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Modelling of reaction kinetics in anaerobic ecosystems with considerations of thermodynamic principles

Hoh, Choon-Yee (1996) Modelling of reaction kinetics in anaerobic ecosystems with considerations of thermodynamic principles. PhD thesis, Murdoch University.

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The classical Michaelis-Menten Model is widely used as the basis for modelling of a number of biological systems. As the model does not consider the inhibitory effect of end products that accumulate in virtually all bioprocesses, it is often modified to prevent the overestimation of reaction rates when products have accumulated. Traditional approaches of model modification use the inclusion of irreversible, competitive and non competitive inhibition factors. The use of these factors is demonstrated in this thesis to be insufficient for the prediction of product inhibition and violating the laws of thermodynamics because they predicted positive reaction rates for reactions that were endergonic due to high end-product concentrations. This thesis developed a simple but practical model, the Equilibrium-Based Model, that includes the fundamentals of steady state kinetics as well as thermodynamic theory. When compared with Michaelis-Menten based models that use traditional inhibition factors, the Equilibrium-Based Model correctly predicts that a reaction stops when the free energy change is zero (no driving force) due to the increase of product and the decrease of substrate concentrations. As the new model takes into account all of the substrates and products, it was able to predict the inhibitory effect of multiple end-products. Moreover, the new model also considers the energetic effects of the reaction pH and temperature. The predictions of the model were confirmed with a variety of laboratory experiments using anaerobic bacteria. Experiments with bacterial H2 oxidation which confirmed the dependence of H2 threshold value (left over H2 concentration) on the energetic conditions, further showed that the threshold value and consequently, the reaction energetics can have major effects on the rates of H2 degradation. In contrast to the Michaelis-Menten Model, the Equilibrium-Based Model accurately predicted the threshold level and its effect on the reaction kinetics, hence further validates the need of thermodynamic considerations in the modelling of biological processes that occur close to the dynamic equilibrium.

When implemented into an established anaerobic digester model, the Equilibrium-Based Model was able to predict realistic behaviour of a laboratory anaerobic digester. With the consideration of reaction energetics, the model correctly predicted end-product inhibition such as H2 inhibition of propionate degradation, without the need for any empirical inhibition factors. The model also provided fundamental scientific explanations for different accumulation patterns in H2 and specific organic fatty acids during the overloading and shockloading of anaerobic digesters. Furthermore, it could explain why temperature and pH changes can initiate severe changes in the behaviour of anaerobic digesters. The model further revealed a plausible explanation for the role of H2 degrading homoacetogenic bacteria for being able to consume rather than produce hydrogen when the H2 concentration in anaerobic digesters is elevated with increasing loading rate. This was later confirmed by laboratory experiments. In summary, the Equilibrium-Based Model, which was developed using the fundamental theories of thermodynamics and kinetics, provides a scientifically correct and more realistic basis for a variety of models that describe bioprocesses that proceed close to the equilibrium such as the anaerobic digestion processes studied in this thesis. The possible use of this model in other biological systems is evident but requires further investigation.

Item Type: Thesis (PhD)
Murdoch Affiliation(s): School of Biological and Environmental Sciences
Notes: Note to the author: If you would like to make your thesis openly available on Murdoch University Library's Research Repository, please contact: Thank you.
Supervisor(s): Cord-Ruwisch, Ralf
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