Chemical analog computers for clock frequency control based on p modules

  • Authors:

  • Thomas Hinze;Christian Bodenstein;Benedict Schau;Ines Heiland;Stefan Schuster

  • Affiliations:

  • School of Biology and Pharmacy, Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany;School of Biology and Pharmacy, Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany;School of Biology and Pharmacy, Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany;School of Biology and Pharmacy, Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany;School of Biology and Pharmacy, Department of Bioinformatics, Friedrich Schiller University Jena, Jena, Germany

  • Venue:
  • CMC'11 Proceedings of the 12th international conference on Membrane Computing
  • Year:
  • 2011

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Abstract

Living organisms comprise astonishing capabilities of information processing for efficient adaptation to environmental changes. Resulting chemical control loops and regulator circuits are expected to exhibit a high functional similarity to technical counterparts subsumed by analog computers. A fascinating example is given by circadian clocks providing an endogenous biological rhythm adapted to the daily variation of sunlight and darkness. Its underlying biochemical principle of operation suggests a general functional scheme corresponding to frequency control using phase-locked loops (PLL). From a systems biology point of view, clock systems can be decomposed into specific modules like low-pass filters, arithmetic signal comparators, and controllable core oscillators. Each of them processes analog chemical signals on the fly. We introduce P modules in order to capture structure, behaviour, and interface of pure chemical analog computer models in terms of building blocks along with two simulation case studies. The first one is focused on chemical analog computer components including a controllable Goodwin-type core oscillator while the second one evolves an entire PLL-based frequency control by means of a pure chemical circadian clock model.