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J Chem Phys. 2011 Oct 7;135(13):134109. doi: 10.1063/1.3634003.

Correction factors for boundary diffusion in reaction-diffusion master equations.

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  • 1Okinawa Institute of Science and Technology, 1919-1, Tancha, Onna-Son, Kunigami, Okinawa 904-0412, Japan. andre.leier@oist.jp

Abstract

The reaction-diffusion master equation (RDME) has been widely used to model stochastic chemical kinetics in space and time. In recent years, RDME-based trajectorial approaches have become increasingly popular. They have been shown to capture spatial detail at moderate computational costs, as compared to fully resolved particle-based methods. However, finding an appropriate choice for the discretization length scale is essential for building a reasonable RDME model. Moreover, it has been recently shown [R. Erban and S. J. Chapman, Phys. Biol. 4, 16 (2007); R. Erban and S. J. Chapman, Phys. Biol. 6, 46001 (2009); D. Fange, O. G. Berg, P. Sjöberg, and J. Elf, Proc. Natl. Acad. Sci. U.S.A. 107, 46 (2010)] that the reaction rates commonly used in RDMEs have to be carefully reassessed when considering reactive boundary conditions or binary reactions, in order to avoid inaccurate--and possibly unphysical--results. In this paper, we present an alternative approach for deriving correction factors in RDME models with reactive or semi-permeable boundaries. Such a correction factor is obtained by solving a closed set of equations based on the moments at steady state, as opposed to modifying probabilities for absorption or reflection. Lastly, we briefly discuss existing correction mechanisms for bimolecular reaction rates both in the limit of fast and slow diffusion, and argue why our method could also be applied for such purpose.

© 2011 American Institute of Physics

PMID:
21992284
[PubMed - indexed for MEDLINE]
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