Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Lyapunov-like Conditions of Forward Invariance and Boundedness for a Class of Unstable Systems

We provide Lyapunov-like characterizations of boundedness and convergence of non-trivial solutions for a class of systems with unstable invariant sets. Examples of systems to which the results may apply include interconnections of stable subsystems with one-dimensional unstable dynamics or critically stable dynamics. Systems of this type arise in problems of nonlinear output regulation, parameter estimation and adaptive control. In addition to providing boundedness and convergence criteria the results allow to derive domains of initial conditions corresponding to solutions leaving a given neighborhood of the origin at least once. In contrast to other works addressing convergence issues in unstable systems, our results require neither input-output characterizations for the stable part nor estimates of convergence rates. The results are illustrated with examples, including the analysis of phase synchronization of neural oscillators with heterogenous coupling

Sum-of-Squares approach to feedback control of laminar wake flows

A novel nonlinear feedback control design methodology for incompressible fluid flows aiming at the optimisation of long-time averages of flow quantities is presented. It applies to reduced-order finite-dimensional models of fluid flows, expressed as a set of first-order nonlinear ordinary differential equations with the right-hand side being a polynomial function in the state variables and in the controls. The key idea, first discussed in Chernyshenko et al. 2014, Philos. T. Roy. Soc. 372(2020), is that the difficulties of treating and optimising long-time averages of a cost are relaxed by using the upper/lower bounds of such averages as the objective function. In this setting, control design reduces to finding a feedback controller that optimises the bound, subject to a polynomial inequality constraint involving the cost function, the nonlinear system, the controller itself and a tunable polynomial function. A numerically tractable approach to the solution of such optimisation problems, based on Sum-of-Squares techniques and semidefinite programming, is proposed. To showcase the methodology, the mitigation of the fluctuation kinetic energy in the unsteady wake behind a circular cylinder in the laminar regime at Re=100, via controlled angular motions of the surface, is numerically investigated. A compact reduced-order model that resolves the long-term behaviour of the fluid flow and the effects of actuation, is derived using Proper Orthogonal Decomposition and Galerkin projection. In a full-information setting, feedback controllers are then designed to reduce the long-time average of the kinetic energy associated with the limit cycle. These controllers are then implemented in direct numerical simulations of the actuated flow. Control performance, energy efficiency, and physical control mechanisms identified are analysed. Key elements, implications and future work are discussed

On two generalisations of the final value theorem : scientific relevance, first applications, and physical foundations

The present work considers two published generalisations of the Laplace-transform final value theorem (FVT) and some recently appeared applications of one of these generalisations to the fields of physical stochastic processes and Internet queueing. Physical sense of the irrational time functions, involved in the other generalisation, is one of the points of concern. The work strongly extends the conceptual frame of the references and outlines some new research directions for applications of the generalised theorem

The Mean Drift: Tailoring the Mean Field Theory of Markov Processes for Real-World Applications

The statement of the mean field approximation theorem in the mean field theory of Markov processes particularly targets the behaviour of population processes with an unbounded number of agents. However, in most real-world engineering applications one faces the problem of analysing middle-sized systems in which the number of agents is bounded. In this paper we build on previous work in this area and introduce the mean drift. We present the concept of population processes and the conditions under which the approximation theorems apply, and then show how the mean drift is derived through a systematic application of the propagation of chaos. We then use the mean drift to construct a new set of ordinary differential equations which address the analysis of population processes with an arbitrary size

Multigrid Waveform Relaxation on Spatial Finite Element Meshes: The Discrete-Time Case

The efficiency of numerically solving time-dependent partial differential equations on parallel computers can be greatly improved by computing the solution on many time levels simultaneously. The theoretical properties of one such method, namely the discrete-time multigrid waveform relaxation method, are investigated for systems of ordinary differential equations obtained by spatial finite-element discretisation of linear parabolic initial-boundary value problems. The results are compared to the corresponding continuous-time results. The theory is illustrated for a one-dimensional and a two-dimensional model problem and checked against results obtained by numerical experiments

Numerical analysis of parabolic p-Laplacian: Approximation of trajectories

The long time numerical approximation of the parabolic p-Laplacian problem with a time-independent forcing term and sufficiently smooth initial data is studied. Convergence and stability results which are uniform for t is an element of [0, infinity) are established in the L-2, W-1,W-p norms for the backward Euler and the Crank-Nicholson schemes with the finite element method (FEM). This result extends the existing uniform convergence results for exponentially contractive semigroups generated by some semilinear systems to nonexponentially contractive semigroups generated by some quasilinear systems