Unconditional global exponential stability in Lagrange sense of genetic regulatory networks with SUM regulatory logic

In this paper, the global exponential stability in Lagrange sense for genetic regulatory networks (GRNs) with SUM regulatory logic is firstly studied. By constructing appropriate Lyapunov-like functions, several criteria are presented for the boundedness, ultimate boundedness and global exponential attractivity of GRNs. It can be obtained that GRNs with SUM regulatory logic are unconditionally globally exponentially stable in Lagrange sense. These results can be applied to analyze monostable as well as multistable networks. Furthermore, to analyze the stability for GRNs more comprehensively, the existence of equilibrium point of GRNs is proved, and some sufficient conditions of the global exponential stability in Lyapunov sense for GRNs are derived. Finally two numerical examples are given to illustrate the application of the obtained results.     

Robust stabilization and H(∞) controllers design for stochastic genetic regulatory networks with time-varying delays and structured uncertainties

This paper deals with the problem of stabilization design and H(∞) control for a class of genetic regulatory networks (GRNs) with both intrinsic perturbation and extrinsic perturbation. Some delay-dependent mean-square stabilization criteria are put forward for nominal systems and uncertain systems by using an improved free-weighting matrix approach. As a result, the corresponding stabilization controllers and H(∞) controllers of GRNs are constructed with time delays compensated and suboptimal solutions are obtained via exploiting an iterative procedure together with the linear matrix inequality (LMI) method and the cone complementarity liberalization (CCL) algorithm. Finally, three numerical examples are presented to illustrate the effectiveness of the proposed theoretical results.     

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

This 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.     

Design of state estimator for genetic regulatory networks with time-varying delays and randomly occurring uncertainties

In this paper, the design problem of state estimator for genetic regulatory networks with time delays and randomly occurring uncertainties has been addressed by a delay decomposition approach. The norm-bounded uncertainties enter into the genetic regulatory networks (GRNs) in random ways, and such randomly occurring uncertainties (ROUs) obey certain mutually uncorrelated Bernoulli distributed white noise sequences. Under these circumstances, the state estimator is designed to estimate the true concentration of the mRNA and the protein of the uncertain GRNs. Delay-dependent stability criteria are obtained in terms of linear matrix inequalities by constructing a Lyapunov–Krasovskii functional and using some inequality techniques (LMIs). Then, the desired state estimator, which can ensure the estimation error dynamics to be globally asymptotically robustly stochastically stable, is designed from the solutions of LMIs. Finally, a numerical example is provided to demonstrate the feasibility of the proposed estimation schemes.     

Exponential synchronization of discontinuous neural networks with time-varying mixed delays via state feedback and impulsive control

This paper investigates drive-response synchronization for a class of neural networks with time-varying discrete and distributed delays (mixed delays) as well as discontinuous activations. Strict mathematical proof shows the global existence of Filippov solutions to neural networks with discontinuous activation functions and the mixed delays. State feedback controller and impulsive controller are designed respectively to guarantee global exponential synchronization of the neural networks. By using Lyapunov function and new analysis techniques, several new synchronization criteria are obtained. Moreover, lower bound on the convergence rate is explicitly estimated when state feedback controller is utilized. Results of this paper are new and some existing ones are extended and improved. Finally, numerical simulations are given to verify the effectiveness of the theoretical results.     

Sufficient and necessary conditions for Lyapunov stability of genetic networks with SUM regulatory logic

In this paper, a nonlinear model for genetic regulator networks (GRNs) with SUM regulatory logic is presented. Four sufficient and necessary conditions of global asymptotical stability and global exponential stability for the equilibrium point of the GRNs are proposed, respectively. Specifically, three weak sufficient conditions and corresponding corollaries are derived by using comparing theorem and Dini derivative method. Then, a famous GRN model is used as the example to illustrate the effectiveness of our theoretical results. Comparing to the results in the previous literature, some novel ideas, study methods and interesting results are explored.     

Gene regulatory network inference: Data integration in dynamic models—A review

Systems biology aims to develop mathematical models of biological systems by integrating experimental and theoretical techniques. During the last decade, many systems biological approaches that base on genome-wide data have been developed to unravel the complexity of gene regulation. This review deals with the reconstruction of gene regulatory networks (GRNs) from experimental data through computational methods. Standard GRN inference methods primarily use gene expression data derived from microarrays. However, the incorporation of additional information from heterogeneous data sources, e.g. genome sequence and protein–DNA interaction data, clearly supports the network inference process. This review focuses on promising modelling approaches that use such diverse types of molecular biological information. In particular, approaches are discussed that enable the modelling of the dynamics of gene regulatory systems. The review provides an overview of common modelling schemes and learning algorithms and outlines current challenges in GRN modelling.     

