Graduate Student / Postdoc Seminar

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An Event-Driven Kinetic Monte Carlo Algorithm for Reaction-Diffusion Systems

Speaker: Aleksandar Donev, Courant

Location: Warren Weaver Hall 1302

Date: Friday, December 3, 2010, 1 p.m.

Synopsis:

I will present an asynchronous event-driven algorithm for simulating reaction-diffusion particle systems. Systems of diffusing reactive particles can successfully model a variety of processes, from signal transduction in chemotaxis to radiation damage in steel alloys. Our First Passage Kinetic Monte Carlo algorithm [A. Donev et al., J. Comp. Phys., 229(9):3214-3236, 2010, arXiv:0905.3576] replaces the tedious sequence of diffusive hops needed to bring reactants into proximity with super hops sampled from a time-dependent Green's function derived from the theory of first-passage processes. The algorithm has been used to study annealing of microstructural damage in irradiated metals and extends the simulated time horizon from minutes to tens and hundreds of years while retaining uncompromising accuracy. Recent work in other groups has applied the algorithm to biochemical reactions in the cytoplasm (http://www.e-cell.org/ecell/software/bd-simulator-prototype).

Joint work with V. V. Bulatov, Lawrence Livermore National Laboratory

Note: This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344 (LLNL-ABS-409991).