Algorithms for Simulation of Macromolecular Diffusion and Association

DBI 9974555，斯基尔，伊利诺伊大学，乌尔巴纳香槟。用于模拟大分子扩散和缔合的算法项目摘要这项提议的研究目标是改进计算方法并开发用于模拟大分子间扩散相遇的软件。细胞内的许多生物分子缔合反应是由定向扩散控制的。在分子细节上理解这种相遇的性质将提供对潜在的关联机制的洞察。这对蛋白质工程和设计以及对几个细胞过程的调控都有影响。拟议的研究将使分子细节的扩散过程模拟成为可能。特别针对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)开发生物分子模拟的更详细的数学描述，(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，建议对生物分子的几何形状、电荷分布和流体动力学相互作用进行更详细的表示。为了更快地计算布朗运动的轨迹并更有选择性地生成它们，将设计和实现算法。编写的软件要体现增强的能力，并在分布式和共享内存计算机上高效地并行运行。这项活动将包括对具有挑战性的跨学科工作的人员进行继续教育。它将提供记录在案的软件，该功能也将作为基于网络的生物学工作台(http://biology.ncsa.uiuc.edu).)的一部分提供

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).