A geometric and structural approach to the analysis and design of biological circuit dynamics: a theory tailored for synthetic biology

Much of the progress in developing our ability to successfully design genetic circuits with predictable dynamics has followed the strategy of molding biological systems to fit into conceptual frameworks used in other disciplines, most notably the engineering sciences. Because biological systems have fundamental differences from systems in these other disciplines, this approach is challenging and the insights obtained from such analyses are often not framed in a biologically-intuitive way. Here, we present a new theoretical framework for analyzing the dynamics of genetic circuits that is tailored towards the unique properties associated with biological systems and experiments. Our framework approximates a complex circuit as a set of simpler circuits, which the system can transition between by saturating its various internal components. These approximations are connected to the intrinsic structure of the system, so this representation allows the analysis of dynamics which emerge solely from the system's structure. Using our framework, we analyze the presence of structural bistability in a leaky autoactivation motif and the presence of structural oscillations in the Repressilator

Recent advances on filtering and control for nonlinear stochastic complex systems with incomplete information: A survey

This Article is provided by the Brunel Open Access Publishing Fund - Copyright @ 2012 Hindawi PublishingSome recent advances on the filtering and control problems for nonlinear stochastic complex systems with incomplete information are surveyed. The incomplete information under consideration mainly includes missing measurements, randomly varying sensor delays, signal quantization, sensor saturations, and signal sampling. With such incomplete information, the developments on various filtering and control issues are reviewed in great detail. In particular, the addressed nonlinear stochastic complex systems are so comprehensive that they include conventional nonlinear stochastic systems, different kinds of complex networks, and a large class of sensor networks. The corresponding filtering and control technologies for such nonlinear stochastic complex systems are then discussed. Subsequently, some latest results on the filtering and control problems for the complex systems with incomplete information are given. Finally, conclusions are drawn and several possible future research directions are pointed out.This work was supported in part by the National Natural Science Foundation of China under Grant nos. 61134009, 61104125, 61028008, 61174136, 60974030, and 61074129, the Qing Lan Project of Jiangsu Province of China, the Project sponsored by SRF for ROCS of SEM of China, the Engineering and Physical Sciences Research Council EPSRC of the UK under Grant GR/S27658/01, the Royal Society of the UK, and the Alexander von Humboldt Foundation of Germany

Design of feedback control systems for stable plants with saturating actuators

A systematic control design methodology is introduced for multi-input/multi-output stable open loop plants with multiple saturations. This new methodology is a substantial improvement over previous heuristic single-input/single-output approaches. The idea is to introduce a supervisor loop so that when the references and/or disturbances are sufficiently small, the control system operates linearly as designed. For signals large enough to cause saturations, the control law is modified in such a way as to ensure stability and to preserve, to the extent possible, the behavior of the linear control design. Key benefits of the methodology are: the modified compensator never produces saturating control signals, integrators and/or slow dynamics in the compensator never windup, the directional properties of the controls are maintained, and the closed loop system has certain guaranteed stability properties. The advantages of the new design methodology are illustrated in the simulation of an academic example and the simulation of the multivariable longitudinal control of a modified model of the F-8 aircraft

Design of feedback control systems for unstable plants with saturating actuators

A new control design methodology is introduced for multi-input/multi-output systems with unstable open loop plants and saturating actuators. A control system is designed using well known linear control theory techniques and then a reference prefilter is introduced so that when the references are sufficiently small, the control system operates linearly as designated. For signals large enough to cause saturations, the control law is modified in such a way to ensure stability and to preserve, to the extent possible, the behavior of the linear control design. Key benefits of this methodology are: the modified feedback system never produces saturating control signals, integrators and/or slow dynamics in the compensator never windup, the directionaL properties of the controls are maintained, and the closed loop system has certain guaranteed stability properties. The advantages of the new design methodology are illustrated in the simulation of an approximation of the AFTI-16 (Advanced Fighter Technology Integration) aircraft multivariable longitudinal dynamics

Variance-constrained multiobjective control and filtering for nonlinear stochastic systems: A survey

The multiobjective control and filtering problems for nonlinear stochastic systems with variance constraints are surveyed. First, the concepts of nonlinear stochastic systems are recalled along with the introduction of some recent advances. Then, the covariance control theory, which serves as a practical method for multi-objective control design as well as a foundation for linear system theory, is reviewed comprehensively. The multiple design requirements frequently applied in engineering practice for the use of evaluating system performances are introduced, including robustness, reliability, and dissipativity. Several design techniques suitable for the multi-objective variance-constrained control and filtering problems for nonlinear stochastic systems are discussed. In particular, as a special case for the multi-objective design problems, the mixed H 2 / H ∞ control and filtering problems are reviewed in great detail. Subsequently, some latest results on the variance-constrained multi-objective control and filtering problems for the nonlinear stochastic systems are summarized. Finally, conclusions are drawn, and several possible future research directions are pointed out

Nonlinear analysis of dynamical complex networks

Copyright © 2013 Zidong Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Complex networks are composed of a large number of highly interconnected dynamical units and therefore exhibit very complicated dynamics. Examples of such complex networks include the Internet, that is, a network of routers or domains, the World Wide Web (WWW), that is, a network of websites, the brain, that is, a network of neurons, and an organization, that is, a network of people. Since the introduction of the small-world network principle, a great deal of research has been focused on the dependence of the asymptotic behavior of interconnected oscillatory agents on the structural properties of complex networks. It has been found out that the general structure of the interaction network may play a crucial role in the emergence of synchronization phenomena in various fields such as physics, technology, and the life sciences

Torque Saturation in Bipedal Robotic Walking through Control Lyapunov Function Based Quadratic Programs

This paper presents a novel method for directly incorporating user-defined control input saturations into the calculation of a control Lyapunov function (CLF)-based walking controller for a biped robot. Previous work by the authors has demonstrated the effectiveness of CLF controllers for stabilizing periodic gaits for biped walkers, and the current work expands on those results by providing a more effective means for handling control saturations. The new approach, based on a convex optimization routine running at a 1 kHz control update rate, is useful not only for handling torque saturations but also for incorporating a whole family of user-defined constraints into the online computation of a CLF controller. The paper concludes with an experimental implementation of the main results on the bipedal robot MABEL

State estimation for discrete-time neural networks with Markov-mode-dependent lower and upper bounds on the distributed delays

Copyright @ 2012 Springer VerlagThis paper is concerned with the state estimation problem for a new class of discrete-time neural networks with Markovian jumping parameters and mixed time-delays. The parameters of the neural networks under consideration switch over time subject to a Markov chain. The networks involve both the discrete-time-varying delay and the mode-dependent distributed time-delay characterized by the upper and lower boundaries dependent on the Markov chain. By constructing novel Lyapunov-Krasovskii functionals, sufficient conditions are firstly established to guarantee the exponential stability in mean square for the addressed discrete-time neural networks with Markovian jumping parameters and mixed time-delays. Then, the state estimation problem is coped with for the same neural network where the goal is to design a desired state estimator such that the estimation error approaches zero exponentially in mean square. The derived conditions for both the stability and the existence of desired estimators are expressed in the form of matrix inequalities that can be solved by the semi-definite programme method. A numerical simulation example is exploited to demonstrate the usefulness of the main results obtained.This work was supported in part by the Royal Society of the U.K., the National Natural Science Foundation of China under Grants 60774073 and 61074129, and the Natural Science Foundation of Jiangsu Province of China under Grant BK2010313