A hybrid cybernetic modeling for the growth of Escherichia coli in glucose-pyruvate mixtures

Flux balance analysis in combination with the decomposition of metabolic networks into elementary modes has provided a route to modeling cellular metabolism. It is dependent, however, on the availability of external fluxes such as substrate uptake or growth rates before estimates of intracellular fluxes become available. The framework classically does not allow modeling of metabolic regulation or the formulation of dynamic models except through dynamic measurement of external fluxes. The cybernetic modeling approach of Ramkrishna and coworkers provides a dynamic framework for modeling metabolic systems because of its focus on describing regulatory processes based on cybernetic arguments which have the capacity to describe both external and internal fluxes. The approach presented in this thesis uses the decomposition of network into elementary modes with cybernetic control on the selective combination of elementary modes so that global objectives such as the maximization of carbon uptake or growth rate are met. The hybrid cybernetic model in this thesis uses pseudo-steady state balances for each mode which greatly simplify the computational effort required for the analysis of these models. The main objective of this thesis is to report on the performance of hybrid cybernetic models in predicting bioprocess performance in batch and continuous reactors and evaluating the effect of regulatory processes on reactor behavior. The preliminary simulations of the hybrid cybernetic models with the simplified network and the reduced network have successfully shown the same performances of those models. Based on preliminary observations, the hybrid cybernetic model for the anaerobic growth of E. coli in glucose-pyruvate mixtures is validated by batch experiments. The anaerobic batch cultures in glucose-pyruvate mixtures showed the preculturing effects as simulated by the previous cybernetic model. The identified hybrid cybernetic model has shown the steady state multiplicity of continuous reactor in glucose-pyruvate mixtures, confirmed experimentally at dilution rates 0.308 and 0.318 h-1. Also, the hybrid cybernetic model of the more detailed metabolic network presents oscillatory behavior of continuous bioreactor in glucose-only media under the dilution rate of 0.03 h-1