InterJournal Complex Systems, 1919
Status: Accepted
Manuscript Number: [1919]
Submission Date: 2006
A molecular network rewiring rule that represents spatial constraint
Author(s): Hideaki Suzuki

Subject(s): CX.67



Network artificial chemistry (NAC) is an approach to emulating molecular interaction in a solvent with a mathematical graph. To emulate molecules' spatial movement in a 3D space, we have to appropriately design rewiring rules for the NAC's weakest edges (van der Waals edges) so that the edges imitate the contact relation between molecules or atomic clusters. The paper presents one candidate solution for this problem. First, an energy function of network is introduced, and a rewiring rule is formulated using the criterion of the minimization of the energy. The energy consists of the node degree's diversity term and the second shortest path term, and its minimization makes a network have topological properties of a regular graph. Second, we conduct a NAC simulation using the established rewiring rule and compare the results with those of a random walk simulation that emulates Brownian motion of hard spheres in a 3D Euclid space. It is shown that the two experimental results are in good agreement with each other in terms of such network properties as the cluster coefficient and average path length or the joining and cutting probabilities of edges. This is an invited paper in the session titled "Life and Computation".

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