Evolving beyond perfection: an investigation of the effects of long-term evolution on fractal gene regulatory networks

This paper continues a theme of exploring algorithms based on principles of biological development for tasks such as pattern generation, machine learning and robot control. Previous work has investigated the use of genes expressed as fractal proteins to enable greater evolvability of gene regulatory networks (GRNs). Here, the evolution of such GRNs is investigated further to determine whether evolution exhibits natural tendencies towards efficiency and graceful degradation of developmental programs. Experiments where "perfect" GRNs are evolved for a further thousand generations without the addition of any further selection pressure, confirm this hypothesis. After further evolution, the perfect GRNs operate in a more efficient manner (using fewer proteins) and show an improved ability to function correctly with missing genes. When the algorithm is applied to applications (e.g. robot control) this equates to efficient and fault-tolerant controllers.     

Robust stability of stochastic delayed genetic regulatory networks

Gene regulation is an intrinsically noisy process, which is subject to intracellular and extracellular noise perturbations and environment fluctuations. In this paper, we consider the robust stability analysis problem of genetic regulatory networks with time-varying delays and stochastic perturbation. Different from other papers, the genetic regulate system considers not only stochastic perturbation but also parameter disturbances, it is in close proximity to the real gene regulation process than determinate model. Based on the Lyapunov functional theory, sufficient conditions are given to ensure the stability of the genetic regulatory networks. All the stability conditions are given in terms of LMIs which are easy to be verified. Illustrative examples are presented to show the effectiveness of the obtained results.     

Chaotic motifs in gene regulatory networks

Chaos should occur often in gene regulatory networks (GRNs) which have been widely described by nonlinear coupled ordinary differential equations, if their dimensions are no less than 3. It is therefore puzzling that chaos has never been reported in GRNs in nature and is also extremely rare in models of GRNs. On the other hand, the topic of motifs has attracted great attention in studying biological networks, and network motifs are suggested to be elementary building blocks that carry out some key functions in the network. In this paper, chaotic motifs (subnetworks with chaos) in GRNs are systematically investigated. The conclusion is that: (i) chaos can only appear through competitions between different oscillatory modes with rivaling intensities. Conditions required for chaotic GRNs are found to be very strict, which make chaotic GRNs extremely rare. (ii) Chaotic motifs are explored as the simplest few-node structures capable of producing chaos, and serve as the intrinsic source of chaos of random few-node GRNs. Several optimal motifs causing chaos with atypically high probability are figured out. (iii) Moreover, we discovered that a number of special oscillators can never produce chaos. These structures bring some advantages on rhythmic functions and may help us understand the robustness of diverse biological rhythms. (iv) The methods of dominant phase-advanced driving (DPAD) and DPAD time fraction are proposed to quantitatively identify chaotic motifs and to explain the origin of chaotic behaviors in GRNs.     

Passivity of memristor-based BAM neural networks with different memductance and uncertain delays

This paper addresses the passivity problem for a class of memristor-based bidirectional associate memory (BAM) neural networks with uncertain time-varying delays. In particular, the proposed memristive BAM neural networks is formulated with two different types of memductance functions. By constructing proper Lyapunov–Krasovskii functional and using differential inclusions theory, a new set of sufficient condition is obtained in terms of linear matrix inequalities which guarantee the passivity criteria for the considered neural networks. Finally, two numerical examples are given to illustrate the effectiveness of the proposed theoretical results.     

具有三时滞Lotka-Volterra互惠系统的Hopf分支

建立了具有三个时滞的Lotka-Volterra互惠系统;获得了正平衡点和Hopf分支存在的条件等;并对所获得的结果进行了数值模拟．     

Spatiotemporal dynamics of the Calvin cycle: multistationarity and symmetry breaking instabilities

The possibility of controlling the Calvin cycle has paramount implications for increasing the production of biomass. Multistationarity, as a dynamical feature of systems, is the first obvious candidate whose control could find biotechnological applications. Here we set out to resolve the debate on the multistationarity of the Calvin cycle. Unlike the existing simulation-based studies, our approach is based on a sound mathematical framework, chemical reaction network theory and algebraic geometry, which results in provable results for the investigated model of the Calvin cycle in which we embed a hierarchy of realistic kinetic laws. Our theoretical findings demonstrate that there is a possibility for multistationarity resulting from two sources, homogeneous and inhomogeneous instabilities, which partially settle the debate on multistability of the Calvin cycle. In addition, our tractable analytical treatment of the bifurcation parameters can be employed in the design of validation experiments.     

Finite-time and fixed-time synchronization analysis of inertial memristive neural networks with time-varying delays

This paper investigates the finite-time synchronization and fixed-time synchronization problems of inertial memristive neural networks with time-varying delays. By utilizing the Filippov discontinuous theory and Lyapunov stability theory, several sufficient conditions are derived to ensure finite-time synchronization of inertial memristive neural networks. Then, for the purpose of making the setting time independent of initial condition, we consider the fixed-time synchronization. A novel criterion guaranteeing the fixed-time synchronization of inertial memristive neural networks is derived. Finally, three examples are provided to demonstrate the effectiveness of our main results.