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Robust network clocks: Design of genetic oscillators as a complex combinatorial optimization problem

Yasuaki Kobayashi, Tatsuo Shibata, Yoshiki Kuramoto, and Alexander S. Mikhailov
Phys. Rev. E 83, 060901(R) – Published 3 June 2011

Abstract

Complex combinatorial optimization can be used to design network systems having desired dynamics and that are robust against structural perturbations. Here genetic networks exhibiting limit-cycle oscillations with prescribed periods and, furthermore, that are robust against the deletion of links and nodes or the application of noise are constructed. Large ensembles of robust genetic clocks with different periods could thus be obtained, and some of their statistical properties have been investigated. Similar methods can be used to design robust network oscillators of various origins.

    • Received 28 February 2011

    DOI:https://doi.org/10.1103/PhysRevE.83.060901

    ©2011 American Physical Society

    Authors & Affiliations

    Yasuaki Kobayashi1,*, Tatsuo Shibata2,3, Yoshiki Kuramoto4, and Alexander S. Mikhailov1

    • 1Department of Physical Chemistry, Fritz Haber Institute of the Max Planck Society, Faradayweg 4-6, D-14195 Berlin, Germany
    • 2Laboratory for Physical Biology, RIKEN Center for Developmental Biology, Kobe 650-0047, Japan
    • 3PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama, Japan
    • 4Research Institute for Mathematical Science, Kyoto University, Kyoto 606-8502, Japan

    • *yasuaki@fhi-berlin.mpg.de

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    Issue

    Vol. 83, Iss. 6 — June 2011

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