Modeling of the Main Metabolism in Escherichia coli and Ruled-Based Dynamic Simulation of the Batch Culture

Mathematical models for the main metabolic pathways such as glycolysis, TCA cycle, glyoxylate pathway, anapleorotic pathway etc. were considered to simulate the dynamic behavior of the metabolism of Escherichia coli in the batch culture. A rule -based approach was employed to express the metabolic changes caused by gene-level regulation in response to the change in culture environment and/or cellpsilas state. It was shown that the transition from glycolysis to gluconeogenesis as the carbon source changes from glucose to acetate during the batch culture could be simulated as observed in experiments. This approach enables us to simulate the metabolic changes in the specific gene knockout mutants.