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System identification of bio-technological processes

Project members: M. Verhaegen, H.H.J. Bloemen (Biotechnology, Delft University of Technology)

The purpose of metabolic modeling is, in the first place, to understand the in vivo kinetics of the metabolism of a (micro) organism, and in the second place, to possibly reprogram this metabolism. The models often describe the metabolism under the assumption that the amount of enzymes remains constant, e.g. [27]. Both to reveal the metabolism and to verify the metabolic models, pulse experiments are conducted to a steady state culture of the particular organism. In order to be able to neglect the biosynthesis of new enzymes, the data should be collected within a time window of a few minutes after the pulse. This motivates the development of rapid sampling techniques to analyze the dynamics of the different metabolites in this time window (see, e.g., [31]). Besides, often measurements are available of the oxygen $\mathrm{O}_2$ and carbon dioxide $\mathrm{CO}_2$ concentrations in the off-gas of a fermenter, measured by a gas analyzer, and of the dissolved oxygen (DO) concentration in the fermentation broth.

The latter measurement can be used to reconstruct the dynamics of the oxygen uptake rate (OUR) and carbon dioxide evolution (CER) after the pulse, and in turn can be used to analyze the metabolism and to verify the metabolic models. To reconstruct the OUR and CER first a model is required that describes the dynamic relation between the OUR and CER (the impulse of the model) and the measured quantities provided by the gas analyzer and the DO sensor (the outputs of the model). Using this off-gas model, the OUR and CER can be reconstructed from the data (collected during the pulse experiment) by using estimation techniques.

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