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Artificial Life

Winter 2009, Vol. 15, No. 1, Pages 71-88
(doi: 10.1162/artl.2009.15.1.15105)
© 2008 Massachusetts Institute of Technology
A Topological Approach to Chemical Organizations
Article PDF (539.79 KB)
Abstract

Large chemical reaction networks often exhibit distinctive features that can be interpreted as higher-level structures. Prime examples are metabolic pathways in a biochemical context. We review mathematical approaches that exploit the stoichiometric structure, which can be seen as a particular directed hypergraph, to derive an algebraic picture of chemical organizations. We then give an alternative interpretation in terms of set-valued set functions that encapsulate the production rules of the individual reactions. From the mathematical point of view, these functions define generalized topological spaces on the set of chemical species. We show that organization-theoretic concepts also appear in a natural way in the topological language. This abstract representation in turn suggests the exploration of the chemical meaning of well-established topological concepts. As an example, we consider connectedness in some detail.