Chemical Organizations in Natural Reaction Networks
The theory of chemical organizations is applied to several reaction network models, including a photochemical network of the Martian atmosphere, a Petri net model of bacteriophage lambda, and three models of Escherichia coli. All investigated networks are found to feature non-trivial hierarchies of organizations. In several instances, organizations - subnetworks that are algebraically closed and self-maintaining - are related to biological functions and states. It is shown that the theory of chemical organizations can be used as a capable novel network analysis technique for model validation and prediction, that is also suitable for genomewide models provided by systems biology approaches.