Innovative Supercomputing for Breakthrough Molecular Dynamics

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提供了一个礼物，让社区可以使用他们在NRBSC/PSC托管的一台超级计算机（Anton）。这份礼物确实是前所未有的，它将使医学研究界能够研究迄今为止完全无法触及的生物时间尺度上的重要突出问题。许多重要的生物分子过程发生在毫秒级的时间内。MD模拟提供了对蛋白质，细胞膜，RNA和DNA在原子水平上的详细行为的见解，但由于离散时间步长在飞秒（10-15秒）的顺序上，目前的模拟通常不能达到超过100纳秒的生物时间，每天的时钟时间为中等大小的分子系统。因此，大多数现有的MD模拟仍然停留在纳秒的模拟时间范围内，只有少数运行扩展到微秒。相比之下，安东的原型机现在能够以大约快两个数量级的速度模拟类似的分子系统。如此剧烈的加速可以改变分子结构和功能的研究方式。第一次，科学家可能可视化和预测至关重要的生化现象，包括蛋白质功能基础的结构变化，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。在这个水平上，MD模拟可以开始回答重要的开放式生物医学问题，为药物开发做出重大贡献，并为在更长时间尺度上运行的细胞和组织的布朗动力学和相关随机扩散反应算法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Anton超级计算机。将实施国家分配机制，并开发强大的新型开源数据分析方法。该项目将使突破性的科学，也可能迎来一个专门的计算机开发的生物医学建模和模拟的新时代，跨越分子到细胞和组织尺度的空间和时间。

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.