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

Abstract

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.

Authors:
 [1];  [1]
  1. Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore 560012 (India)
Publication Date:
OSTI Identifier:
21592618
Resource Type:
Journal Article
Journal Name:
Journal of Computational Physics
Additional Journal Information:
Journal Volume: 230; Journal Issue: 24; Other Information: DOI: 10.1016/j.jcp.2011.07.032; PII: S0021-9991(11)00515-8; Copyright (c) 2011 Elsevier Science B.V., Amsterdam, The Netherlands, All rights reserved.; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0021-9991
Country of Publication:
United States
Language:
English
Subject:
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSICS; CALCULATION METHODS; COMPUTERIZED SIMULATION; DIFFERENTIAL EQUATIONS; KINETICS; LANGEVIN EQUATION; MATHEMATICAL MODELS; PROTEINS; STOCHASTIC PROCESSES; EQUATIONS; ORGANIC COMPOUNDS; SIMULATION

Citation Formats

Dana, Saswati, E-mail: saswatid@rishi.serc.iisc.ernet.in, and Raha, Soumyendu, E-mail: raha@serc.iisc.ernet.in. Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-{alpha} method. United States: N. p., 2011. Web. doi:10.1016/j.jcp.2011.07.032.
Dana, Saswati, E-mail: saswatid@rishi.serc.iisc.ernet.in, & Raha, Soumyendu, E-mail: raha@serc.iisc.ernet.in. Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-{alpha} method. United States. doi:10.1016/j.jcp.2011.07.032.
Dana, Saswati, E-mail: saswatid@rishi.serc.iisc.ernet.in, and Raha, Soumyendu, E-mail: raha@serc.iisc.ernet.in. Sat . "Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-{alpha} method". United States. doi:10.1016/j.jcp.2011.07.032.
@article{osti_21592618,
title = {Physically consistent simulation of mesoscale chemical kinetics: The non-negative FIS-{alpha} method},
author = {Dana, Saswati, E-mail: saswatid@rishi.serc.iisc.ernet.in and Raha, Soumyendu, E-mail: raha@serc.iisc.ernet.in},
abstractNote = {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.},
doi = {10.1016/j.jcp.2011.07.032},
journal = {Journal of Computational Physics},
issn = {0021-9991},
number = 24,
volume = 230,
place = {United States},
year = {2011},
month = {10}
}