Mathematical modelling and experiment design for hypothesis testing and model validation for PSEUDOMONAS PUTIDA (Partner 11 of SYSMO)

White Biotechnology (the exploitation of the catalytic properties of microorganisms for industrial applications) is increasingly recognized as one of the pillars of the knowledge-base Economy that Europe is bound to drive into. The purpose of this project is to develop the necessary knowledge base and the material and conceptual (computational) resources to establish the soil bacterium Pseudomonas putida as the vehicle for implementing biological activities into a whole range of industrially-related processes. Mathematical modelling has become a common approach in most engineering disciplines. In general, this approach yields models that give a very accurate description of the system. However, predictions from such models are not meaningful or useful unless the model can be validated against collected experimental data. To achieve this, we must estimate certain parameters within the model to match the model predictions with collected data / the identification problem. The work in this proposal sets out to integrate modelling, experiment design and validation, and control and optimisation into a single framework that would lead to increased productivity and reduced experimental costs. The integration of these three research tools represents a unique, novel, and interdisciplinary approach to addressing the complicated research and industrial problem of model-based control and optimisation of the culture processes. It builds on existing work carried out by the authors and seeks to integrate various models developed with the ultimate goal of model-based control and optimisation of culture processes.

White Biotechnology (the exploitation of the catalytic properties of microorganisms for industrial applications) is increasingly recognized as one of the pillars of the knowledge-base Economy that Europe is bound to drive into. The purpose of this project is to develop the necessary knowledge base and the material and conceptual (computational) resources to establish the Gram negative soil bacterium Pseudomonas putida strain KT2440 as the vehicle for implementing biological activities into a whole range of industrially-related processes. The specific goal of the overall proposal is therefore to exploit the full biotechnological efficacy of Pseudomonas putida KT2440 by developing new optimization strategies that achieve quantum increases in cell factory performance through a systems biology understanding of key metabolic and regulatory parameters that control cellular responses to key stresses generated during biotechnological application of this versatile bacterium. Dynamic mechanistic modelling has become a common approach in most engineering disciplines. In general, this approach yields nonlinear parametric models that, once the parameters have been identified, give a very accurate mathematical description of the system, much more so than high dimensional linear models obtained using classical identification algorithms. However, predictions from such a model are not meaningful or useful unless the model can be validated against collected experimental data. The work in this proposal sets out to integrate modelling, experiment design and validation, and control and optimisation into a single framework that would lead to increased productivity, regulated quality, and reduced experimental costs. The integration of these three research tools represents a unique, novel, and interdisciplinary approach to addressing the complicated research and industrial problem of model-based control and optimisation of the P. putida culture processes.