Quasi-Integral Control for Robustness to Perturbations of Integrated Genetic Devices in Living Cells for Biotechnology

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The objective of this research is to develop the theoretical underpinnings for the design of integral feedback controllers that can be added to genetic circuits to make their operation robust to a number of common perturbations. Integral controllers provide model-free compensation of constant or slowly varying disturbances and uncertainties. The tremendous progress of molecular biology technologies has enabled engineering of the genetic circuitry that controls the way cells sense and respond to external stimuli. This opens up the path to a number of impactful applications, ranging from regenerative medicine, wherein healthy cells could be reprogrammed into any required cell type to replace damaged cells, to biofuel production, to biosensing. For engineered cells to be dependable, their genetic circuitry needs to function robustly in the face of changes and uncertainties in the environment. Unfortunately, today's state-of-the-art genetic circuitry lacks robustness, and often fails to function properly outside of nominal pre-set conditions. This precludes the use of engineered cells in real-life applications. This project seeks to develop a genetic-circuit analog to the proportional-integral (PI) controllers that are ubiquitous in industry for enhancing the robustness of electromechanical systems. This will ultimately lead to engineered cells dependable enough to be used in real-life applications, resulting in cutting edge progress in medicine, environment, and energy.The goal of this project is to create a novel mathematical framework for the analysis and design of in vivo nonlinear quasi-integral controllers that make the operation of in-cell integrated genetic devices sufficiently robust for biotechnology applications. Engineered living cells, wherein in-cell genetic devices reconfigure the way cells sense, compute, and respond to the environment hold tremendous promise for a number of biotechnology applications from regenerative medicine, to biofuel production, to biosensing. While a number of success stories are available, for engineered living cells to reach their full potential a major roadblock needs to be overcome: lack of robustness. The reality is that genetic devices are subject to significant perturbations in the cellular context, which often hamper the devices' functionality. In this project quasi-integral controllers will be designed and implemented through core biomolecular processes, to restore robustness of integrated genetic devices to unwanted perturbations that affect the cellular context. The physics of the systems considered lead to dynamical structures that are subject to singularities, potential instabilities, and integrator windup problems. The analysis and design of stability, robustness, and performance of such structures is largely unexplored. This project includes the following tasks: create a new class of nonlinear dynamical system structures that captures the physical mechanisms of core biomolecular processes that can realize quasi-integral feedback in living cells; create new control theory to determine the stability, robustness, and performance properties of this class of dynamical system structures; and validate the previous findings with experimental demonstration of in-cell quasi-integral feedback.