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

本研究的目的是发展的积分反馈控制器的设计，可以添加到遗传电路，使他们的操作强大的一些常见的扰动的理论基础。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已经使控制细胞感知和响应外部刺激的方式的遗传电路的工程成为可能。这为许多有影响力的应用开辟了道路，从再生医学，其中健康细胞可以重新编程为任何所需的细胞类型以取代受损细胞，到生物燃料生产，再到生物传感。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发挥强大的作用。不幸的是，当今最先进的遗传电路缺乏鲁棒性，并且通常在标称预设条件之外无法正常工作。这排除了工程细胞在现实生活中的应用。本计画旨在开发一种类比于比例积分控制器的基因电路，以提升机电系统的强健性。这将最终导致工程细胞足够可靠，可用于现实生活中的应用，从而在医学，环境和能源的尖端进步。本项目的目标是创建一个新的数学框架，用于分析和设计体内非线性准积分控制器，使细胞内集成的遗传设备的操作足够强大的生物技术应用。工程活细胞，其中细胞内遗传装置重新配置细胞感知，计算和响应环境的方式，为再生医学，生物燃料生产，生物传感等许多生物技术应用带来了巨大的希望。虽然有许多成功的故事，但工程活细胞要充分发挥其潜力，需要克服一个主要的障碍：缺乏鲁棒性。现实情况是，基因装置在细胞环境中受到重大干扰，这通常会妨碍装置的功能。在该项目中，准积分控制器将通过核心生物分子过程设计和实现，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。考虑的系统的物理导致的动力学结构，受到奇点，潜在的不稳定性，和积分饱和问题。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学系统结构，该结构捕获了可以在活细胞中实现准积分反馈的核心生物分子过程的物理机制;创建新的控制理论，以确定这类动力学系统结构的稳定性，鲁棒性和性能特性;并通过细胞内准积分反馈的实验演示验证先前的发现。

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.