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

Lecca, P.

International Journal of Data Mining and Bioinformatics 1(4): 315-336

2008

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 pi-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 pi-calculus and has been applied to simulate the passive glucose cellular transport.

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