Cellular Automata Approach for Characterizing of DNA Tile Computing
Miki Hirabayashi, Syunsuke Kinoshita, Shukichi Tanaka, Hajime Honda, Hiroaki Kojima and Kazuhiro Oiwa
An cellular automata (CA) analysis on technical problems in DNA tile computing is presented. Using a CA model, various complex systems can be simulated by updating the states of calculation cells based on the local interaction rules. This approach is suitable to verify qualitative features of DNA computing, because it is operated through the local interaction between complimentary strands of DNAs. Here we investigate the cryptosystem using a DNA motif called a triple crossover (TX) tile using a CA model. We aim at improving the problems that prevent the system from realizing the sufficient performance in the selfassembly process of a calculation sheet of TX tiles. Our results indicate that such problems connect deeply into stability issues of local interaction. There are several problems to solve in order to realize practical applications of DNA computing such as DNA cryptosystem.We expect that CA analyses will provide effective solutions to them.
Keywords: DNA computing, self-assembly, DNA cryptosystem, pattern formation, DNA nanostructure, cellular automata approach.