Publications - Published papers

Please find below publications of our group. Currently, we list 501 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

A Topological Approach to Chemical Organization

Gil Benkö, Florian Centler, Peter Dittrich, Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler

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Alife 15: 71-88 (2009)

Abstract


Large chemical reaction networks often exhibit distinctive features which can be interpreted as higher-level structures. Prime examples are metabolic pathways in a biochemical context. In this contribution 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 the 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 suggest to explore the chemical meaning of well-established topological concepts. As an example, we consider connectedness in some details.

Keywords


chemical reaction networks, hypergraphs, stoichiometric matrix, flux analysis, generalized topology, closure functions, organization theory, connectedness