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Applications of Membrane Computing in Systems and Synthetic Biology pp 65–96Cite as

Molecular Diffusion and Compartmentalization in Signal Transduction Pathways: An Application of Membrane Systems to the Study of Bacterial Chemotaxis

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Part of the book series: Emergence, Complexity and Computation ((ECC,volume 7))

Abstract

In this chapter we present an application of membrane systems to the study of intracellular diffusive processes. In particular, a class of membrane systems, called \(\tau \)-DPP, is used for the modeling, simulation and analysis of bacterial chemotaxis. Two different models of this signal transduction pathway are presented. The first is a single volume model used to investigate the properties of bacterial chemotaxis and to analyze the effects of different perturbations (deletion of chemotactic proteins, addition of distinct amounts of external ligand, effect of different methylation states of the receptors) on the system dynamics. The second model represents a multivolume extension of the former, and it is exploited for the analysis of the diffusive processes that give rise to the formation of concentration gradients throughout the bacterial cytoplasm. The outcome of stochastic simulations of both models are exploited to analyze the process of synchronization of flagella, in order to evaluate the running and tumbling time intervals of bacterial cells.

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Acknowledgments

Giancarlo Mauri and Dario Pescini acknowledge the partial funding by Regione Lombardia, research project “Network Enabled Drug Design (NEDD)”.

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Authors and Affiliations

  1. Dipartimento di Scienze Umane e Sociali, Università degli Studi di Bergamo, Piazzale S. Agostino 2, 24129 , Bergamo, Italy

    Paolo Cazzaniga

  2. Dipartimento di Informatica, Università degli Studi di Milano, Via Comelico 39, 20135 , Milano, Italy

    Daniela Besozzi

  3. Dipartimento di Statistica e Metodi Quantitativi, Università degli Studi di Milano-Bicocca, Via Bicocca degli Arcimboldi 8, 20126 , Milano, Italy

    Dario Pescini

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

    Giancarlo Mauri

Authors
  1. Paolo Cazzaniga
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  2. Daniela Besozzi
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  3. Dario Pescini
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  4. Giancarlo Mauri
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Correspondence to Paolo Cazzaniga .

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Editors and Affiliations

  1. The School of Mathematical and Computer Sciences, Heriot-Watt University, Eindhoven, United Kingdom

    Pierluigi Frisco

  2. The Department of Computer Science, University of Sheffield, Sheffield, United Kingdom

    Marian Gheorghe

  3. Department of Computer Science and Artificial Intelligence, University of Sevilla, Sevilla, Spain

    Mario J. Pérez-Jiménez

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Cazzaniga, P., Besozzi, D., Pescini, D., Mauri, G. (2014). Molecular Diffusion and Compartmentalization in Signal Transduction Pathways: An Application of Membrane Systems to the Study of Bacterial Chemotaxis. In: Frisco, P., Gheorghe, M., Pérez-Jiménez, M. (eds) Applications of Membrane Computing in Systems and Synthetic Biology. Emergence, Complexity and Computation, vol 7. Springer, Cham. https://doi.org/10.1007/978-3-319-03191-0_3

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  • DOI: https://doi.org/10.1007/978-3-319-03191-0_3

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  • Online ISBN: 978-3-319-03191-0

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