Pollack, Jordan, Mark A. Bedau, Phil Husbands, Richard A. Watson, and Takashi Ikegami. “Spacial representation for artificial chemistry based on small-world networks.” (2004): 507-513.
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A method to simulate molecular reactions with a graph whose nodes represent molecules or atomic modules and whose edges represent the bond/contact relation is proposed. The graph is updated by two actions: passive rewiring of contact edges that gives the graph a small-world property and active rewiring by active nodes’ programs that rewire bond and contact edges. As examples, the replication of a chain molecule and the partitioning of a network are successfully simulated.