Australian Journal of Chemistry Australian Journal of Chemistry Society
An international journal for chemical science
RESEARCH FRONT

An Approach Toward Emulating Molecular Interaction with a Graph

Hideaki Suzuki
+ Author Affiliations
- Author Affiliations

National Institute of Information and Communications Technology, Kobe 651-2492, Japan. Email: hsuzuki@nict.go.jp

Australian Journal of Chemistry 59(12) 869-873 https://doi.org/10.1071/CH06182
Submitted: 30 May 2006  Accepted: 16 August 2006   Published: 20 December 2006

Abstract

Network artificial chemistry (NAC) uses a mathematical graph to emulate molecular interaction in a solvent. To emulate molecules' movement in a three-dimensional space, rewiring rules for NAC graphs’ edges must be designed to enable the edges to imitate the relations between molecules or atomic clusters. Our research formulated the ‘network energy’ representing this constraint and rewired the NAC graph to minimize the required energy. Experimental results for the NAC rewiring are compared with a hard-sphere random walk simulation.


Acknowledgements

This study was supported in part by Doshisha University's Research Promotion Funds, ‘Academic Frontier, Intelligent Information Science’, in Japan.


References


[1]   W. Fontana, Algorithmic chemistry, in Artificial Life II: Proceedings of an Interdisciplinary Workshop on the Synthesis and Simulation of Living Systems (Santa Fe Institute Studies in the Sciences of Complexity, Vol. 10) (Ed. C. G. Langton) 1992, pp. 159–209 (Addison-Wesley: Boston, MA).

[2]   P. Dittrich, J. Ziegler, W. Banzhaf, Artif. Life 2001, 7,  225.
        | CrossRef |   

[3]   W. Fontana, L. W. Buss, Bull. Math. Biol. 1994, 56,  1.
         

[4]   H. Suzuki, Artif. Life 2000, 6,  103.
        | CrossRef |   

[5]   Y. Suzuki, H. Tanaka, Chemical evolution among artificial proto-cells, in Artificial Life VII: Proceedings of the Seventh International Conference on Artificial Life (Eds M. A. Bedau et al.) 2000, pp. 54–63 (MIT Press: Cambridge, MA).

[6]   P. Dittrich, W. Banzhaf, Artif. Life 1998, 4,  203.
        | CrossRef |   

[7]   P. Speroni di Fenizio, W. Banzhaf, Stability of metabolic and balanced organisations, in Advances in Artificial Life (6th European Conference on Artificial Life Proceedings) (Eds J. Kelemen, P. Sosik) 2001, pp. 196–205 (Springer: Berlin).

[8]   N. Ono, H. Suzuki, String rewriter that allows the maintenance of different types of self-replicators, in Proceedings of the Fifth International Conference on Humans and Computers (HC-2002) 2002, pp. 173–178.

[9]   H. Suzuki, N. Ono, Universal replication in a string rewriting system, in Proceedings of the Fifth International Conference on Humans and Computers (HC-2002) 2002, pp. 179–184.

[10]   N. Ono, T. Ikegami, Artificial chemistry: computational studies on the emergence of self-reproducing units, in Advances in Artificial Life (6th European Conference on Artificial Life Proceedings) (Eds J. Kelemen, P. Sosik) 2001, pp. 186–195 (Springer: Berlin).

[11]   D. Madina, N. Ono, T. Ikegami, Cellular evolution in a 3D lattice artificial chemistry, in Advances in Artificial Life (7th European Conference on Artificial Life Proceedings) (Eds W. Banzhaf, T. Christaller, P. Dittrich, J. T. Kim, J. Ziegler) 2003, pp. 59–68 (Springer: Berlin).

[12]   B. McMullin, D. Groß, Towards the implementation of evolving autopoietic artificial agents, in Advances in Artificial Life (6th European Conference on Artificial Life Proceedings) (Eds J. Kelemen, P. Sosik) 2001, pp. 440–443 (Springer: Berlin).

[13]   P. Speroni di Fenizio, P. Dittrich, W. Banzhaf, Spontaneous formation of proto-cells in an universal artificial chemistry on a planar graph, in Advances in Artificial Life (6th European Conference on Artificial Life Proceedings) (Eds J. Kelemen, P. Sosik) 2001, pp. 206–215 (Springer: Berlin).

[14]   H. Suzuki, Spacial representation for artificial chemistry based on small-world networks, in Proceedings of the Ninth International Conference on the Simulation and Synthesis of Living Systems (Artificial Life IX) (Eds J. Pollack, M. Bedau, P. Husbands, T. Ikegami, R. A. Watson) 2004, pp. 507–513.

[15]   H. Suzuki, Network artificial chemistry—molecular interaction represented by a graph, in Workshop and Tutorial Proceedings of the Ninth International Conference on the Simulation and Synthesis of Living Systems (Alife IX) (Eds M. Bedau, P. Husbands, T. Hutton, S. Kumar, H. Suzuki) 2004, pp. 63–70.

[16]   H. Suzuki, Mathematical folding of node chains in network artificial chemistry, in Proceedings 6th International Workshop on Information Processing in Cells and Tissues (IPCAT) 2005, pp. 52–68.

[17]   H. Suzuki, Mathematical folding that constructs data-flow computers in network artificial chemistry, in 8th European Conference on Artificial Life (ECAL) Workshop Proceedings 2005.

[18]   H. Suzuki, N. Ono, Statistical mechanical rewiring in network artificial chemistry, in 8th European Conference on Artificial Life (ECAL) Workshop Proceedings 2005.

[19]   G. M. Barrow, Physical Chemistry 1988, Ch. 15–17 (McGraw-Hill: New York, NY).

[20]   G. K. Vemulapalli, Physical Chemistry 1993, Ch. 23–33 (Prentice–Hall: Englewood Cliffs, NJ).

[21]   X. Burda, J. D. Correia, A. Krzywicki, Phys. Rev. E 2001, 64,  046118.
        | CrossRef |   

[22]   J. Berg, M. Lässig, Phys. Rev. Lett. 2002, 89,  228701.
        | CrossRef |   

[23]   D. J. Watts, S. H. Strogatz, Nature 1998, 393,  440.
        | CrossRef |   

[24]   J. Davidsen, H. Ebel, S. Bornholdt, Phys. Rev. Lett. 2002, 88,  128701.
        | CrossRef |   

[25]   R. Albert, A. L. Barabási, Rev. Mod. Phys. 2002, 74,  47.
        | CrossRef |   

[26]   www.aisee.com



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