Filtering for nonlinear genetic regulatory networks with stochastic disturbances

In this paper, the filtering problem is investigated for nonlinear genetic regulatory networks with stochastic disturbances and time delays, where the nonlinear function describing the feedback regulation is assumed to satisfy the sector condition, the stochastic perturbation is in the form of a scalar Brownian motion, and the time delays exist in both the translation process and the feedback regulation process. The purpose of the addressed filtering problem is to estimate the true concentrations of the mRNA and protein. Specifically, we are interested in designing a linear filter such that, in the presence of time delays, stochastic disturbances as well as sector nonlinearities, the filtering dynamics of state estimation for the stochastic genetic regulatory network is exponentially mean square stable with a prescribed decay rate lower bound beta. By using the linear matrix inequality (LMI) technique, sufficient conditions are first derived for ensuring the desired filtering performance for the gene regulatory model, and the filter gain is then characterized in terms of the solution to an LMI, which can be easily solved by using standard software packages. A simulation example is exploited in order to illustrate the effectiveness of the proposed design procedures

Synchronization of stochastic genetic oscillator networks with time delays and Markovian jumping parameters

The official published version of the article can be found at the link below.Genetic oscillator networks (GONs) are inherently coupled complex systems where the nodes indicate the biochemicals and the couplings represent the biochemical interactions. This paper is concerned with the synchronization problem of a general class of stochastic GONs with time delays and Markovian jumping parameters, where the GONs are subject to both the stochastic disturbances and the Markovian parameter switching. The regulatory functions of the addressed GONs are described by the sector-like nonlinear functions. By applying up-to-date ‘delay-fractioning’ approach for achieving delay-dependent conditions, we construct novel matrix functional to derive the synchronization criteria for the GONs that are formulated in terms of linear matrix inequalities (LMIs). Note that LMIs are easily solvable by the Matlab toolbox. A simulation example is used to demonstrate the synchronization phenomena within biological organisms of a given GON and therefore shows the applicability of the obtained results.This work was supported in part by the Biotechnology and Biological Sciences Research Council (BBSRC) of the UK under Grants BB/C506264/1 and 100/EGM17735, the Royal Society of the UK, the National Natural Science Foundation of China under Grant 60804028, the Teaching and Research Fund for Excellent Young Teachers at Southeast University of China, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050, and the Alexander von Humboldt Foundation of Germany

Robust filtering for stochastic genetic regulatory networks with time-varying delay

This is the post print version of the article. The official published version can be obtained from the link - Copyright 2009 Elsevier LtdThis paper addresses the robust filtering problem for a class of linear genetic regulatory networks (GRNs) with stochastic disturbances, parameter uncertainties and time delays. The parameter uncertainties are assumed to reside in a polytopic region, the stochastic disturbance is state-dependent described by a scalar Brownian motion, and the time-varying delays enter into both the translation process and the feedback regulation process. We aim to estimate the true concentrations of mRNA and protein by designing a linear filter such that, for all admissible time delays, stochastic disturbances as well as polytopic uncertainties, the augmented state estimation dynamics is exponentially mean square stable with an expected decay rate. A delay-dependent linear matrix inequality (LMI) approach is first developed to derive sufficient conditions that guarantee the exponential stability of the augmented dynamics, and then the filter gains are parameterized in terms of the solution to a set of LMIs. Note that LMIs can be easily solved by using standard software packages. A simulation example is exploited in order to illustrate the effectiveness of the proposed design procedures.This work was supported in part by the Biotechnology and Biological Sciences Research Council (BBSRC) of the U.K. under Grants BB/C506264/1 and 100/EGM17735, an International Joint Project sponsored by the Royal Society of the U.K., the Research Grants Council of Hong Kong under Grant HKU 7031/06P, the National Natural Science Foundation of China under Grant 60804028, and the Alexander von Humboldt Foundation of Germany

On robust stability of stochastic genetic regulatory networks with time delays: A delay fractioning approach

Copyright [2009] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.Robust stability serves as an important regulation mechanism in system biology and synthetic biology. In this paper, the robust stability analysis problem is investigated for a class of nonlinear delayed genetic regulatory networks with parameter uncertainties and stochastic perturbations. The nonlinear function describing the feedback regulation satisfies the sector condition, the time delays exist in both translation and feedback regulation processes, and the state-dependent Brownian motions are introduced to reflect the inherent intrinsic and extrinsic noise perturbations. The purpose of the addressed stability analysis problem is to establish some easy-to-verify conditions under which the dynamics of the true concentrations of the messenger ribonucleic acid (mRNA) and protein is asymptotically stable irrespective of the norm-bounded modeling errors. By utilizing a new Lyapunov functional based on the idea of “delay fractioning”, we employ the linear matrix inequality (LMI) technique to derive delay-dependent sufficient conditions ensuring the robust stability of the gene regulatory networks. Note that the obtained results are formulated in terms of LMIs that can easily be solved using standard software packages. Simulation examples are exploited to illustrate the effectiveness of the proposed design procedures

Time-and event-driven communication process for networked control systems: A survey

