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Membrane Systems and Tools Combining Dynamical Structures with Reaction Kinetics for Applications in Chronobiology

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Applications of Membrane Computing in Systems and Synthetic Biology

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

Abstract

This chapter addresses three coordinated chronobiological studies demonstrating the convergence of experimental observations, fine-grained spatio-temporal modelling, and predictive simulation. Due to the discrete manner of molecular assembly in cell signalling and gene regulation, we define a framework of membrane systems equipped with discretised forms of reaction kinetics in concert with variable intramolecular structures. Our first study is dedicated to circadian clocks inducing daily biological rhythms. As an inspiring example, the KaiABC core oscillator reaches its functionality by cyclically varying protein structures. Within our second study, we present a meta-model of an entire circadian clockwork able to adapt its oscillation to an external stimulus in terms of a frequency control system acting in a phase-locked loop. Substrate concentration courses resulting from gene expression reflect its oscillatory behaviour utilised in a periodical trigger for subsequent processes. In this context, our third study cytometrically quantifies the dynamical behaviour of a bistable toggle switch resulting from mutual gene regulation.

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Notes

  1. 1.

    See the BioNetGen Documentation. A BioNetGen tutorial can be found online at: http://bionetgen.org/index.php/BioNetGen_Tutorial

  2. 2.

    www.biosystemsanalysis.de

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Authors and Affiliations

  1. Institute of Computer Science and Information and Media Technology, Brandenburg University of Technology, Postfach 10 13 44, 03013, Cottbus, Germany

    Thomas Hinze, Petra Hofstedt & Peter Sauer

  2. School of Biology and Pharmacy, Department of Bioinformatics, Friedrich Schiller University of Jena, Ernst-Abbe-Platz 1–4, 07743, Jena, Germany

    Thomas Hinze, Christian Bodenstein, Gabi Escuela, Gerd Grünert & Peter Dittrich

  3. Theoretical Systems Biology Group, Institute of Food Research, Norwich Research Park, Colney, Norwich, NR4 7UA, UK

    Jörn Behre

  4. Department of Biochemistry and Biophysics, University of Stockholm, Svante Arrhenius väg 16C, SE-106 91, Stockholm, Sweden

    Sikander Hayat

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  1. Thomas Hinze
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  2. Jörn Behre
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  3. Christian Bodenstein
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  4. Gabi Escuela
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Correspondence to Thomas Hinze .

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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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Hinze, T. et al. (2014). Membrane Systems and Tools Combining Dynamical Structures with Reaction Kinetics for Applications in Chronobiology. 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_5

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  • DOI: https://doi.org/10.1007/978-3-319-03191-0_5

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