Name
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. |
Year | DOI | Venue |
|---|---|---|
2009 | 10.1162/artl.2009.15.1.15105 | Artificial Life |
Keywords | Field | DocType |
organization theory,connectedness.,chemical reaction networks,chemical meaning,topological approach,chemical species,topological language,generalized topology,set-valued set function,generalized topological space,flux analysis,large chemical reaction network,closure functions,well-established topological concept,mathematical approach,stoichiometric matrix,hypergraphs,mathematical point,chemical organization,metabolic pathway,connectedness,topological space | Set function,Prime (order theory),Topology,Social connectedness,Algebraic number,Topological space,Computer science,Chemical species,Constraint graph,Exploit | Journal |
Volume | Issue | ISSN |
15 | 1 | 1064-5462 |
Citations | PageRank | References |
9 | 1.59 | 13 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Gil Benkö | 1 | 57 | 5.54 |
| Florian Centler | 2 | 69 | 10.73 |
| Peter Dittrich | 3 | 161 | 19.50 |
| Christoph Flamm | 4 | 374 | 31.28 |
| Bärbel M. R. Stadler | 5 | 52 | 11.64 |
| Peter F. Stadler | 6 | 256 | 62.77 |