Multi-enzyme Process Modeling

The subject of this thesis is to develop a methodological framework that can systematically guide mathematical model building for better understanding of multi-enzyme processes. In this way, opportunities for process improvements
can be identified by analyzing simulations of either existing or potential process configurations operated under different conditions. In these cases, process engineering, enzyme immobilization and protein engineering are presented as
fields that can offer feasible solutions for better process configurations or biocatalyst modification to enhance actual process implementation, especially at an industrial level.
Multi-enzyme processes are characterized by a high degree of complexity due to the mixture of enzymes that catalyze several reactions. Therefore, it is necessary to understand how enzymes act in a coordinated and interactive way, and also how enzymes are affected (in a positive or negative way) by the presence of the other enzymes and compounds in the media.
In this thesis the concept of multi-enzyme in-pot term is adopted for processes that are carried out by the combination of enzymes in a single reactor and implemented at pilot or industrial scale. In order to understand the difference
between multi-enzyme processes, a number of concepts are discussed in the second chapter of this thesis and has also been published as a review. Furthermore, a classification of multi-enzyme processes is suggested to clarify the ambiguous definitions found in the scientific literature.
Reliable mathematical models of such multi-catalytic schemes can exploit the potential benefit of these processes. In this way, the best outcome of the process can be obtained understanding the types of modification that are required for
process optimization. An effective evaluation of these processes is achieved by applying a methodological framework which provides a systematic way of modeling, a structure, guidance, documentation and support to the modeler.
The methodological framework developed here brings many benefits to multienzyme process modeling. This framework identifies generic features of the process and provides the information required to structure the process model
by using a step-by-step procedure with the required tools and methods. In this way, this framework increases efficiency of the model development process with respect to time and resources needed (fast and effective model development).
Furthermore, this methodology incorporates state-of-the-art methods and provides background and insight into their applications for model development purposes.
The methodological framework, which comprises five steps, is the main result of this thesis. The novel feature of this methodology is the emphasis on the multi-enzyme process concepts that is introduced in all steps. In this way,
the most relevant and necessary modeling issues can be precisely identified in order to achieve reliable mathematical structures of the processes. In the same way, specific mathematical techniques, for model quality evaluation such as
uncertainty and sensitivity analyses, are included in this methodology. Multienzyme process modeling is tremendously benefited with the introduction of these analyses which mark a big difference in the formulation of reliable models
for the multi-enzyme processes. In this way the model parameters that drives the main dynamic behavior can be identified and thus a better understanding of this type of processes.
In order to develop, test and verify the methodology, three case studies were selected, specifically the bi-enzyme process for the production of lactobionic acid, the bi-enzyme process for the production of N-acetyl-D-neuraminic acid, and the tri-enzyme process for the production of 1-phenylethylamine. Furthermore, different capabilities of the methodology are developed due to the valuable contributions of each case study. In this way, the methodology was also proven to be useful for a fast model formulation of multi-enzyme processes. Additionally, programming codes were developed using MATLAB (The Mathworks, Natick, MA) which were also used as computational tools to support the implementation, solution and analysis of all the mathematical problems faced in the case studies.