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

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

Leader-following Consensus of Multi-agent Systems over Finite Fields

The leader-following consensus problem of multi-agent systems over finite fields ${\mathbb F}_p$ is considered in this paper. Dynamics of each agent is governed by a linear equation over ${\mathbb F}_p$, where a distributed control protocol is utilized by the followers.Sufficient and/or necessary conditions on system matrices and graph weights in ${\mathbb F}_p$ are provided for the followers to track the leader

Design of linear Boolean network codes for combination networks

Network coding is a promising technique to improve the throughput of communication networks. In the thesis, we investigate linear Boolean network codes on a special class of multicast networks, called combination networks. Using companion matrices of primitive polynomials over finite fields, we design a class of symmetric linear Boolean network codes from Reed-Solomon codes for single-source combination networks. We also prove that, for some cases, the linear Boolean network codes are optimal in the sense of minimum network uses. In the thesis, we further consider two-source network coding problem for combination networks and other specific networks. We develop a method to evaluate an outer bound for these two-source networks. By designing linear Boolean network codes which achieve extreme points of rate regions, we show that the outer bound is actually tight for some of these networks

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

Limit Synchronization in Markov Decision Processes

Markov decision processes (MDP) are finite-state systems with both strategic and probabilistic choices. After fixing a strategy, an MDP produces a sequence of probability distributions over states. The sequence is eventually synchronizing if the probability mass accumulates in a single state, possibly in the limit. Precisely, for 0 <= p <= 1 the sequence is p-synchronizing if a probability distribution in the sequence assigns probability at least p to some state, and we distinguish three synchronization modes: (i) sure winning if there exists a strategy that produces a 1-synchronizing sequence; (ii) almost-sure winning if there exists a strategy that produces a sequence that is, for all epsilon > 0, a (1-epsilon)-synchronizing sequence; (iii) limit-sure winning if for all epsilon > 0, there exists a strategy that produces a (1-epsilon)-synchronizing sequence. We consider the problem of deciding whether an MDP is sure, almost-sure, limit-sure winning, and we establish the decidability and optimal complexity for all modes, as well as the memory requirements for winning strategies. Our main contributions are as follows: (a) for each winning modes we present characterizations that give a PSPACE complexity for the decision problems, and we establish matching PSPACE lower bounds; (b) we show that for sure winning strategies, exponential memory is sufficient and may be necessary, and that in general infinite memory is necessary for almost-sure winning, and unbounded memory is necessary for limit-sure winning; (c) along with our results, we establish new complexity results for alternating finite automata over a one-letter alphabet

Control of movement time and sequential action through attractor dynamics : a simulation study demonstrating object interception and coordination

The timing of movements and of action sequences is difficult when on-line coupling to sensory information is a requirement. That requirement arises in most behavior-based robot architectures, in which relatively low-level and often noisy sensor input is used to initiate and steer action. We show how an attractor dynamics approach to the generation of behavior in such architectures can be extended to the timing of motor acts. We propose a two-layer architecture, in which a competitive "neural" dynamics controls the qualitative dynamics of a second, "timing" layer. At that second layer, periodic attractors generate timed movement. By activating such limit cycles over limited time intervals, discrete movements and movement sequences can be obtained. We demonstrate the approach by simulating two tasks that involve control of timing: the interception of moving objects by a simple two-degree-of-freedom robot arm and the temporal coordination of the end-effector motions of two six-degree-of-freedom robot arms.Fundação para a Ciência e a Tecnoloia (FCT

A Prescription for Partial Synchrony

Algorithms in message-passing distributed systems often require partial synchrony to tolerate crash failures. Informally, partial synchrony refers to systems where timing bounds on communication and computation may exist, but the knowledge of such bounds is limited. Traditionally, the foundation for the theory of partial synchrony has been real time: a time base measured by counting events external to the system, like the vibrations of Cesium atoms or piezoelectric crystals. Unfortunately, algorithms that are correct relative to many real-time based models of partial synchrony may not behave correctly in empirical distributed systems. For example, a set of popular theoretical models, which we call M_*, assume (eventual) upper bounds on message delay and relative process speeds, regardless of message size and absolute process speeds. Empirical systems with bounded channel capacity and bandwidth cannot realize such assumptions either natively, or through algorithmic constructions. Consequently, empirical deployment of the many M_*-based algorithms risks anomalous behavior. As a result, we argue that real time is the wrong basis for such a theory. Instead, the appropriate foundation for partial synchrony is fairness: a time base measured by counting events internal to the system, like the steps executed by the processes. By way of example, we redefine M_* models with fairness-based bounds and provide algorithmic techniques to implement fairness-based M_* models on a significant subset of the empirical systems. The proposed techniques use failure detectors — system services that provide hints about process crashes — as intermediaries that preserve the fairness constraints native to empirical systems. In effect, algorithms that are correct in M_* models are now proved correct in such empirical systems as well. Demonstrating our results requires solving three open problems. (1) We propose the first unified mathematical framework based on Timed I/O Automata to specify empirical systems, partially synchronous systems, and algorithms that execute within the aforementioned systems. (2) We show that crash tolerance capabilities of popular distributed systems can be denominated exclusively through fairness constraints. (3) We specify exemplar system models that identify the set of weakest system models to implement popular failure detectors