Copyright © 2014 Lei Zou 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.In recent years, theoretical and practical research topics on networked control systems (NCSs) have gained an increasing interest from many researchers in a variety of disciplines owing to the extensive applications of NCSs in practice. In particular, an urgent need has arisen to understand the effects of communication processes on system performances. Sampling and protocol are two fundamental aspects of a communication process which have attracted a great deal of research attention. Most research focus has been on the analysis and control of dynamical behaviors under certain sampling procedures and communication protocols. In this paper, we aim to survey some recent advances on the analysis and synthesis issues of NCSs with different sampling procedures (time-and event-driven sampling) and protocols (static and dynamic protocols). First, these sampling procedures and protocols are introduced in detail according to their engineering backgrounds as well as dynamic natures. Then, the developments of the stabilization, control, and filtering problems are systematically reviewed and discussed in great detail. Finally, we conclude the paper by outlining future research challenges for analysis and synthesis problems of NCSs with different communication processes.This work was supported in part by the National Natural Science Foundation of China under Grants 61329301, 61374127, and 61374010, the Royal Society of the UK, and the Alexander von Humboldt Foundation of Germany

Parameters identification of unknown delayed genetic regulatory networks by a switching particle swarm optimization algorithm

The official published version can be found at the link below.This paper presents a novel particle swarm optimization (PSO) algorithm based on Markov chains and competitive penalized method. Such an algorithm is developed to solve global optimization problems with applications in identifying unknown parameters of a class of genetic regulatory networks (GRNs). By using an evolutionary factor, a new switching PSO (SPSO) algorithm is first proposed and analyzed, where the velocity updating equation jumps from one mode to another according to a Markov chain, and acceleration coefficients are dependent on mode switching. Furthermore, a leader competitive penalized multi-learning approach (LCPMLA) is introduced to improve the global search ability and refine the convergent solutions. The LCPMLA can automatically choose search strategy using a learning and penalizing mechanism. The presented SPSO algorithm is compared with some well-known PSO algorithms in the experiments. It is shown that the SPSO algorithm has faster local convergence speed, higher accuracy and algorithm reliability, resulting in better balance between the global and local searching of the algorithm, and thus generating good performance. Finally, we utilize the presented SPSO algorithm to identify not only the unknown parameters but also the coupling topology and time-delay of a class of GRNs.This research was partially supported by the National Natural Science Foundation of PR China (Grant No. 60874113), the Research Fund for the Doctoral Program of Higher Education (Grant No. 200802550007), the Key Creative Project of Shanghai Education Community (Grant No. 09ZZ66), the Key Foundation Project of Shanghai (Grant No. 09JC1400700), the Engineering and Physical Sciences Research Council EPSRC of the UK under Grant No. GR/S27658/01, the International Science and Technology Cooperation Project of China under Grant No. 2009DFA32050, an International Joint Project sponsored by the Royal Society of the UK, and the Alexander von Humboldt Foundation of Germany

Stochastic models and numerical algorithms for a class of regulatory gene networks

Regulatory gene networks contain generic modules like those involving feedback loops, which are essential for the regulation of many biological functions. We consider a class of self-regulated genes which are the building blocks of many regulatory gene networks, and study the steady state distributions of the associated Gillespie algorithm by providing efficient numerical algorithms. We also study a regulatory gene network of interest in synthetic biology and in gene therapy, using mean-field models with time delays. Convergence of the related time-nonhomogeneous Markov chain is established for a class of linear catalytic networks with feedback loop

Stability Analysis of Delayed Genetic Regulatory Networks via a Relaxed Double Integral Inequality

Time delay arising in a genetic regulatory network may cause the instability. This paper is concerned with the stability analysis of genetic regulatory networks with interval time-varying delays. Firstly, a relaxed double integral inequality, named as Wirtinger-type double integral inequality (WTDII), is established to estimate the double integral term appearing in the derivative of Lyapunov-Krasovskii functional with a triple integral term. And it is proved theoretically that the proposed WTDII is tighter than the widely used Jensen-based double inequality and the recently developed Wiringter-based double inequality. Then, by applying the WTDII to the stability analysis of a delayed genetic regulatory network, together with the usage of useful information of regulatory functions, several delay-range- and delay-rate-dependent (or delay-rate-independent) criteria are derived in terms of linear matrix inequalities. Finally, an example is carried out to verify the effectiveness of the proposed method and also to show the advantages of the established stability criteria through the comparison with some literature

Global synchronization for discrete-time stochastic complex networks with randomly occurred nonlinearities and mixed time delays

Copyright [2010] IEEE. This material is posted here with permission of the IEEE. Such permission of the IEEE does not in any way imply IEEE endorsement of any of Brunel University's products or services. Internal or personal use of this material is permitted. However, permission to reprint/republish this material for advertising or promotional purposes or for creating new collective works for resale or redistribution must be obtained from the IEEE by writing to [email protected]. By choosing to view this document, you agree to all provisions of the copyright laws protecting it.In this paper, the problem of stochastic synchronization analysis is investigated for a new array of coupled discrete-time stochastic complex networks with randomly occurred nonlinearities (RONs) and time delays. The discrete-time complex networks under consideration are subject to: (1) stochastic nonlinearities that occur according to the Bernoulli distributed white noise sequences; (2) stochastic disturbances that enter the coupling term, the delayed coupling term as well as the overall network; and (3) time delays that include both the discrete and distributed ones. Note that the newly introduced RONs and the multiple stochastic disturbances can better reflect the dynamical behaviors of coupled complex networks whose information transmission process is affected by a noisy environment (e.g., Internet-based control systems). By constructing a novel Lyapunov-like matrix functional, the idea of delay fractioning is applied to deal with the addressed synchronization analysis problem. By employing a combination of the linear matrix inequality (LMI) techniques, the free-weighting matrix method and stochastic analysis theories, several delay-dependent sufficient conditions are obtained which ensure the asymptotic synchronization in the mean square sense for the discrete-time stochastic complex networks with time delays. The criteria derived are characterized in terms of LMIs whose solution can be solved by utilizing the standard numerical software. A simulation example is presented to show the effectiveness and applicability of the proposed results