CS Forum: "Cellular automata materialised as DNA-based reaction-diffusion systems" Ibuki Kawamata, Tohoku University

CS department's public guest lecture, open to everyone free-of-charge.

Professor Ibuki Kawamata
Tohoku University, Japan

Host: Professor Pekka Orponen
Time: 14:15 (coffee at 14:00)
Venue: T3, CS building

Cellular automata materialised as DNA-based reaction-diffusion systems

Abstract:

We consider the implementation of cellular automata by means of DNA computing. The proposed approach is as reaction-diffusion systems built on a structured hydrogel matrix that mimics cellular compartments of biological tissues. Since a cellular automaton is thus materialised by a hydrogel matrix, the system is called a gellular automaton, and it is theoretically capable of pattern formation and computation by chemical reactions.

In the presentation, I will discuss both experimental and theoretical aspects of gellular automata. On the experimental side, a demonstration of pattern formation along with technical issues to realise the system are explained. Since gellular automata are fundamentally asynchronous and require restricted transition rules (such as boolean totalistic, non-camouflage), their computational capability is not obvious. To tackle the problem, we have theoretically analysed the properties of gellular automata using several types of simulations.

In the future, combined with multifunctionality of DNA molecules, the programmability of gellular automata would enable bottom-up fabrication of complex systems, such as self-healing composites and artificial organs.

Bio:

Ibuki Kawamata received a Ph. D. from the Department of Computer Science, Graduate School of Information Science and Technology, The University of Tokyo in 2014. He is now an assistant professor at the Department of Robotics, Graduate School of Engineering, Tohoku University, Japan. His research fields are molecular robotics, DNA computing and DNA nanotechnology, and he is currently working on two topics. One is implementing a computation framework using DNA-based reaction-diffusion systems, and the other is constructing mechanical DNA nanostructures capable of conformational change.

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Prof. Ibuki Kawamata is visiting Prof. Pekka Orponen on 19-23 Feb and is available for dicussion during his visit.