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.
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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