Abstract
An Analysis on the self-assembly process in DNA tile computing is presented using the cellular automata approach. It is known that a cellular automata model can simulate various complex systems by updating the states of calculation cells based on the local interaction rules. Generally DNA computing is operated through the local interaction between complimentary strands. Therefore the cellular automata approach is suitable to investigate qualitative features of such systems. Focusing on the cryptosystem using a DNA motif called a triple crossover (TX) tile, we construct a new cellular automata model. Our objective is to find a solution to improve the fragmentation problem in the self-assembly process of a calculation sheet of TX tiles, because the fragmentation prevents the system from realizing the sufficient performance. Our results suggest that such fragmentation occurs when the error correction function is lost due to the strong stability of local interaction. It is expected that these findings using cellular automata simulations provide effective information to solve the problems to develop practical applications of DNA-based computation.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
Similar content being viewed by others
References
Chopard, B., Droz, M.: Cellular Automata Modeling of Physical Systems. Cambridge University Press, Cambridge (1998)
Mao, C., LaBean, T.H., Reif, J.H., Seeman, N.C.: Logical computation using algorithmic self-assembly of DNA triple-crossovermolecules. Nature 407, 493–496 (2000)
Hirabayashi, M., Nishikawa, A., Tanaka, F., Hagiya, M., Kojima, H., Oiwa, K.: Analysis on Secure and Effective Applications of a DNA - Based Cryptosystem. In: 6th IEEE International Conference on Bio-Inspired Computing: Theory and Applications, pp. 205–210 (2011)
Hirabayashi, M., Nishikawa, A., Tanaka, F., Hagiya, M., Kojima, H., Oiwa, K.: Implementation of tile sequencing for DNA logical computation toward next-generation information security. In: 5th IEEE International Conference on Bio-Inspired Computing: Theory and Applications, pp. 1296–1307 (2010)
Hirabayashi, M., Kojima, H., Oiwa, K.: Effective algorithm to encrypt information based on self-assembly of DNA tiles. Nucleic Acids Symposium Series, vol. 53. Oxford Press (2009)
Hirabayashi, M., Kojima, H., Oiwa, K.: Design of true random one-time-pads in DNA XOR cryptosystem. In: 4th International Workshop on Natural Computing, vol. 2, pp. 174–183 (2010)
Chen, Z., Xu, J.: One-Time-Pads Encryption in the Tile Assembly Model. In: Third International Conference on Bio-Inspired Computing: Theories and Applications, pp. 23–29 (2008)
Shannon, C.: Communication Theory of Secrecy Systems. Bell System Technical Journal 28(4), 656–715 (1949)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Hirabayashi, M., Kinoshita, S., Tanaka, S., Honda, H., Kojima, H., Oiwa, K. (2012). Cellular Automata Analysis on Self-assembly Properties in DNA Tile Computing. In: Sirakoulis, G.C., Bandini, S. (eds) Cellular Automata. ACRI 2012. Lecture Notes in Computer Science, vol 7495. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-33350-7_56
Download citation
DOI: https://doi.org/10.1007/978-3-642-33350-7_56
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-33349-1
Online ISBN: 978-3-642-33350-7
eBook Packages: Computer ScienceComputer Science (R0)