Title: The small-voxel tracking algorithm for simulating chemical reactions among diffusing molecules

Simulating the evolution of a chemically reacting system using the bimolecular propensity function, as is done by the stochastic simulation algorithm and its reaction-diffusion extension, entails making statistically inspired guesses as to where the reactant molecules are at any given time. Those guesses will be physically justified if the system is dilute and well-mixed in the reactant molecules. Otherwise, an accurate simulation will require the extra effort and expense of keeping track of the positions of the reactant molecules as the system evolves. One molecule-tracking algorithm that pays careful attention to the physics of molecular diffusion is the enhanced Green's function reaction dynamics (eGFRD) of Takahashi, Tănase-Nicola, and ten Wolde [Proc. Natl. Acad. Sci. U.S.A. 107, 2473 (2010)]. We introduce here a molecule-tracking algorithm that has the same theoretical underpinnings and strategic aims as eGFRD, but a different implementation procedure. Called the small-voxel tracking algorithm (SVTA), it combines the well known voxel-hopping method for simulating molecular diffusion with a novel procedure for rectifying the unphysical predictions of the diffusion equation on the small spatiotemporal scale of molecular collisions. Indications are that the SVTA might be more computationally efficient than eGFRD for the problematic class of non-dilute systems. A widely applicable,more » user-friendly software implementation of the SVTA has yet to be developed, but we exhibit some simple examples which show that the algorithm is computationally feasible and gives plausible results.« less

Dan T Gillespie Consulting, 30504 Cordoba Pl., Castaic, California 91384 (United States)

Department of Physics, Oxford College of Emory University, 100 Hamill St., Oxford, Georgia 30054 (United States)

Publication Date:

OSTI Identifier:

22413331

Resource Type:

Journal Article

Resource Relation:

Journal Name: Journal of Chemical Physics; Journal Volume: 141; Journal Issue: 23; Other Information: (c) 2014 AIP Publishing LLC; Country of input: International Atomic Energy Agency (IAEA)

Country of Publication:

United States

Language:

English

Subject:

97 MATHEMATICAL METHODS AND COMPUTING; ALGORITHMS; CHEMICAL REACTIONS; COLLISIONS; COMPUTER CODES; DIFFUSION; DIFFUSION EQUATIONS; FUNCTIONS; MOLECULES; SIMULATION