Algorithms for Simulation of Macromolecular Diffusion and Association

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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).