Monostability and multistability of genetic regulatory networks with different types of regulation functions

The official published version of the article can be found at the link below.Monostability and multistability are proven to be two important topics in synthesis biology and system biology. In this paper, both monostability and multistability are analyzed in a unified framework by applying control theory and mathematical tools. The genetic regulatory networks (GRNs) with multiple time-varying delays and different types of regulation functions are considered. By putting forward a general sector-like regulation function and utilizing up-to-date techniques, a novel Lyapunov–Krasovskii functional is introduced for achieving delay dependence to ensure less conservatism. A new condition is then proposed for the general stability of a GRN in the form of linear matrix inequalities (LMIs) that are dependent on the upper and lower bounds of the delays. Our general stability conditions are applicable to several frequently used regulation functions. It is shown that the existing results for monostability of GRNs are special cases of our main results. Five examples are employed to illustrate the applicability and usefulness of the developed theoretical results.This work was supported in part by the Biotechnology and Biological Sciences Research Council (BBSRC) of the U.K. under Grant BB/C506264/1, the Royal Society of the U.K., the National Natural Science Foundation of China under Grants 60504008 and 60804028, the Program for New Century Excellent Talents in Universities of China, and the Alexander von Humboldt Foundation of Germany

A Marginalist Model of Network Formation

We develop a network-formation model where the quality of a link depends on the amount invested in it and is determined by a link-formation "technology" , an increasing strictly concave function which is the only exogenous ingredient in the model. The revenue from the investments in links is the information that the nodes receive through the network. Two approaches are considered. First, assuming that the investments in links are made by a planner, the basic question is that of the efficient investments, either relative to a given infrastructure (i.e. a set of feasible links) or in absolute terms. It is proved that efficient networks belong to a special class of weighted nested split graph networks. Second, assuming that links are the result of investments of the node-players involved, there is the question of stability in the underlying network-formation game, be it restricted to a given infrastructure or unrestricted. Necessary and sufficient conditions for stability of the complete and star networks, and nested split graph networks in general, are obtained.This research is supported by the Spanish Ministerio de Economía y Competitividad under projects ECO2015-66027-P and ECO2015-67519-P (MINECO/FEDER). Both authors also bene t from the Basque Government Departa-mento de Educación, Política Lingüística y Cultura funding for Grupos Consolidados IT869-13 and IT568-13

Networked Control System Design and Parameter Estimation

Networked control systems (NCSs) are a kind of distributed control systems in which the data between control components are exchanged via communication networks. Because of the attractive advantages of NCSs such as reduced system wiring, low weight, and ease of system diagnosis and maintenance, the research on NCSs has received much attention in recent years. The first part (Chapter 2 - Chapter 4) of the thesis is devoted to designing new controllers for NCSs by incorporating the network-induced delays. The thesis also conducts research on filtering of multirate systems and identification of Hammerstein systems in the second part (Chapter 5 - Chapter 6). Network-induced delays exist in both sensor-to-controller (S-C) and controller-to-actuator (C-A) links. A novel two-mode-dependent control scheme is proposed, in which the to-be-designed controller depends on both S-C and C-A delays. The resulting closed-loop system is a special jump linear system. Then, the conditions for stochastic stability are obtained in terms of a set of linear matrix inequalities (LMIs) with nonconvex constraints, which can be efficiently solved by a sequential LMI optimization algorithm. Further, the control synthesis problem for the NCSs is considered. The definitions of H₂ and H∞ norms for the special system are first proposed. Also, the plant uncertainties are considered in the design. Finally, the robust mixed H₂/H∞ control problem is solved under the framework of LMIs. To compensate for both S-C and C-A delays modeled by Markov chains, the generalized predictive control method is modified to choose certain predicted future control signal as the current control effort on the actuator node, whenever the control signal is delayed. Further, stability criteria in terms of LMIs are provided to check the system stability. The proposed method is also tested on an experimental hydraulic position control system. Multirate systems exist in many practical applications where different sampling rates co-exist in the same system. The l₂-l∞ filtering problem for multirate systems is considered in the thesis. By using the lifting technique, the system is first transformed to a linear time-invariant one, and then the filter design is formulated as an optimization problem which can be solved by using LMI techniques. Hammerstein model consists of a static nonlinear block followed in series by a linear dynamic system, which can find many applications in different areas. New switching sequences to handle the two-segment nonlinearities are proposed in this thesis. This leads to less parameters to be estimated and thus reduces the computational cost. Further, a stochastic gradient algorithm based on the idea of replacing the unmeasurable terms with their estimates is developed to identify the Hammerstein model with two-segment nonlinearities. Finally, several open problems are listed as the future research directions

