Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting

Membrane systems were originally introduced as models of computation inspired by the structure and the functioning of living cells. More recently, membrane systems have been shown to be suitable also to model cellular processes. Inspired by brane calculi, a new model of membrane system with peripheral proteins has been recently introduced. Such model has compartments (enclosed by membranes), floating objects, and objects attached to the internal and external surfaces of the membranes. The objects can be processed/transported inside/across the compartments and the transport is regulated by opportune objects attached to the membranes surfaces. We present a stochastic simulator of this model, with a style of syntax based on chemical reactions. We show that the simulator can be particularly useful in modelling biological processes that involve compartments, surface and integral membrane proteins, transport and processing of chemical substances. As examples we present the simulation of circadian clock and the G-protein cycle in yeast

Modeling and Simulating Biological Processes with Stochastic Multiset Rewriting

Membrane systems are models of computation inspired by the structure and the function of biological cells. The model was introduced in 1998 by Gh. Păun and since then many results have been obtained, mostly concerning the computational power of the model (for an updated bibliography the reader can consult the web-page [24]). More recently, membrane systems have been applied to systems biology and several models have been proposed for simulating biological processes (e.g., see the monograph dedicated to membrane systems applications, [9]). In the original definition, membrane systems are composed of an hierarchical nesting of membranes that enclose regions in which floating objects exist. Each region can have associated rules for evolving these objects (called evolution rules, modelling the biochemical reactions present in cell regions), and/or rules for moving objects across membranes (called symport/antiport rules, modelling some kind of transport rules present in cells). Recently, inspired by brane calculus, [4], a model of a membrane system, having objects attached to th