TY - GEN
T1 - Discrete DNA reaction-diffusion model for implementing simple cellular automaton
AU - Kawamata, Ibuki
AU - Yoshizawa, Satoru
AU - Takabatake, Fumi
AU - Sugawara, Ken
AU - Murata, Satoshi
N1 - Funding Information:
We appreciate Masami Hagiya to motivate this research. Helpful advice from the experimental viewpoints were given by Hiroyuki Asanuma, Takashi Arimura, Yusuke Hara, and Nobuyoshi Miyamoto. We thank Teijiro Isokawa and Ferdinand Peper for discussion including the suggestion to simulate a normal automaton by a cellular automaton. This research was supported by Grant-in-Aid for Scientific Research on Innovative Areas “Molecular Robotics” (No. 24104005) and Grant-in-Aid for Young Scientists (Start-up, 26880002).
Publisher Copyright:
© Springer International Publishing Switzerland 2016.
PY - 2016
Y1 - 2016
N2 - 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.
AB - 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.
KW - Cellular automaton
KW - DNA chemical reaction network
KW - Maze solving
KW - Pattern formation
KW - Spatio-temporal evolution
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U2 - 10.1007/978-3-319-41312-9_14
DO - 10.1007/978-3-319-41312-9_14
M3 - Conference contribution
AN - SCOPUS:84977538937
SN - 9783319413112
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 168
EP - 181
BT - Unconventional Computation and Natural Computation - 15th International Conference, UCNC 2016, Proceedings
A2 - Condon, Anne
A2 - Amos, Martyn
PB - Springer Verlag
T2 - 15th International Conference on Unconventional Computation and Natural Computation, UCNC 2016
Y2 - 11 July 2016 through 15 July 2016
ER -