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Updated: Jul 12, 2026

The Use of Chemostats in Microbial Systems Biology
Published on: October 14, 2013
Stochastic P systems and the simulation of biochemical processes with dynamic compartments
Antoine Spicher1, Olivier Michel, Mikolaj Cieslak
1IBISC-FRE 2873 CNRS & Université d'Evry, Genopole Tour Evry 2, 523 place des terrasses de l'Agora, 91000 Evry, France. aspicher@ibisc.fr
Abstract:
We introduce a sequential rewriting strategy for P systems based on Gillespie's stochastic simulation algorithm, and show that the resulting formalism of stochastic P systems makes it possible to simulate biochemical processes in dynamically changing, nested compartments. Stochastic P systems have been implemented using the spatially explicit programming language MGS. Implementation examples include models of the Lotka-Volterra auto-catalytic system, and the life cycle of the Semliki Forest virus.
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