Structure-Preserving Model Reduction of Physical Network Systems

This paper considers physical network systems where the energy storage is naturally associated to the nodes of the graph, while the edges of the graph correspond to static couplings. The first sections deal with the linear case, covering examples such as mass-damper and hydraulic systems, which have a structure that is similar to symmetric consensus dynamics. The last section is concerned with a specific class of nonlinear physical network systems; namely detailed-balanced chemical reaction networks governed by mass action kinetics. In both cases, linear and nonlinear, the structure of the dynamics is similar, and is based on a weighted Laplacian matrix, together with an energy function capturing the energy storage at the nodes. We discuss two methods for structure-preserving model reduction. The first one is clustering; aggregating the nodes of the underlying graph to obtain a reduced graph. The second approach is based on neglecting the energy storage at some of the nodes, and subsequently eliminating those nodes (called Kron reduction).</p

A new computational approach to the synthesis of fixed order controllers

The research described in this dissertation deals with an open problem concerning the synthesis of controllers of xed order and structure. This problem is encountered in a variety of applications. Simply put, the problem may be put as the determination of the set, S of controller parameter vectors, K = (k1; k2; : : : ; kl), that render Hurwitz a family (indexed by F) of complex polynomials of the form fP0(s; ) + Pl i=1 Pi(s; )ki; 2 Fg, where the polynomials Pj(s; ); j = 0; : : : ; l are given data. They are specied by the plant to be controlled, the structure of the controller desired and the performance that the controllers are expected to achieve. Simple examples indicate that the set S can be non-convex and even be disconnected. While the determination of the non-emptiness of S is decidable and amenable to methods such as the quantier elimination scheme, such methods have not been computationally tractable and more importantly, do not provide a reasonable approximation for the set of controllers. Practical applications require the construction of a set of controllers that will enable a control engineer to check the satisfaction of performance criteria that may not be mathematically well characterized. The transient performance criteria often fall into this category. From the practical viewpoint of the construction of approximations for S, this dissertation is dierent from earlier work in the literature on this problem. A novel feature of the proposed algorithm is the exploitation of the interlacing property of Hurwitz polynomials to provide arbitrarily tight outer and inner approximation to S. The approximation is given in terms of the union of polyhedral sets which are constructed systematically using the Hermite-Biehler theorem and the generalizations of the Descartes' rule of signs

Design and analysis of genetic feedback architectures for synthetic biology

Synthetic Biology seeks to design and assemble novel biological systems with favourable properties. It allows us to comprehend and modify the fundamental mechanisms of life and holds significant promise in revolutionizing current technologies ranging from medicine and biomanufacturing to energy and environmental protection. Biological processes constitute remarkably complex dynamical systems operating impeccably well in messy and constantly changing environments. Their ability to do so is rooted in sophisticated molecular control architectures crafted by natural evolutionary innovation over billions of years. Such control architectures, often blended with human-engineering approaches, are the key to realizing efficient and reliable synthetic biological systems. Aiming to accelerate the development of the latter, the present thesis addresses some fundamental challenges in biomolecular systems and control design. We begin by elucidating biological mechanisms of temporal gradient computation, enabling cells to adjust their behaviour in response to anticipated environmental changes. Specifically, we introduce biomolecular motifs capable of functioning as highly tunable and accurate signal differentiators to input molecular signals around their nominal operation. We investigate strategies to deal with high-frequency input signal components which can be detrimental to the performance of most differentiators. We ascertain the occurrence of such motifs in natural regulatory networks and demonstrate the potential of synthetic experimental realizations. Our motifs can serve as reliable speed biosensors and can form the basis for derivative feedback control. Motivated by the pervasiveness of Proportional-Integral-Derivative (PID) controllers in modern technological applications, we present the realization of a PID controller via biomolecular reactions employing, among others, our differentiator motifs. This biomolecular architecture represents a PID control law with set point weighting and filtered derivative action, offering robust regulation of a single-output biological process with enhanced dynamic performance and low levels of stochastic noise. It is characterized by significant ease of tuning and can be of particular experimental interest in molecular programming applications. Finally, we investigate efficient regulation strategies for multi-output biological processes with internal coupling interactions, expanding previously established single-output control approaches. More specifically, we propose control schemes allowing for robust manipulation of the outputs in various ways, namely manipulation of their product/ratio, linear combinations of them as well as manipulation of each of the outputs independently. Our analysis is centered around two-output biological processes, yet the scalability of the proposed regulation strategies to processes with a higher number of outputs is highlighted. In parallel, their experimental implementability is explored in both in vivo and in vitro settings

Non-Parametric Bayesian Methods for Linear System Identification

Recent contributions have tackled the linear system identification problem by means of non-parametric Bayesian methods, which are built on largely adopted machine learning techniques, such as Gaussian Process regression and kernel-based regularized regression. Following the Bayesian paradigm, these procedures treat the impulse response of the system to be estimated as the realization of a Gaussian process. Typically, a Gaussian prior accounting for stability and smoothness of the impulse response is postulated, as a function of some parameters (called hyper-parameters in the Bayesian framework). These are generally estimated by maximizing the so-called marginal likelihood, i.e. the likelihood after the impulse response has been marginalized out. Once the hyper-parameters have been fixed in this way, the final estimator is computed as the conditional expected value of the impulse response w.r.t. the posterior distribution, which coincides with the minimum variance estimator. Assuming that the identification data are corrupted by Gaussian noise, the above-mentioned estimator coincides with the solution of a regularized estimation problem, in which the regularization term is the l2 norm of the impulse response, weighted by the inverse of the prior covariance function (a.k.a. kernel in the machine learning literature). Recent works have shown how such Bayesian approaches are able to jointly perform estimation and model selection, thus overcoming one of the main issues affecting parametric identification procedures, that is complexity selection. While keeping the classical system identification methods (e.g. Prediction Error Methods and subspace algorithms) as a benchmark for numerical comparison, this thesis extends and analyzes some key aspects of the above-mentioned Bayesian procedure. In particular, four main topics are considered. 1. PRIOR DESIGN. Adopting Maximum Entropy arguments, a new type of l2 regularization is derived: the aim is to penalize the rank of the block Hankel matrix built with Markov coefficients, thus controlling the complexity of the identified model, measured by its McMillan degree. By accounting for the coupling between different input-output channels, this new prior results particularly suited when dealing for the identification of MIMO systems To speed up the computational requirements of the estimation algorithm, a tailored version of the Scaled Gradient Projection algorithm is designed to optimize the marginal likelihood. 2. CHARACTERIZATION OF UNCERTAINTY. The confidence sets returned by the non-parametric Bayesian identification algorithm are analyzed and compared with those returned by parametric Prediction Error Methods. The comparison is carried out in the impulse response space, by deriving “particle” versions (i.e. Monte-Carlo approximations) of the standard confidence sets. 3. ONLINE ESTIMATION. The application of the non-parametric Bayesian system identification techniques is extended to an online setting, in which new data become available as time goes. Specifically, two key modifications of the original “batch” procedure are proposed in order to meet the real-time requirements. In addition, the identification of time-varying systems is tackled by introducing a forgetting factor in the estimation criterion and by treating it as a hyper-parameter. 4. POST PROCESSING: MODEL REDUCTION. Non-parametric Bayesian identification procedures estimate the unknown system in terms of its impulse response coefficients, thus returning a model with high (possibly infinite) McMillan degree. A tailored procedure is proposed to reduce such model to a lower degree one, which appears more suitable for filtering and control applications. Different criteria for the selection of the order of the reduced model are evaluated and compared