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Innovative Supercomputing for Breakthrough Molecular Dynamics

创新超级计算突破分子动力学

基本信息

批准号：
7945309
负责人：
Markus Dittrich
金额：
$ 134.66万
依托单位：
CARNEGIE-MELLON UNIVERSITY
依托单位国家：
美国
项目类别：
财政年份：
2009
资助国家：
美国
起止时间：
2009-09-30 至 2012-11-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7945309
关键词：
Acceleration Algorithms Arts Award Behavior Binding Biochemical Phenomena Biological Biomedical Research Biotechnology Calendar Cell Membrane Proteins Cells Chemicals Communities Computer software Computers DNA Data Data Analyses Data Storage and Retrieval Diffusion Disease Drug Interactions Equilibrium Gifts Goals Grant Health High Performance Computing Investigation Ion Channel Maintenance Membrane Proteins Methods Mission Molecular Molecular Structure Names National Center for Research Resources Nucleic Acids Policies Process Production Proteins Reaction Research Resource Sharing Resources Running Science Scientist Services Signal Transduction Simulate Supercomputing System Technology Testing Time Tissues Training United States National Institutes of Health abstracting base biomedical resource design drug candidate drug development innovation insight millisecond models and simulation molecular dynamics molecular size nanosecond new technology novel open source protein function protein structure prototype simulation software development supercomputer

项目摘要

DESCRIPTION (provided by applicant): A partnership between D.E. Shaw Research (DESRES) and the National Resource for Biomedical Supercomputing (NRBSC) at the Pittsburgh Supercomputing Center (PSC) will enable breakthrough advances in Molecular Dynamics (MD) research. DESRES has recently developed new supercomputing technology that can accelerate MD simulations by about 100-fold. For this project, DESRES has offered a gift of community access to one of their supercomputers (Anton) hosted at the NRBSC/PSC. This gift is truly unprecedented, and would allow the MD research community to investigate important outstanding questions on scales of biological time that up until now have been completely inaccessible. Many important biomolecular processes occur over times on the order of milliseconds. MD simulations provide insights into the behavior of proteins, cell membranes, RNA, and DNA at an atomic level of detail, but with discrete time steps on the order of femtoseconds (10-15 seconds), current simulations typically can reach no more than about 100 nanoseconds of biological time per day of wall-clock time for medium-size molecular systems. Thus, most existing MD simulations remain in the nanosecond range of simulated time, with only a few runs extending to a microsecond. In contrast, an Anton prototype is now able to run simulations of comparable molecular systems at rates about two orders of magnitude faster. Such dramatic acceleration could literally transform the way that molecular structure and function are studied. For the first time, scientists might visualize and predict critically important biochemical phenomena, including the structural changes that underlie protein function, and the interactions between two proteins or between a protein and a candidate drug molecule. At that level, MD simulations could begin to answer important open biomedical questions, contribute substantially to drug development, and provide direct inputs to simulations of cells and tissues run with Brownian Dynamics and related stochastic diffusion-reaction algorithms at even longer time-scales. In this highly innovative project, DESRES and the NRBSC will partner to make an Anton supercomputer available to the national research community. A national allocation mechanism will be implemented, and powerful new open-source data analysis methods will be developed as well. This project will enable breakthrough science, and may also usher in a new era of specialized computers developed for biomedical modeling and simulation, spanning molecular to cellular and tissue scales of space and time. PUBLIC HEALTH RELEVANCE: New supercomputing technology, approximately one hundred times faster than pre-existing resources, will be made available to the national research community for the first time ever. This new technology will enable breakthrough advances in the modeling and simulation of molecular structure and function (Molecular Dynamics). Such dramatic acceleration may literally transform the way that scientists visualize and predict important chemical interactions that underlie health and disease, including how protein structure changes as the molecules carry out their functions, and how protein molecules bind to new candidate drug molecules. These advances will be made possible through a partnership between D.E. Shaw Research and the National Resource for Biomedical Supercomputing at the Pittsburgh Supercomputing Center.

描述(由申请人提供)：D.E.Shaw Research(DESRES)和匹兹堡超级计算中心(PSC)的国家生物医学超级计算资源(NRBSC)之间的合作伙伴关系将使分子动力学(MD)研究取得突破性进展。DESRES最近开发了新的超级计算技术，可以将MD模拟速度提高约100倍。对于这个项目，DESRES提供了一份礼物，可以让社区访问他们在NRBSC/PSC托管的一台超级计算机(ANTON)。这份礼物真的是史无前例的，它将允许MD研究界在生物时间尺度上调查重要的悬而未决的问题，到目前为止，这些问题是完全无法获得的。许多重要的生物分子过程发生在毫秒量级的时间内。MD模拟提供了对蛋白质、细胞膜、RNA和DNA在原子细节水平上的行为的深入了解，但由于离散的时间步长在飞秒(10-15秒)的数量级，当前的模拟通常可以达到中等大小分子系统的挂钟时间的每天不超过大约100纳秒的生物时间。因此，大多数现有的MD模拟仍然停留在模拟时间的纳秒范围内，只有少数几次运行延伸到一微秒。相比之下，Anton的原型现在能够以大约两个数量级的速度运行可比的分子系统的模拟。这种戏剧性的加速可能会真正改变人们研究分子结构和功能的方式。科学家们可能会首次可视化并预测至关重要的生化现象，包括支撑蛋白质功能的结构变化，以及两种蛋白质之间或蛋白质与候选药物分子之间的相互作用。在这一水平上，MD模拟可以开始回答重要的公开生物医学问题，为药物开发做出重大贡献，并为在更长时间尺度上用布朗动力学和相关的随机扩散-反应算法运行的细胞和组织的模拟提供直接输入。在这个高度创新的项目中，DESRES和NRBSC将合作为国家研究界提供一台ANTON超级计算机。将实施国家分配机制，并将开发强大的新的开源数据分析方法。该项目将使科学取得突破性进展，并可能开启为生物医学建模和模拟开发的专用计算机的新时代，跨越分子、细胞和组织的空间和时间尺度。与公共健康相关：新的超级计算技术将有史以来第一次提供给国家研究界，其速度大约是现有资源的100倍。这项新技术将使分子结构和功能的建模和模拟(分子动力学)取得突破性进展。这种戏剧性的加速可能会从字面上改变科学家对构成健康和疾病基础的重要化学相互作用的可视化和预测方式，包括蛋白质结构在分子执行其功能时如何变化，以及蛋白质分子如何与新的候选药物分子结合。这些进展将通过D.E.Shaw Research和匹兹堡超级计算中心的国家生物医学超级计算资源之间的合作实现。