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

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 M G S . Implementation examples include models of the Lotka–Volterra auto-catalytic system, and the life cycle of the Semliki Forest virus.