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A simple method for simulating biochemical reaction networks

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Abstract

We propose a simple method of simulating chemical reaction networks by using a multiset rewriting system: abstract rewriting system on multisets (ARMS). We simulate the oregonator model, a mathematical model of the Belousov-Zhabotinskii reaction, and we obtain the same behavior when the differential equations or the Gillespie method are used. We also compose a 1- and 2-dimensional cellular automata by using ARMS, and confirm that it shows the pattern forming that is observed in the BZ reaction.

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Authors and Affiliations

  1. Nagoya University, Furocho, Chikusa-ku, Nagoya, 464-8603, Japan

    Mai Umeki & Yasuhiro Suzuki

Authors
  1. Mai Umeki
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  2. Yasuhiro Suzuki
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Corresponding author

Correspondence to Yasuhiro Suzuki.

Additional information

This work was presented in part at the First European Workshop on Artificial Life and Robotics, Vienna, Austria, July 12–13, 2007

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Umeki, M., Suzuki, Y. A simple method for simulating biochemical reaction networks. Artif Life Robotics 13, 566–569 (2009). https://doi.org/10.1007/s10015-008-0625-2

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  • DOI: https://doi.org/10.1007/s10015-008-0625-2

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