Summary
The theory of chemical organizations is employed as a novel method to analyze and understand biological network models. The method allows us to decompose a chemical reaction network into sub-networks that are (algebraically) closed and self-maintaining. Such sub-networks are termed organizations. Although only stoichiometry is considered to compute organizations, the analysis allows us to narrow down the potential dynamic behavior of the network: organizations 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 organizations are found to coincide with inducible biochemical pathways.
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Centler, F., Fenizio, P.S., Matsumaru, N., Dittrich, P. (2007). Chemical Organizations in the Central Sugar Metabolism of Escherichia coli . In: Deutsch, A., Brusch, L., Byrne, H., Vries, G.d., Herzel, H. (eds) Mathematical Modeling of Biological Systems, Volume I. Modeling and Simulation in Science, Engineering and Technology. Birkhäuser Boston. https://doi.org/10.1007/978-0-8176-4558-8_10
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DOI: https://doi.org/10.1007/978-0-8176-4558-8_10
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