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Optogenetic modulation of adenosine triphosphatase (ATPase) expression represents a novel approach to maximize bioprocess efficiency by leveraging enforced adenosine triphosphate (ATP) turnover. In this study, we experimentally implement a model-based open-loop optimization scheme for optogenetic modulation of the expression of ATPase. Increasing the intracellular concentration of ATPase, and thus the level of ATP turnover, in bioprocesses with product synthesis coupled with ATP generation, can lead to increased product formation and substrate uptake. Previous simulation studies formulated optimal control problems using dynamic constraint-based models to find optimal light inputs in fermentations with optogenetically mediated ATPase expression. However, using these models poses challenges due to resulting bilevel optimizations and complex parameterization. Here, we outline a simplified unsegregated and quasi-unstructured kinetic modeling approach that reduces the number of dynamic states and leads to single-level optimizations. The models can be augmented with Gaussian processes to compensate for model uncertainties. We implement optimal control constrained by knowledge-based and hybrid models for optogenetic ATPase expression in $\textit{Escherichia coli}$ with lactate as the main product. To do so, we genetically engineer $\textit{E. coli}$ to obtain optogenetic expression of ATPase using the CcaS/CcaR system. This represents the first experimental implementation of model-based optimization of ATPase expression in bioprocesses., Comment: 24 pages, 5 figures, journal submission

Biotechnology offers many opportunities for the sustainable manufacturing of valuable products. The toolbox to optimize bioprocesses includes \textit{extracellular} process elements such as the bioreactor design and mode of operation, medium formulation, culture conditions, feeding rates, etc. However, these elements are frequently insufficient for achieving optimal process performance or precise product composition. One can use metabolic and genetic engineering methods for optimization at the intracellular level. Nevertheless, those are often of static nature, failing when applied to dynamic processes or if disturbances occur. Furthermore, many bioprocesses are optimized empirically and implemented with little-to-no feedback control to counteract disturbances. The concept of cybergenetics has opened new possibilities to optimize bioprocesses by enabling online modulation of the gene expression of metabolism-relevant proteins via external inputs (e.g., light intensity in optogenetics). Here, we fuse cybergenetics with model-based optimization and predictive control for optimizing dynamic bioprocesses. To do so, we propose to use dynamic constraint-based models that integrate the dynamics of metabolic reactions, resource allocation, and inducible gene expression. We formulate a model-based optimal control problem to find the optimal process inputs. Furthermore, we propose using model predictive control to address uncertainties via online feedback. We focus on fed-batch processes, where the substrate feeding rate is an additional optimization variable. As a simulation example, we show the optogenetic control of the ATPase enzyme complex for dynamic modulation of enforced ATP wasting to adjust product yield and productivity.

The control of manufacturing processes must satisfy high quality and efficiency requirements while meeting safety requirements. A broad spectrum of monitoring and control strategies, such as model- and optimization-based controllers, are utilized to address these issues. Driven by rising demand for flexible yet energy and resource-efficient operations existing approaches are challenged due to high uncertainties and changes. Machine learning algorithms are becoming increasingly important in tackling these challenges, especially due to the growing amount of available data. The ability for automatic adaptation and learning from human operators offer new opportunities to increase efficiency yet provide flexible operation. Combining machine learning algorithms with safe or robust controls offers novel reliable operation methods. This chapter highlights ways to fuse machine learning and control for the safe and improved operation of chemical and biochemical processes. We outline and summarize both - learning models for control and learning the control components. We offer a general overview, including a literature review, to provide a guideline for utilizing machine learning techniques in control structures.

Model-based optimization approaches for monitoring and control, such as model predictive control and optimal state and parameter estimation, have been used for decades in many engineering applications. Models describing the dynamics, constraints, and desired performance criteria are fundamental to model-based approaches. Thanks to recent technological advancements in digitalization, machine learning methods such as deep learning, and computing power, there has been an increasing interest in using machine learning methods alongside model-based approaches for control and estimation. The number of new methods and theoretical findings using machine learning for model-based control and optimization is increasing rapidly. This paper outlines the basic ideas and principles behind an easy-to-use Python toolbox that allows to quickly and efficiently solve machine-learning-supported optimization, model predictive control, and estimation problems. The toolbox leverages state-of-the-art machine learning libraries to train components used to define the problem. It allows to efficiently solve the resulting optimization problems. Machine learning can be used for a broad spectrum of tasks, ranging from model predictive control for stabilization, setpoint tracking, path following, and trajectory tracking to moving horizon estimation and Kalman filtering. For linear systems, it enables quick code generation for embedded MPC applications. HILO-MPC is flexible and adaptable, making it especially suitable for research and fundamental development tasks. Due to its simplicity and numerous already implemented examples, it is also a powerful teaching tool. The usability is underlined, presenting a series of application examples.