Collaborative Research: A Petaflop Cyberinfrastructure for Computing Free Energy Landscapes of Macro- and Biomolecular Systems

合作研究：用于计算宏观和生物分子系统自由能景观的千万亿次网络基础设施

• 批准号: 0904685
• 负责人: David Landau
• 金额: $ 38.2万
• 依托单位: University of Georgia Research Foundation Inc
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-01 至 2015-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=0904685&HistoricalAwards=false
• 关键词: Collaborative; Research; Petaflop; Cyberinfrastructure; Computing

The objective of this research is to develop a petascale cyberinfrastructure for the efficient calculation of free energy landscapes for complex macro- and biomolecular systems. The approach is to develop a cyberinfrastructure for performing Wang-Landau calculations of free energy distributions on petaflop architectures and, to demonstrate its effectiveness, apply it to two outstanding science problems (conformations of a linker protein in solution and self-assembly of lipids). Free energy is a measure of the energy of the system that takes into account entropic and thermal effects. Understanding the relative free energies of, and barriers between, various conformations of macromolecular and biological molecules, including proteins, and of phase transitions between disordered and self-assembled structures, is an extremely important area of chemistry, biochemistry and biophysics and is an area where increased computational capabilities hold the promise of significant progress. The intellectual merit of the proposed research is that it has the potential to result in new algorithms for performing free energy calculations on petascale architectures, in addition to yielding insights into conformational equilibria and self-assembly in macro- and biomolecular systems. The broader impacts of the proposed research include the development of a robust open source petascale cyberinfrastructure for performing free energy calculations made possible only through a strong synergy between physics, chemistry, biology, engineering, and computer science. Through the research performed and educational and outreach programs at the participating institutions, the project exposes high school, undergraduate and graduate students and postdoctoral researchers to the frontiers of computational physics, chemistry and materials research.

本研究的目的是开发一个千万亿级的网络基础设施，用于有效计算复杂的宏观和生物分子系统的自由能景观。该方法是开发一种网络基础设施，用于在petaflop架构上执行Wang-Landau自由能分布计算，并将其应用于两个突出的科学问题（溶液中连接蛋白的构象和脂质自组装），以证明其有效性。自由能是考虑了熵和热效应的系统能量的量度。了解大分子和生物分子（包括蛋白质）的各种构象之间的相对自由能和屏障，以及无序和自组装结构之间的相变，是化学、生物化学和生物物理学的一个极其重要的领域，也是一个计算能力增强有望取得重大进展的领域。这项研究的智力价值在于，除了对宏观和生物分子系统的构象平衡和自组装有深入的了解外，它还有可能产生在千万亿次架构上执行自由能计算的新算法。拟议研究的更广泛影响包括开发一个强大的开源千兆级网络基础设施，用于执行自由能计算，这只有通过物理、化学、生物、工程和计算机科学之间的强大协同才能实现。通过在参与机构进行的研究、教育和推广计划，该项目使高中生、本科生、研究生和博士后研究人员接触到计算物理、化学和材料研究的前沿。