Algorithms for Simulation of Macromolecular Diffusion and Association

大分子扩散和缔合模拟算法

• 批准号: 9974555
• 负责人: Robert Skeel
• 金额: $ 39.96万
• 依托单位: University of Illinois at Urbana-Champaign
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-10-01 至 2002-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=9974555&HistoricalAwards=false
• 关键词: Algorithms; Simulation; Macromolecular; Diffusion; Association

DBI 9974555, Skeel, U of I, Urbana Champaign. Algorithms for simulation of macromolecular Diffusion and AssociationProject SummaryThe research objective of this proposal is to advance computational methodology and develop software for modeling dffusional encounters between macromolecules. A number of biomolecular association reactions in the cell are controlled by steered dffusion. Understanding the nature of the encounter in molecular detail will provide insights into underlying mechanisms of association. This has implications for protein engineering and design as well as regulation for several cellular processes. The proposed research will enable simulations of diffusional processes in molecular detail. Especially targeted is the calculation of diffusion-limited reaction rates. To improve computational tools, the work has as its aims (i) to develop a more detailed mathematical description of the biomolecular simulation, (ii) to construct more efficient algorithms for solving the equations, and (iii) to implement the methods in well designed software that runs on parallel computers. More specifically, it is proposed to develop more detailed representations of the biomolecules' geometry, the distributionof electric charge, and hydrodynamic interactions. Algorithms are to be devised and implemented for more rapid calculation of trajectories of Brownian motion and more selective generation of them. Software is to be written that embodies the enhanced capabilities and runs effciently in parallel on both distributed and shared-memory computers. This activity is to include the further education of personnel in challenging interdisciplinary work. It will make available documented software, and the capability will also become available as part of the Web-based Biology Workbench (http://biology.ncsa.uiuc.edu).

DBI 9974555，斯基尔，伊利诺伊大学厄巴纳香槟分校。模拟大分子扩散和关联的算法项目概述本提案的研究目标是推进计算方法和开发模拟大分子之间扩散相遇的软件。细胞中的许多生物分子结合反应是由定向扩散控制的。从分子细节上理解这种相遇的本质，将有助于深入了解关联的潜在机制。这对蛋白质工程和设计以及几个细胞过程的调节具有启示意义。提出的研究将使分子扩散过程的详细模拟成为可能。特别有针对性的是扩散限制反应速率的计算。为了改进计算工具，这项工作的目标是(i)对生物分子模拟进行更详细的数学描述，（ii）构建更有效的求解方程的算法，以及（iii）在并行计算机上运行的精心设计的软件中实现这些方法。更具体地说，建议开发更详细的生物分子几何形状，电荷分布和流体动力学相互作用的表示。为了更快地计算布朗运动轨迹和更有选择性地生成它们，需要设计和实现算法。要编写的软件包含增强的功能，并在分布式和共享内存计算机上并行有效地运行。这项活动将包括对具有挑战性的跨学科工作人员的进一步教育。它将提供文档化的软件，并且该功能也将成为基于web的生物学工作台（http://biology.ncsa.uiuc.edu）的一部分。