Modeling and Estimation of Biological Plants

Estimating the state of a dynamic system is an essential task for achieving important objectives such as process monitoring, identification, and control. Unlike linear systems, no systematic method exists for the design of observers for nonlinear systems. Although many researchers have devoted their attention to these issues for more than 30 years, there are still many open questions. We envisage that estimation plays a crucial role in biology because of the possibility of creating new avenues for biological studies and for the development of diagnostic, management, and treatment tools. To this end, this thesis aims to address two types of nonlinear estimation techniques, namely, the high-gain observer and the moving-horizon estimator with application to three different biological plants. After recalling basic definitions of stability and observability of dynamical systems and giving a bird's-eye survey of the available state estimation techniques, we are interested in the high-gain observers. These observers may be used when the system dynamics can be expressed in specific a coordinate under the so-called observability canonical form with the possibility to assign the rate of convergence arbitrarily by acting on a single parameter called the high-gain parameter. Despite the evident benefits of this class of observers, their use in real applications is questionable due to some drawbacks: numerical problems, the peaking phenomenon, and high sensitivity to measurement noise. The first part of the thesis aims to enrich the theory of high-gain observers with novel techniques to overcome or attenuate these challenging performance issues that arise when implementing such observers. The validity and applicability of our proposed techniques have been shown firstly on a simple one-gene regulatory network, and secondly on an SI epidemic model. The second part of the thesis studies the problem of state estimation using the moving horizon approach. The main advantage of MHE is that information about the system can be explicitly considered in the form of constraints and hence improve the estimates. In this work, we focus on estimation for nonlinear plants that can be rewritten in the form of quasi-linear parameter-varying systems with bounded unknown parameters. Moving-horizon estimators are proposed to estimate the state of such systems according to two different formulations, i.e., "optimistic" and "pessimistic". In the former case, we perform estimation by minimizing the least-squares moving-horizon cost with respect to both state variables and parameters simultaneously. In the latter, we minimize such a cost with respect to the state variables after picking up the maximum of the parameters. Under suitable assumptions, the stability of the estimation error given by the exponential boundedness is proved in both scenarios. Finally, the validity of our obtained results has been demonstrated through three different examples from biological and biomedical fields, namely, an example of one gene regulatory network, a two-stage SI epidemic model, and Amnioserosa cell's mechanical behavior during Dorsal closure

Contraction analysis of nonlinear systems and its application

The thesis addresses various issues concerning the convergence properties of switched systems and differential algebraic equation (DAE) systems. Specifically, we focus on contraction analysis problem, as well as tackling problems related to stabilization and synchronization. We consider the contraction analysis of switched systems and DAE systems. To address this, a transformation is employed to convert the contraction analysis problem into a stabilization analysis problem. This transformation involves the introduction of virtual systems, which exhibit a strong connection with the Jacobian matrix of the vector field. Analyzing these systems poses a significant challenge due to the distinctive structure of their Jacobian matrices. Regarding the switched systems, a time-dependent switching law is established to guarantee uniform global exponential stability (UGES). As for the DAE system, we begin by embedding it into an ODE system. Subsequently, the UGES property is ensured by analyzing its matrix measure. As our first application, we utilize our approach to stabilize time-invariant switched systems and time-invariant DAE systems, respectively. This involves designing control laws to achieve system contractivity, thereby ensuring that the trajectory set encompasses the equilibrium point. In oursecond application, we propose the design of a time-varying observer by treating the system’s output as an algebraic equation of the DAE system. In our study on synchronization problems, we investigate two types of synchronization issues: the trajectory tracking of switched oscillators and the pinning state synchronization. In the case of switched oscillators, we devise a time-dependent switching law to ensure that these oscillators effectively follow the trajectory of a time-varying system. As for the pinning synchronization problem, we define solvable conditions and, building upon these conditions, we utilize contraction theory to design dynamic controllers that guarantee synchronization is achieved among the agents

Optimization-based Robustness and Stabilization in Decentralized Control

This dissertation pertains to the stabilization, robustness, and optimization of Finite Dimensional Linear Time Invariant (FDLTI) decentralized control systems. We study these concepts for FDLTI systems subject to decentralizations that emerge from imposing sparsity constraints on the controller. While these concepts are well-understood in absence of an information structure, they continue to raise fundamental interesting questions regarding an optimal controller, or on suitable notions of robustness in presence of information structures. Two notions of stabilizability with respect to decentralized controllers are considered. First, the seminal result of Wang & Davison in 1973 regarding internal stabilizability of perfectly decentralized system and its connection to the decentralized fixed-modes of the plant is revisited. This seminal result would be generalized to any arbitrary sparsity-induced information structure by providing an inductive proof that verifies and shows that those mode of the plant that are fixed with respect to the static controllers would remain fixed with respect to the dynamic ones. A constructive proof is also provided to show that one can move any non-fixed mode of the plant to any arbitrary location within desired accuracy provided that they remain symmetric in the complex plane. A synthesizing algorithm would then be derived from the inductive proof. A second stronger notion of stability referred to as "non-overshooting stability" is then addressed. A key property called "feedthrough consistency" is derived, that when satisfied, makes extension of the centralized results to the decentralized case possible. Synthesis of decentralized controllers to optimize an H_Infinity norm for model-matching problems is considered next. This model-matching problem corresponds to an infinite-dimensional convex optimization problem. We study a finite-dimensional parametrization, and show that once the poles are chosen for this parametrization, the remaining problem of coefficient optimization can be cast as a semidefinite program (SDP). We further demonstrate how to use first-order methods when the SDP is too large or when a first-order method is otherwise desired. This leaves the remaining choice of poles, for which we develop and discuss several methods to better select the most effective poles among many candidates, and to systematically improve their location using convex optimization techniques. Controllability of LTI systems with decentralized controllers is then studied. Whether an LTI system is controllable (by LTI controllers) with respect to a given information structure can be determined by testing for fixed modes, but this gives a binary answer with no information about robustness. Measures have already been developed to determine how far a system is from having a fixed mode when one considers complex or real perturbations to the state-space matrices. These measures involve intractable minimizations of a non-convex singular value over a power-set, and hence cannot be computed except for the smallest of the plants. We replace these problem by equivalent optimization problems that involve a binary vector rather than the power-set minimization and prove their equality. Approximate forms are also provided that would upper bound the original metrics, and enable us to utilize MINLP techniques to derive scalable upper bounds. We also show that we can formulate lower bounds for these measures as polynomial optimization problems,and then use sum-of-squares methods to obtain a sequence of SDPs, whose solutions would lower bound these metrics