Discrete DNA reaction-diffusion model for implementing simple cellular automaton

Ibuki Kawamata, Satoru Yoshizawa, Fumi Takabatake, Ken Sugawara, Satoshi Murata

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Citations (Scopus)

Abstract

We introduce a theoretical model of DNA chemical reactiondiffusion network capable of performing a simple cellular automaton. The model is based on well-characterized enzymatic bistable switch that was reported to work in vitro. Our main purpose is to propose an autonomous, feasible, and macro DNA system for experimental implementation. As a demonstration, we choose a maze-solving cellular automaton. The key idea to emulate the automaton by chemical reactions is assuming a space discretized by hydrogel capsules which can be regarded as cells. The capsule is used both to keep the state uniform and control the communication between neighboring capsules. Simulations under continuous and discrete space are successfully performed. The simulation results indicate that our model evolves as expected both in space and time from initial conditions. Further investigation also suggests that the ability of the model can be extended by changing parameters. Possible applications of this research include pattern formation and a simple computation. By overcoming some experimental difficulties, we expect that our framework can be a good candidate to program and implement a spatio-temporal chemical reaction system.

Original languageEnglish
Title of host publicationUnconventional Computation and Natural Computation - 15th International Conference, UCNC 2016, Proceedings
PublisherSpringer Verlag
Pages168-181
Number of pages14
Volume9726
ISBN (Print)9783319413112
DOIs
Publication statusPublished - 2016
Event15th International Conference on Unconventional Computation and Natural Computation, UCNC 2016 - Manchester, United Kingdom
Duration: 2016 Jul 112016 Jul 15

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume9726
ISSN (Print)03029743
ISSN (Electronic)16113349

Other

Other15th International Conference on Unconventional Computation and Natural Computation, UCNC 2016
CountryUnited Kingdom
CityManchester
Period16/7/1116/7/15

Keywords

  • Cellular automaton
  • DNA chemical reaction network
  • Maze solving
  • Pattern formation
  • Spatio-temporal evolution

ASJC Scopus subject areas

  • Computer Science(all)
  • Theoretical Computer Science

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  • Cite this

    Kawamata, I., Yoshizawa, S., Takabatake, F., Sugawara, K., & Murata, S. (2016). Discrete DNA reaction-diffusion model for implementing simple cellular automaton. In Unconventional Computation and Natural Computation - 15th International Conference, UCNC 2016, Proceedings (Vol. 9726, pp. 168-181). (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); Vol. 9726). Springer Verlag. https://doi.org/10.1007/978-3-319-41312-9_14