟与先前数据之间的关系。他们使用eode和控制理论进行稳定性分析、不确定性估计和系统识别。研究人员通过各种纳米和生物纳米材料的实际应用来验证他们的技术。所选择的应用的重要性源于这样一个事实，即材料在历史上在人类进步中发挥了关键作用。人类进步的时代，如铁器时代和青铜器时代，都是以促进这些进步的材料命名的，这一事实表明了它们的重要性。纳米和生物纳米材料是基于对原子尺度的基本理解而设计的，有望带来另一场革命，导致诸如节能汽车、抗灾结构和治疗疾病的新方法等产品的出现。研究人员的技术消除了这种发展的一个重要障碍。此外，参与的学生获得跨学科研究方面的培训。在hbcu中加入一名共同任命的合作者，确保未被充分代表的学生也能从这项工作中受益。

Conventional parallelization strategies do not scalewell when the computational effort arises from theneed to simulate to long time spans, rather than fromlarge state space. Molecular Dynamics simulationsconstitute an important class of applications wherethis proves to be a bottleneck. The investigatorsdevelop a new approach to parallelization of MolecularDynamics, which is based on the observation thatsimulations typically occur in a context rich in datafrom other related simulations. They use such data toparallelize the time domain, which yields a morescalable algorithm. This approach is based on theobservation that long time-spans are often encounteredin simulations with multiple time scales. The finescales are responsible for the large computationaleffort. However, the important contribution of thefine-scales is often to the effect they have on thecoarse scale. The investigators use reduced ordermodeling to identify important coarse scale effects.They use clustering and machine learning todynamically determine the relationship between thesimulation being performed and prior data. They useODE and controls theory for stability analysis,uncertainty estimation, and system identification.The investigators validate their techniques using avariety of realistic applications in nano and bio-nanomaterials. The importance of the applications chosenarises from the fact that materials have historicallyplayed a pivotal role in human progress. An indicationof their importance lies in the fact that eras ofhuman progress, such as the iron age and the bronzeage, are named after the materials that contributed tosuch progress. Nano and bio-nano materials, designedbased on fundamental understanding at the atomicscale, promise yet another revolution, leading toproducts such as fuel efficient cars, disasterresistant structures, and new ways of treatingdiseases. The investigators' techniques remove animportant impediment to such developments.Furthermore, the students involved obtain training ininterdisciplinary research. Inclusion of acollaborator with a joint appointment at an HBCUensures that under-represented students too benefitfrom this work.