An Approach Toward Emulating Molecular Interaction with a Graph

Hideaki Suzuki

doi:10.1071/CH06182

RESEARCH FRONT

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An Approach Toward Emulating Molecular Interaction with a Graph

Hideaki Suzuki ^A

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^A 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

An Approach Toward Emulating Molecular Interaction with a Graph

Abstract

Acknowledgements

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