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

  • Thomas Hinze
  • Jörn Behre
  • Christian Bodenstein
  • Gabi Escuela
  • Gerd Grünert
  • Petra Hofstedt
  • Peter Sauer
  • Sikander Hayat
  • Peter Dittrich
Chapter
Part of the Emergence, Complexity and Computation book series (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.

Keywords

Circadian Clock Gene Regulatory Network Membrane System Derivation Tree Reaction Rule 
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 International Publishing Switzerland 2014

Authors and Affiliations

  • Thomas Hinze
    • 1
    • 2
  • Jörn Behre
    • 3
  • Christian Bodenstein
    • 2
  • Gabi Escuela
    • 2
  • Gerd Grünert
    • 2
  • Petra Hofstedt
    • 1
  • Peter Sauer
    • 1
  • Sikander Hayat
    • 4
  • Peter Dittrich
    • 2
  1. 1.Institute of Computer Science and Information and Media TechnologyBrandenburg University of TechnologyCottbusGermany
  2. 2.School of Biology and Pharmacy, Department of BioinformaticsFriedrich Schiller University of JenaJenaGermany
  3. 3.Theoretical Systems Biology GroupInstitute of Food ResearchNorwichUK
  4. 4.Department of Biochemistry and BiophysicsUniversity of StockholmStockholmSweden

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