title: A graph-based reflexive artificial chemistry.
abstract: The conceptual divide between formal systems of computation and abstract models of chemistry is considered. As an attempt to concretely bridge this divide, a formalism is proposed that describes a constructive artificial chemistry on a space of directed graph structures. The idea for the formalism originates in computer science theory, with the traditional abstraction of a physical machine, the finite-state machine (FSM). In the FSM, the machine (state-transition graph) and input string (series of binary digits) are fundamentally distinct objects, separated by nature of the underlying formalism. This distinction is dissolved in the proposed system, resulting in a construction process that is reflexive: graphs interact with their own topological structure to generate a product. It is argued that this property of reflexivity is a key element missing from earlier model chemistries. Examples demonstrate the continuous emergence complex self-similar topologies, novel reaction pathways, and seemingly open-ended diversity. Implications of these findings are discussed.
authors.affiliation: Department of General Systems Studies, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan. chris@sacral.c.u-tokyo.ac.jp
authors.forename: Chris
authors.initials: C
authors.lastname: Salzberg
mesh_terms: D055598:Chemical Phenomena; D002621:Chemistry; D003196:Computer Graphics; D020342:Finite Element Analysis; D008958:Models, Molecular