Stochastic P systems and the simulation of biochemical processes with dynamic compartments

Antoine Spicher1, Olivier Michel1, Mikolaj Cieslak2, Jean-Louis Giavatto1, and Przemyslaw Prusinkiewicz2.
1 IBISC-FRE 2873 CNRS & Université d'Évry, Genopole Tour Évry 2, 523 place des terrasses del'Agora, 91000 Évry, France
2 Department of Computer Science, University of Calgary, 2500 University Drive N.W., Calgary, AB, Canada T2N 1N4

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.

Reference

Antoine Spicher, Olivier Michel, Mikolaj Cieslak, Jean-Louis Giavitto, and Przemyslaw Prusinkiewicz: Stochastic P systems and the simulation of biochemical processes with dynamic compartments. Biosystems 91(3), pp. 458-472.

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