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Modelling Spatial Heterogeneity and Macromolecular Crowding with Membrane Systems

  • Ettore Mosca
  • Paolo Cazzaniga
  • Dario Pescini
  • Giancarlo Mauri
  • Luciano Milanesi
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6501)

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 multi-volume 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 reaction-diffusion and crowded systems, the correctness and accuracy of our simulation methods.

Keywords

Spatial Heterogeneity Cellular Automaton Brownian Dynamic Stochastic Simulation Algorithm Chemical Master Equation 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Ettore Mosca
    • 1
  • Paolo Cazzaniga
    • 2
  • Dario Pescini
    • 2
  • Giancarlo Mauri
    • 2
  • Luciano Milanesi
    • 1
  1. 1.Institute for Biomedical TechnologiesNational Research CouncilSegrateItaly
  2. 2.Department of Informatics, Systems and CommunicationsUniversity of Milan-BicoccaMilanItaly

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