We develop the robust control theories of stopping-time nonlinear systems and switching-control nonlinear systems. We formulate a robust optimal stopping-time control problem for a state-space nonlinear system and give the connection between various notions of lower value function for the associated game (and storage function for the associated dissipative system) with solutions of the appropriate variational inequality (VI). We show that the stopping-time rule can be obtained by solving the VI in the viscosity sense. It also happens that a positive definite supersolution of the VI can be used for stability analysis. We also show how to solve the VI for some prototype examples with one-dimensional state space. For the robust optimal switching-control problem, we establish the Dynamic Programming Principle (DPP) for the lower value function of the associated game and employ it to derive the appropriate system of quasivariational inequalities (SQVI) for the lower value vector function. Moreover we formulate the problem in the <I>L</I>₂-gain/dissipative system framework. We show that, under appropriate assumptions, continuous switching-storage (vector) functions are characterized as viscosity supersolutions of the SQVI, and that the minimal such storage function is equal to the lower value function for the game. We show that the control strategy achieving the dissipative inequality is obtained by solving the SQVI in the viscosity sense; in fact this solution is also used to address stability analysis of the switching system. In addition we prove the comparison principle between a viscosity subsolution and a viscosity supersolution of the SQVI satisfying a boundary condition and use it to give an alternative derivation of the characterization of the lower value function. Finally we solve the SQVI for a simple one-dimensional example by a direct geometric construction. / Ph. D.

This thesis is concerned with large-scale systems of Ordinary Differential Equations that model Biomolecular Reaction Networks (BRNs) in Systems and Synthetic Biology. It addresses the strategies of model reduction and decomposition used to overcome the challenges posed by the high dimension and stiffness typical of these models. A number of developments of these strategies are identified, and their implementation on various BRN models is demonstrated. The goal of model reduction is to construct a simplified ODE system to closely approximate a large-scale system. The error estimation problem seeks to quantify the approximation error; this is an example of the trajectory comparison problem. The first part of this thesis applies semi-definite programming (SDP) and dissipativity theory to this problem, producing a single a priori upper bound on the difference between two models in the presence of parameter uncertainty and for a range of initial conditions, for which exhaustive simulation is impractical. The second part of this thesis is concerned with the BRN decomposition problem of expressing a network as an interconnection of subnetworks. A novel framework, called layered decomposition, is introduced and compared with established modular techniques. Fundamental properties of layered decompositions are investigated, providing basic criteria for choosing an appropriate layered decomposition. Further aspects of the layering framework are considered: we illustrate the relationship between decomposition and scale separation by constructing singularly perturbed BRN models using layered decomposition; and we reveal the inter-layer signal propagation structure by decomposing the steady state response to parametric perturbations. Finally, we consider the large-scale SDP problem, where large scale SDP techniques fail to certify a system’s dissipativity. We describe the framework of Structured Storage Functions (SSF), defined where systems admit a cascaded decomposition, and demonstrate a significant resulting speed-up of large-scale dissipativity problems, with applications to the trajectory comparison technique discussed above.