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

Authors:
Paola Lecca
Affiliations:
Microsoft Research University of Trento, Centre for Computational and System Biology, Italy
Venue:
International Journal of Data Mining and Bioinformatics
Year:
2007

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Abstract

Realistic simulations of the biological systems evolutionrequire a mathematical model of the stochasticity of the involvedprocesses and a formalism for specifying the concurrent nature ofthe biochemical interactions. A time-dependent extension of theGillespie algorithm implementing the race condition of thestochastic π-calculus formalism satisfies both theserequirements. This paper formulates those modifications to theoriginal Gillespie algorithm necessary when the time dependence ofthe reaction propensity is due to changes either of volume ortemperature. This re-formulation has been incorporated in theframework of stochastic π-calculus and has been applied tosimulate the passive glucose cellular transport.