Modelling spatial heterogeneity and macromolecular crowding with membrane systems

Authors:
Ettore Mosca;Paolo Cazzaniga;Dario Pescini;Giancarlo Mauri;Luciano Milanesi
Affiliations:
Institute for Biomedical Technologies, National Research Council, Segrate, MI, Italy;Department of Informatics, Systems and Communications, University of Milan-Bicocca, Milan, Italy;Department of Informatics, Systems and Communications, University of Milan-Bicocca, Milan, Italy;Department of Informatics, Systems and Communications, University of Milan-Bicocca, Milan, Italy;Institute for Biomedical Technologies, National Research Council, Segrate, MI, Italy
Venue:
CMC'10 Proceedings of the 11th international conference on Membrane computing
Year:
2010

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Abstract

In biological processes, intrinsic noise, spatial heterogeneity and molecular crowding deeply affect the system dynamics. The classic stochastic methods lack of the necessary features needed for the description of these phenomena. Membrane systems are a suitable framework to embed these characteristics; in particular, the variants of τ-DPP and Sτ -DPP allow the modelling and stochastic simulations of multivolume biochemical systems, in which diffusion and size of volumes and chemicals are taken into account improving the description of these biological systems. In this paper we show, by means of two models of reactiondiffusion and crowded systems, the correctness and accuracy of our simulation methods.