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

本研究的目的是为积分反馈控制器的设计提供理论基础，这些控制器可以添加到遗传电路中，使其对许多常见的扰动具有鲁棒性。积分控制器提供恒定或缓慢变化的干扰和不确定性的无模型补偿。分子生物学技术的巨大进步使基因回路的工程设计成为可能，基因回路控制着细胞感知和响应外部刺激的方式。这为许多有影响力的应用开辟了道路，从再生医学，其中健康细胞可以被重新编程成任何所需的细胞类型来取代受损细胞，到生物燃料生产，到生物传感。为了使工程细胞可靠，它们的遗传电路需要在面对环境的变化和不确定性时功能强大。不幸的是，当今最先进的基因电路缺乏稳健性，并且经常无法在规定的预设条件之外正常运行。这就阻碍了工程细胞在现实生活中的应用。该项目旨在开发一种遗传电路模拟比例积分（PI）控制器，这种控制器在工业中无处不在，用于增强机电系统的鲁棒性。这最终将导致足够可靠的工程细胞用于实际应用，从而在医学、环境和能源领域取得前沿进展。该项目的目标是为体内非线性准积分控制器的分析和设计创建一个新的数学框架，使细胞内集成遗传设备的操作足够健壮，适用于生物技术应用。工程活细胞，其中细胞内的遗传设备重新配置细胞感知、计算和响应环境的方式，为再生医学、生物燃料生产和生物传感等许多生物技术应用带来了巨大的希望。虽然有许多成功的案例，但要使工程活细胞充分发挥其潜力，需要克服一个主要障碍：缺乏健壮性。现实情况是，遗传设备在细胞环境中受到显著的扰动，这通常会妨碍设备的功能。在这个项目中，准积分控制器将通过核心生物分子过程来设计和实现，以恢复集成遗传设备对影响细胞环境的不必要扰动的鲁棒性。所考虑的系统的物理特性导致了受奇点、潜在不稳定性和积分器缠绕问题影响的动态结构。这种结构的稳定性、鲁棒性和性能的分析和设计在很大程度上是未知的。该项目包括以下任务：创建一类新的非线性动力系统结构，捕获核心生物分子过程的物理机制，可以在活细胞中实现准积分反馈；创建新的控制理论来确定这类动力系统结构的稳定性、鲁棒性和性能特性；并通过单元内准积分反馈的实验验证了之前的研究结果。

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.