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A Multi-volume Approach to Stochastic Modeling with Membrane Systems

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Algorithmic Bioprocesses

Part of the book series: Natural Computing Series ((NCS))

Abstract

In the last decades, experimental investigations have evidenced the role of biological noise in cellular processes, and several stochastic approaches have been proposed to modeling and simulation of biochemical networks. Here, we review the main stochastic procedures defined for single-volume biochemical systems (SSA, tau-leaping), and discuss their practical utility and limitations. Then, within the framework of membrane systems, we propose a multi-volume generalization of the tau-leaping algorithm, called τ-DPP, feasible for the stochastic analysis of complex biochemical systems. Finally, we present a case-study application of τ-DPP to an intracellular genetic oscillator, coupled with an intercellular communication mechanism.

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Author information

Authors and Affiliations

  1. Dipartimento di Informatica e Comunicazione, Università degli Studi di Milano, Via Comelico 39, 20135, Milano, Italy

    Daniela Besozzi

  2. Dipartimento di Informatica, Sistemistica e Comunicazione, Università degli Studi di Milano—Bicocca, Viale Sarca 336, 20126, Milano, Italy

    Paolo Cazzaniga, Dario Pescini & Giancarlo Mauri

Authors
  1. Daniela Besozzi
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  2. Paolo Cazzaniga
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  3. Dario Pescini
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  4. Giancarlo Mauri
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Corresponding author

Correspondence to Daniela Besozzi .

Editor information

Editors and Affiliations

  1. Dept. Computer Science, University of British Columbia, Main Mall 201-2366, Vancouver, V6T 1Z4, Canada

    Anne Condon

  2. Dept. Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel

    David Harel

  3. Leiden Inst. Advanced Computer Science, Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, Netherlands

    Joost N. Kok

  4. Turku Centre for Computer Science, Lemminkaisenkatu 14 A, Turku, 20520, Finland

    Arto Salomaa

  5. Computer Science, Computation,, California Inst. of Technology, Pasadena, 91125, U.S.A.

    Erik Winfree

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© 2009 Springer-Verlag Berlin Heidelberg

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Besozzi, D., Cazzaniga, P., Pescini, D., Mauri, G. (2009). A Multi-volume Approach to Stochastic Modeling with Membrane Systems. In: Condon, A., Harel, D., Kok, J., Salomaa, A., Winfree, E. (eds) Algorithmic Bioprocesses. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88869-7_26

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  • DOI: https://doi.org/10.1007/978-3-540-88869-7_26

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-88868-0

  • Online ISBN: 978-3-540-88869-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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