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Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-alpha method

Dana, Saswati and Raha, Soumyendu (2011) Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-alpha method. In: Journal of Computational Physics, 230 (24). pp. 8813-8834.

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Official URL: http://dx.doi.org/10.1016/j.jcp.2011.07.032


Biochemical pathways involving chemical kinetics in medium concentrations (i.e., at mesoscale) of the reacting molecules can be approximated as chemical Langevin equations (CLE) systems. We address the physically consistent non-negative simulation of the CLE sample paths as well as the issue of non-Lipschitz diffusion coefficients when a species approaches depletion and any stiffness due to faster reactions. The non-negative Fully Implicit Stochastic alpha (FIS alpha) method in which stopped reaction channels due to depleted reactants are deleted until a reactant concentration rises again, for non-negativity preservation and in which a positive definite Jacobian is maintained to deal with possible stiffness, is proposed and analysed. The method is illustrated with the computation of active Protein Kinase C response in the Protein Kinase C pathway. (C) 2011 Elsevier Inc. All rights reserved.

Item Type: Journal Article
Publication: Journal of Computational Physics
Publisher: Elsevier Science
Additional Information: Copyright of this article belongs to Elsevier Science.
Keywords: Chemical Langevin equations;Stiff stochastic differential equations;Meso-scale kinetics;Implicit method of numerical integration
Department/Centre: Division of Interdisciplinary Sciences > Supercomputer Education & Research Centre
Date Deposited: 21 Dec 2011 09:07
Last Modified: 21 Dec 2011 09:07
URI: http://eprints.iisc.ac.in/id/eprint/42631

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