Mapping Fitness and Free Energy Landscapes of Proteins

绘制蛋白质的健康度和自由能景观

• 批准号: 10577469
• 负责人: Ronald Levy
• 金额: $ 21.46万
• 依托单位: TEMPLE UNIV OF THE COMMONWEALTH
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-05-01 至 2024-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10577469
• 关键词: 7 year old; Algorithmic Software; Biophysics; Computational Biology; Computer Systems; Computers; Computing Methodologies; Development; Equipment; Free Energy; Funding; High Performance Computing; Hybrids; Life Cycle Stages; Machine Learning; Problem Solving; Protein Dynamics; Proteins; Research; Research Personnel; Research Project Grants; Research Support; Resources; Scientist; Structure; System; United States National Institutes of Health; computational chemistry; computer cluster; computing resources; experience; fitness; high end computer; molecular dynamics; parent grant; structural biology

Abstract, Funds are requested to purchase computer equipment to support the research projects described in the parent grant NIH 1R35GM132090 “Mapping Fitness and Free Energy Landscapes of Proteins” (R.M. Levy, PI). The PI is a computational scientist with forty years of experience in computational structural biology and biophysics. The research described in the parent grant is focused on the development and application of computational methods for studying the structure, function, and dynamics of proteins. All of the projects supported by NIH 1R35GM132090 rely on access to state-of-the-art computational resources. Since 2015, advances in software and algorithms have led to a significantly greater focus on GPU implementations for machine learning and for solving problems in computational chemistry, biophysics, and structural biology. Access to the latest GPU hardware is essential for the successful completion of the research described in the parent grant. The PI requests a supplement to purchase 8 NVIDIA A100 40GB PCIe GPUs, with double the number of GPU cores and triple the bandwidth relative to the current consumer-level GPUs the PI currently has access to, and they are much better optimized for high-performance computing. The new GPUs will be connected to an existing shared computer cluster, the Center for Biophysics and Computational Biology Research Resource (CB2RR) cluster, which supports NIH funded researchers. The GPUs will be connected to the cluster using high- throughput, low overhead InfiniBand HDR 200 Gbps connections, which will be purchased with the GPUs. In addition, funds are requested to upgrade the storage system of the computer cluster with a 500TB RAID-6, as the current hard disks are now out of warranty and at the end of their life cycle. This system will excel at accelerating highly parallelized GPU-only and CPU-GPU hybrid molecular dynamics simulations and machine learning applications as described in NIH 1R35GM132090.

抽象的， 请求资金购买计算机设备以支持父文件中描述的研究项目 授予 NIH 1R35GM132090“绘制蛋白质的健康和自由能量景观”（R.M. Levy，PI）。 是一位计算科学家，在计算结构生物学和生物物理学领域拥有四十年的经验。 家长资助中描述的研究重点是计算的开发和应用 研究蛋白质结构、功能和动力学的方法 NIH 支持的所有项目。 1R35GM132090 依赖于自 2015 年以来软件的进步。 和算法导致人们更加关注机器学习和人工智能的 GPU 实现 解决计算化学、生物物理学和结构生物学中的问题 使用最新的 GPU。 硬件对于成功完成 PI 中描述的研究至关重要。 申请补购8块NVIDIA A100 40GB PCIe GPU，GPU核心数翻倍 相对于 PI 目前可以访问的当前消费级 GPU，带宽增加了三倍，并且它们 新的 GPU 将针对高性能计算进行更好的优化。 共享计算机集群，生物物理学和计算生物学研究资源中心 (CB2RR) 集群，支持 NIH 资助的研究人员。GPU 将使用高性能连接到该集群。 吞吐量、低开销 InfiniBand HDR 200 Gbps 连接，将与 GPU 一起购买。 此外，还需要资金将计算机集群的存储系统升级为500TB RAID-6，如下： 当前的硬盘现已超出保修期，并且该系统将在其生命周期结束时发挥作用。 加速高度并行的仅 GPU 和 CPU-GPU 混合分子动力学模拟和机器 NIH 1R35GM132090 中描述的学习应用程序。