Extension of metabolic control analysis to bioreactor systems

Abstract

This thesis consists of two parts: i) extracellular modeling and ii) intracellular modeling. For the extracellular modeling, we focus on strategies for obtaining kinetic parameters from the continuous stiffed tank bioreactor systems. Kinetics of the cell cultures plays an important role in designing and optimizing biochemical processes. However, such kinetic information is not always available. The process of obtaining detailed kinetic equations and parameters requires multiple steady-state experiments that can be time-consuming and uneconomical. Therefore, to simplify the process, we propose to determine these kinetic parameters using continuous cultures. To do so, we apply the concept of Metabolic Control Analysis (MCA) to continuous stirred tank bioreactor systems. MCA is commonly used to analyze the control of metabolic reactions of living organisms and is based on a set of partial derivatives known as control and elasticity coefficients. These coefficients characterize the responses with respect to changes in enzyme activities or parameters. Indirectly, the kinetics of the cell cultures is embedded in these coefficients. We have developed a methodology to extract kinetic information from the control coefficients. Various approaches are used to estimate the control coefficients: i) dynamic approach (Delgado and Liao, 1992a, b), ii) perturbed steady state approach developed in this study and iii) the combination of the first two approaches. Besides these kinetic information, the coefficients can be utilized to improve the operating conditions. For intracellular modeling, we focus on developing rate expressions for enzymes of Escherichia coli in the glycolysis and the tficarboxylic acid cycle. In order to accommodate the effects of enzymes' inhibitors and activators towards the reaction rates, we adopt the Nfichaelis-Menten form of rate expressions to fit the experimental data obtained from literature. However, due to incomplete kinetic data and inconsistent rate units from various sources, the rate expressions are obtained only for enzymes with adequate information.