Algorithmic issues in queueing systems and combinatorial counting problems

Includes bibliographical references (leaves 111-118).Thesis (Ph. D.)--Massachusetts Institute of Technology, Sloan School of Management, Operations Research Center, 2008.(cont.) However, these randomized algorithms can never provide proven upper or lower bounds on the number of objects they are counting, but can only give probabilistic estimates. We propose a set of deterministic algorithms for counting such objects for three classes of counting problems. They are interesting both because they give an alternative approach to solving these problems, and because unlike MCMC algorithms, they provide provable bounds on the number of objects. The algorithms we propose are for special cases of counting the number of matchings, colorings, or perfect matchings (permanent), of a graph.Multiclass queueing networks are used to model manufacturing, computer, supply chain, and other systems. Questions of performance and stability arise in these systems. There is a body of research on determining stability of a given queueing system, which contains algorithms for determining stability of queueing networks in some special cases, such as the case where there are only two stations. Yet previous attempts to find a general characterization of stability of queueing networks have not been successful.In the first part of the thesis, we contribute to the understanding of why such a general characterization could not be found. We prove that even under a relatively simple class of static buffer priority scheduling policies, stability of deterministic multiclass queueing network is, in general, an undecidable problem. Thus, there does not exist an algorithm for determining stability of queueing networks, even under those relatively simple assumptions. This explains why such an algorithm, despite significant efforts, has not been found to date. In the second part of the thesis, we address the problem of finding algorithms for approximately solving combinatorial graph counting problems. Counting problems are a wide and well studied class of algorithmic problems, that deal with counting certain objects, such as the number of independent sets, or matchings, or colorings, in a graph. The problems we address are known to be #P-hard, which implies that, unless P = #P, they can not be solved exactly in polynomial time. It is known that randomized approximation algorithms based on Monte Carlo Markov Chains (MCMC) solve these problems approximately, in polynomial time.by Dmitriy A. Katz-Rogozhnikov.Ph.D

Mathematical problems for complex networks

Copyright @ 2012 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. This article is made available through the Brunel Open Access Publishing Fund.Complex networks do exist in our lives. The brain is a neural network. The global economy is a network of national economies. Computer viruses routinely spread through the Internet. Food-webs, ecosystems, and metabolic pathways can be represented by networks. Energy is distributed through transportation networks in living organisms, man-made infrastructures, and other physical systems. Dynamic behaviors of complex networks, such as stability, periodic oscillation, bifurcation, or even chaos, are ubiquitous in the real world and often reconfigurable. Networks have been studied in the context of dynamical systems in a range of disciplines. However, until recently there has been relatively little work that treats dynamics as a function of network structure, where the states of both the nodes and the edges can change, and the topology of the network itself often evolves in time. Some major problems have not been fully investigated, such as the behavior of stability, synchronization and chaos control for complex networks, as well as their applications in, for example, communication and bioinformatics

On resilient control of dynamical flow networks

Resilience has become a key aspect in the design of contemporary infrastructure networks. This comes as a result of ever-increasing loads, limited physical capacity, and fast-growing levels of interconnectedness and complexity due to the recent technological advancements. The problem has motivated a considerable amount of research within the last few years, particularly focused on the dynamical aspects of network flows, complementing more classical static network flow optimization approaches. In this tutorial paper, a class of single-commodity first-order models of dynamical flow networks is considered. A few results recently appeared in the literature and dealing with stability and robustness of dynamical flow networks are gathered and originally presented in a unified framework. In particular, (differential) stability properties of monotone dynamical flow networks are treated in some detail, and the notion of margin of resilience is introduced as a quantitative measure of their robustness. While emphasizing methodological aspects -- including structural properties, such as monotonicity, that enable tractability and scalability -- over the specific applications, connections to well-established road traffic flow models are made.Comment: accepted for publication in Annual Reviews in Control, 201

Stability and synchronization of discrete-time Markovian jumping neural networks with mixed mode-dependent time delays

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.In this paper, we introduce a new class of discrete-time neural networks (DNNs) with Markovian jumping parameters as well as mode-dependent mixed time delays (both discrete and distributed time delays). Specifically, the parameters of the DNNs are subject to the switching from one to another at different times according to a Markov chain, and the mixed time delays consist of both discrete and distributed delays that are dependent on the Markovian jumping mode. We first deal with the stability analysis problem of the addressed neural networks. A special inequality is developed to account for the mixed time delays in the discrete-time setting, and a novel Lyapunov-Krasovskii functional is put forward to reflect the mode-dependent time delays. Sufficient conditions are established in terms of linear matrix inequalities (LMIs) that guarantee the stochastic stability. We then turn to the synchronization problem among an array of identical coupled Markovian jumping neural networks with mixed mode-dependent time delays. By utilizing the Lyapunov stability theory and the Kronecker product, it is shown that the addressed synchronization problem is solvable if several LMIs are feasible. Hence, different from the commonly used matrix norm theories (such as the M-matrix method), a unified LMI approach is developed to solve the stability analysis and synchronization problems of the class of neural networks under investigation, where the LMIs can be easily solved by using the available Matlab LMI toolbox. Two numerical examples are presented to illustrate the usefulness and effectiveness of the main results obtained

Animating the development of Social Networks over time using a dynamic extension of multidimensional scaling

The animation of network visualizations poses technical and theoretical challenges. Rather stable patterns are required before the mental map enables a user to make inferences over time. In order to enhance stability, we developed an extension of stress-minimization with developments over time. This dynamic layouter is no longer based on linear interpolation between independent static visualizations, but change over time is used as a parameter in the optimization. Because of our focus on structural change versus stability the attention is shifted from the relational graph to the latent eigenvectors of matrices. The approach is illustrated with animations for the journal citation environments of Social Networks, the (co-)author networks in the carrying community of this journal, and the topical development using relations among its title words. Our results are also compared with animations based on PajekToSVGAnim and SoNIA