Theory of Biomolecular Diffusion

描述（由申请人提供）：扩散控制酶活性、信号转导、基因表达、细胞骨架重塑和细胞间通讯等生物学过程的要素。这项工作的广泛目标是提供新的计算机模拟工具，将使详细分析分子扩散在生物过程中的作用，在亚细胞和细胞水平上，和这些工具的应用，以选定的问题，密切接触的实验工作是可能的。下一个项目期间的具体目标包括以下方面。(a)方法将被开发，以允许更详细的相互作用模型被用于生物分子扩散的布朗动力学模拟。(b)将开发方法，以便在布朗动力学模拟期间更快速地计算大分子（> 100，000个原子）的静电相互作用。(c)方法将被开发，以允许在细胞尺度上的扩散过程的模拟。(d)应用程序将蛋白质-蛋白质扩散遇到，蛋白质-膜扩散遇到，并扩散和神经递质在模型突触的反应。本科生、研究生和博士后的培训将继续是该项目的一个关键方面。

DESCRIPTION (provided by applicant): Diffusion governs elements of such biological processes as enzymatic activity, signal transduction, gene expression, cytoskeletal remodeling,and intercellular communication. The broad objectives of this work are to provide new computer simulation tools that will enable the detailed analysis of the role of molecular diffusion in biological processes at the subcellular and cellular levels, and the application of these tools to selected problems where close contact with experimental work is possible. Specific aims for the next project period include the following. (a) Methods will be developed to allow more detailed interaction models to be used in Brownian dynamics simulations of biomolecular diffusion. (b) Methods will be developed to allow more rapid calculation of electrostatic interactions of large molecules (>100,000 atoms) during Brownian dynamics simulations. (c) Methods will be developed to allow simulations of diffusional processes at cellular scales. (d) Applications will be made to protein-protein diffusional encounter, to protein-membrane diffusional encounter, and to diffusion and reaction of neurotransmitter in model synapses. Training of undergraduate, graduate and postdoctoral students will continue to be a key aspect of this project.