Title: Simulating the cellular passive transport of glucose using a time-dependent extension of Gillespie algorithm for stochastic π-calculus

Authors: Paola Lecca

Addresses: Microsoft Research – University of Trento, Centre for Computational and System Biology, Italy

Abstract: Realistic simulations of the biological systems evolution require a mathematical model of the stochasticity of the involved processes and a formalism for specifying the concurrent nature of the biochemical interactions. A time-dependent extension of the Gillespie algorithm implementing the race condition of the stochastic π-calculus formalism satisfies both these requirements. This paper formulates those modifications to the original Gillespie algorithm necessary when the time dependence of the reaction propensity is due to changes either of volume or temperature. This re-formulation has been incorporated in the framework of stochastic π-calculus and has been applied to simulate the passive glucose cellular transport.

Keywords: chemical kinetics simulation; stochastic π-calculus; Gillespie algorithm; biochemical systems modelling; glucose passive transport; data mining; bioinformatics; cellular transport; cell biology.

DOI: 10.1504/IJDMB.2007.012963

International Journal of Data Mining and Bioinformatics, 2007 Vol.1 No.4, pp.315 - 336

Published online: 02 Apr 2007 *

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