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    A framework for modelling the interactions between biochemical reactions and inorganic ionic reactions in aqueous systems.
    (2022) Brouckaert, Christopher John.; Lokhat, David.
    Bio‐processes interact with the aqueous environment in which they take place. Integrated bio‐process and three‐phase (aqueous–gas–solid) multiple strong and weak acid/base system models are being developed for a range of wastewater treatment applications, including anaerobic digestion, biological sulphate reduction, autotrophic denitrification, biological desulphurization and plant‐wide wastewater treatment systems. In order to model, measure and control such integrated systems, a thorough understanding of the interaction between the bio‐processes and aqueous‐phase multiple strong and weak acid/bases is required. This thesis is based on a series of five papers that were published in Water SA during 2021 and 2022. Chapter 2 (Part 1 of the series) sets out a conceptual framework and a methodology for deriving bioprocess stoichiometric equations. It also introduces the relationship between alkalinity changes in bioprocesses and the underlying reaction stoichiometry, which is a key theme of the series. Chapter 3 (part 2 of the series) presents the stoichiometric equations of the major biological processes and shows how their structure can be analysed to provide insight into how bioprocesses interact with the aqueous environment. Such insight is essential for confident, effective and reliable use of model development protocols and algorithms. Where aqueous ionic chemistry is combined with biological chemistry in a bioprocess model, it is advantageous to deal with the very fast ionic reactions in an equilibrium sub‐model. Chapter 4 (part 5 of the series) presents details of how of such an equilibrium speciation sub‐model can be implemented, based on well‐known open‐source aqueous chemistry models. Specific characteristics of the speciation calculations which can be exploited to reduce the computational burden are highlighted. The approach is illustrated using the ionic equilibrium sub‐model of a plant‐wide wastewater treatment model as an example. Provided that the correct measurements are made that can quantify the material content of the bioprocess products (outputs), the material content of the bioprocess reactants (inputs) can be determined from the bioprocess products via stoichiometry. The links between the modelling and measurement frameworks, which use summary measures such as chemical oxygen demand (COD) and alkalinity, are described in parts 3 and 4 of the series, which are included as appendices to the thesis. An additional paper, presenting case study on modelling an auto‐thermal aerobic bio‐reactor, is included as a third appendix, as it demonstrates the application of some of the principles developed in the series of papers.