Accelerating Biomolecular Simulations on Reconfigurable Computing Hardware

加速可重构计算硬件上的生物分子模拟

• 批准号: 7532368
• 负责人: Pratul K Agarwal
• 金额: $ 23.07万
• 依托单位: UT-BATTELLE, LLC-OAK RIDGE NATIONAL LAB
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-15 至 2010-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7532368
• 关键词: Acceleration; Algorithms; Area; Binding; Biochemical; Biochemical Reaction; Biological; Biology; Catalysis; Cell physiology; Code; Communities; Compatible; Complex; Computer Hardware; Computer software; Computers; Computing Methodologies; DNA; Data; Development; Devices; Docking; Enzymes; Excision; Future; Goals; Health; Heating; Hour; Investigation; Laws; Ligands; Mainstreaming; Medical; Membrane; Memory; Microprocessor; Modification; Movement; Numbers; Performance; Pharmaceutical Preparations; Process; Production; Protein Engineering; Proteins; Public Health; Purpose; Range; Research; Research Personnel; Solutions; Speed; Structure; System; Technology; Time; Transistors; Vendor; Work; computing resources; cost; data structure; design; drug discovery; engineering design; experience; interest; molecular dynamics; molecular recognition; multi-scale modeling; next generation; protein folding; simulation; small molecule; supercomputer

DESCRIPTION (provided by applicant): Accelerating biomolecular simulations will have a direct impact on investigations in many areas of health related research. Simulations of biomolecules are widely used for fundamental understanding of their structure, folding, dynamics and function. The underlying calculations in these simulations are computationally intensive and have benefited considerably from more than an order of magnitude increase in computer processor speeds in last decade alone. There is widespread interest in alternate hardware and software solutions that can speed-up these simulations, as physical challenges in the computing technology are currently placing the limits on future speed increase of processors. Here we propose the development of biomolecular simulations software for adaptive computing that includes Reconfigurable Computing (RC) hardware and General Purpose Graphical Processing Units (GPGPUs) devices. The RC hardware, including Field Programmable Gate Arrays (FPGAs), and GPGPUs provide a tremendous amount of raw computing power even at the desktop level at a fraction of power requirements and cost of multi-processors parallel systems. PMEMD and LAMMPS, widely used biomolecular simulation engines, will be ported and optimized for popular RC/GPGPU devices. Moreover a molecular dynamics (MD) kernel specially designed to efficiently exploit the computational power of current and future RC/GPGPU devices will be developed. The proposed work will benefit the wide community of biochemists, biophysicists and computational chemists. The availability of these codes optimized on adaptive computing hardware will allow the non-expert user to benefit without worrying about the porting and optimizing details. Moreover, the availability of performance profiling utilities and the optimized MD kernel will enable other groups of application code developers to extend our implementation to exploit future FPGA and GPGPU devices enabled platforms. PUBLIC HEALTH RELEVANCE: The development of proposed optimized biomolecular simulations software will have direct impact on health and medical related research in many different areas including biochemical/biophysical characterization of cellular processes, drug-discovery and protein engineering. Biomolecular simulation software is used to investigate biological complexes and activities including protein folding, enzyme catalysis, conformational changes associated with bimolecular function, molecular recognition of proteins, DNA, and biological membrane complexes as well as docking/binding of small compounds to biomolecules.

描述（由申请人提供）：加速生物分子模拟将直接影响与健康相关研究的许多领域的调查。生物分子的模拟广泛用于对其结构，折叠，动力学和功能的基本理解。这些模拟中的基本计算在计算上是密集的，仅在过去十年中，计算机处理器速度的数量级就大大受益。人们对可以加快这些模拟的替代硬件和软件解决方案引起了人们的兴趣，因为计算技术中的物理挑战目前正在对处理器的未来速度提高限制。在这里，我们建议开发用于自适应计算的生物分子仿真软件，其中包括可重构计算（RC）硬件和通用图形处理单元（GPGPUS）设备。 RC硬件，包括现场可编程栅极阵列（FPGA）和GPGPU，即使在台式机级别的功率要求和多处理器平行系统的成本方面，即使在台式机级别上也提供了大量的原始计算功率。 PMEMD和LAMMPS（广泛使用的生物分子模拟引擎）将用于流行的RC/GPGPU设备。此外，将开发出专门设计的分子动力学（MD）内核，以有效利用当前和未来RC/GPGPU设备的计算能力。拟议的工作将使广泛的生物化学家，生物物理学家和计算化学家受益。这些代码在自适应计算硬件上优化的代码的可用性将使非专家用户在不担心移植和优化详细信息的情况下受益。此外，性能分析实用程序的可用性以及优化的MD内核将使其他应用程序代码开发人员扩展我们的实现，以利用未来的FPGA和GPGPU设备启用了启用平台。公共卫生相关性：拟议优化的生物分子仿真软件的开发将直接影响许多不同领域的健康和医学相关研究，包括对细胞过程的生化/生物物理表征，药物分离和蛋白质工程。生物分子仿真软件用于研究生物复合物和活性，包括蛋白质折叠，酶催化，与双分子功能相关的构象变化，蛋白质的分子识别，DNA和生物膜复合物以及对生物分子与生物分子的小小的结合/结合。