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Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting

  • Gil Benkö
  • Christoph Flamm
  • Peter F. Stadler
Part of the Lecture Notes in Computer Science book series (LNCS, volume 2801)

Abstract

We use a Toy Model of chemistry that represents molecules in terms of usual structural formulae to generate large chemical reaction networks. An extremely simplified quantum mechanical energy calculation and a straightforward implementation of reactions as graph rewritings ensure both transparency and closeness to chemical reality, both conditions that are necessary for the analysis of generic properties of large reaction networks. We show that some chemical networks graphs, e.g., repetitive Diels-Alder reactions, have the small-world property and exhibit a scale-free degree distribution. On the other hand, the Formose reaction does not fit well into this paradigm.

Keywords

Metabolic Network Reaction Network Graph Grammar Chemical Network Reaction Rule 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2003

Authors and Affiliations

  • Gil Benkö
    • 1
    • 2
  • Christoph Flamm
    • 2
  • Peter F. Stadler
    • 1
    • 2
    • 3
  1. 1.Lehrstuhl für Bioinformatik, Institut für InformatikUniversität LeipzigLeipzigGermany
  2. 2.Insitut für Theoretische Chemie und Molekulare StrukturbiologieUniversität WienWienAustria
  3. 3.Santa Fe InstituteSanta Fe

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