Fragments and Chemical Organisations

https://doi.org/10.1016/j.entcs.2011.04.003Get rights and content
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Abstract

We describe some aspects of the relationship between the chemical organisations of a reaction network and the chemical organisations of the fragments of this network. The conjecture is that fragments embeddable in a (feasible) organisation of molecules is a (feasible) organisation of fragments. We show this for a certain type of reaction network. However the fragmentation can always be altered such that the result becomes valid for all networks. Of course, this comes at a cost, namely a less coarse-grained fragment system. For the case that we do not change the fragmentation, we give examples for which the statement is true and counterexamples for which it is not. Furthermore we present some interesting examples illustrating our findings and further questions.

Keywords

fragments
rule-based models
model reduction
reaction networks
reaction network
chemical organisation theory
constructive dynamical systems

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1

Many thanks to Jérôme Feret and Tatjana Petrov, who introduced the authors to the concept of fragments. We acknowledge financial support by the German Research Foundation (DFG) Grant DI 852/4-3.