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， 要求资金购买计算机设备以支持父母所描述的研究项目 Grant NIH 1R35GM132090“映射健身和蛋白质的自由能景观”（R.M. Levy，PI）。 pi 是一名计算科学家，在计算结构生物学和生物物理学方面拥有40年的经验。 父母赠款中描述的研究重点是计算的开发和应用 研究蛋白质的结构，功能和动力学的方法。 NIH支持的所有项目 1R35GM132090依靠访问最先进的计算资源。自2015年以来，软件的进步 算法和算法使对机器学习的GPU实施以及针对机器学习和 解决计算化学，生物物理学和结构生物学的问题。访问最新的GPU 硬件对于成功完成父母赠款中描述的研究至关重要。 pi 要求购买8个NVIDIA A100 40GB PCIE GPU的补充，其两倍是GPU核心的数量 相对于当前的消费者级GPU，PI当前可以访问带宽，它们 可以更好地针对高性能计算进行优化。新的GPU将连接到现有的 共享计算机集群，生物物理学和计算生物学研究资源（CB2RR）中心 集群，支持NIH资助的研究人员。 GPU将使用高 - 吞吐量，低顶间Infiniband HDR 200 Gbps连接，将使用GPU购买。 此外，要求资金使用500TB RAID-6升级计算机集群的存储系统，AS 当前的硬盘现在不在保修期内，并且在其生命周期结束时。该系统将在 加速高度平行的仅GPU和CPU-GPU混合动力学模拟和机器 NIH 1R35GM132090中所述的学习应用。