Pattern Formation on Discrete Gel Matrix Based on DNA Computing

Abstract

In this paper, we consider the implementation of a cellular automaton by DNA computing. The proposed system is a reaction–diffusion system built on a structured hydrogel matrix that mimics cellular compartments of biological tissues. Since the cellular automaton is materialized by a hydrogel matrix, the system is called gellular automaton which is theoretically capable of pattern formation and computation by chemical reactions. We focus on technical aspects of the implementation of the gellular automata, such as fabrication of the array of cells, the realization of inter-cellular molecular communication, and how to realize state transitions of cells. Along with the evaluation of each technical element, some simple experimental demonstrations of pattern formation are described.

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Acknowledgements

This research was supported by Grant-in-Aid for Scientific Research on Innovative Areas “Molecular Robotics” Japan Society for the Promotion of Science (JP) (no. 24104005), Grant-in-Aid for Scientific Research(A) 15H01715, and Grant-in-Aid for Young Scientists (Start-up, 26880002).

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Correspondence to Ibuki Kawamata or Satoshi Murata.

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Hosoya, T., Kawamata, I., Nomura, S.M. et al. Pattern Formation on Discrete Gel Matrix Based on DNA Computing. New Gener. Comput. 37, 97–111 (2019). https://doi.org/10.1007/s00354-018-0047-1

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Keywords

  • Chemical implementation of cellular automata
  • Gellular automata
  • Molecular computing
  • DNA computing
  • Reaction–diffusion system