Florian Centler, Pietro Speroni di Fenizio, Naoki Matsumaru, Peter Dittrich (2006)
Chemical organizations in the central sugar metabolism of Escherichia Coli
In: Modeling and Simulation in Science Engineering and Technology, Post-proceedings of ECMTB 2005 
preprint (pdf)

Abstract:

The theory of chemical organisations is employed as a novel method to analyse and understand biological network models. The method allows to decompose a chemical reaction network into sub-networks that are (algebraically) closed and self-maintaining. Such sub-networks are termed organisations. Although only stoichiometry is considered to compute organisations, the analysis allows to narrow down the potential dynamic behaviour of the network: organisations represent potential steady state compositions of the system. When applied to a model of sugar metabolism in E. coli including gene expression, signal transduction, and enzymatic activities, some organisations are found to coincide with inducible biochemical pathways.