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 fault detection for networked systems with communication delay and data missing

n this paper, the robust fault detection problem is investigated for a class of discrete-time networked systems with unknown input and multiple state delays. A novel measurement model is utilized to represent both the random measurement delays and the stochastic data missing phenomenon, which typically result from the limited capacity of the communication networks. The network status is assumed to vary in a Markovian fashion and its transition probability matrix is uncertain but resides in a known convex set of a polytopic type. The main purpose of this paper is to design a robust fault detection filter such that, for all unknown inputs, possible parameter uncertainties and incomplete measurements, the error between the residual signal and the fault signal is made as small as possible. By casting the addressed robust fault detection problem into an auxiliary robust H∞ filtering problem of a certain Markovian jumping system, a sufficient condition for the existence of the desired robust fault detection filter is established in terms of linear matrix inequalities. A numerical example is provided to illustrate the effectiveness and applicability of the proposed technique

Distinct expression and methylation patterns for genes with different fates following a single whole-genome duplication in flowering plants

For most sequenced flowering plants, multiple whole-genome duplications (WGDs) are found. Duplicated genes following WGD often have different fates that can quickly disappear again, be retained for long(er) periods, or subsequently undergo small-scale duplications. However, how different expression, epigenetic regulation, and functional constraints are associated with these different gene fates following a WGD still requires further investigation due to successive WGDs in angiosperms complicating the gene trajectories. In this study, we investigate lotus (Nelumbo nucifera), an angiosperm with a single WGD during the K–pg boundary. Based on improved intraspecific-synteny identification by a chromosome-level assembly, transcriptome, and bisulfite sequencing, we explore not only the fundamental distinctions in genomic features, expression, and methylation patterns of genes with different fates after a WGD but also the factors that shape post-WGD expression divergence and expression bias between duplicates. We found that after a WGD genes that returned to single copies show the highest levels and breadth of expression, gene body methylation, and intron numbers, whereas the long-retained duplicates exhibit the highest degrees of protein–protein interactions and protein lengths and the lowest methylation in gene flanking regions. For those long-retained duplicate pairs, the degree of expression divergence correlates with their sequence divergence, degree in protein–protein interactions, and expression level, whereas their biases in expression level reflecting subgenome dominance are associated with the bias of subgenome fractionation. Overall, our study on the paleopolyploid nature of lotus highlights the impact of different functional constraints on gene fate and duplicate divergence following a single WGD in plant

Rapid Screening for Flavone C-Glycosides in the Leaves of Different Species of Bamboo and Simultaneous Quantitation of Four Marker Compounds by HPLC-UV/DAD

A strategy for analyzing flavone C-glucosides in the leaves of different species of bamboo was developed. Firstly, the flavone C-glycosides were extracted from the bamboo leaves (51 species in 17 genera) with methanol and chromatographed on silica gel 60 plates in automatic developing chamber (ADC2), and a qualitative survey using simple derivatization steps with the NP reagent was carried out. The flavone C-glycosides were found in 40 of 51 species of bamboo examined. Secondly, an HPLC method with photodiode array and multiple wavelength detector was optimized and validated for the simultaneous determination of flavone C-glycosides, including isoorientin, isovitexin, orientin, and vitexin in the leaves of three species of bamboo and the flavone C-glycosides were confirmed by LC/MS. The optimized HPLC method proved to be linear in the concentration range tested (0.2–100 μg/mL, r2 ≥ 0.9997), precise (RSD ≤ 1.56%), and accurate (88–106%). The concentration ranges of isoorientin, isovitexin, orientin, and vitexin in three bamboo leaves samples were 1.00–2.78, 0–0.31, 0–0.07, and 0.20–0.68 mg/g, respectively. The proposed method was validated to be simple and reliable and can be a tool for quality control of bamboo leaf extract or its commercial products

The flavor-changing single-top quark production in the littlest Higgs model with T parity at the LHC

The littlest Higgs model with discrete symmetry named "T-parity"(LHT) is an interesting new physics model which does not suffer strong constraints from electroweak precision data. One of the important features of the LHT model is the existence of new source of FC interactions between the SM fermions and the mirror fermions. These FC interactions can make significant loop-level contributions to the couplings $tcV$, and furthermore enhance the cross sections of the FC single-top quark production processes. In this paper, we study some FC single-top quark production processes, $pp\to t\bar{c}$ and $pp\to tV$, at the LHC in the LHT model. We find that the cross sections of these processes are strongly depended on the mirror quark masses. The processes $pp\to t\bar{c}$ and $pp\to tg$ have large cross sections with heavy mirror quarks. The observation of these FC processes at the LHC is certainly the clue of new physics, and further precise measurements of the cross scetions can provide useful information about the free parameters in the LHT model, specially about the mirror quark masses.Comment: 20 pages, 5 figure

Probing new physics from top quark FCNC processes at linear colliders : a mini review

We briefly review the studies on the top quark FCNC processes at a next-generation linear collider. Such processes, including various FCNC top quark rare decays and top-charm associated productions, are extremely suppressed in the standard model (SM) but could be significantly enhanced in some extensions. We compared the predictions from different typical new physics models: the SM, the minimal supersymmetric model (MSSM), the general two-higgs-doublet model (2HDM) and the topcolor-assisted technicolor (TC2) model. Our conclusion is: (1) While all the new physics models can enhance the rates by several orders relative to the SM predictions, the TC2 model predicts much larger rates than other models; (2) The optimal channel for probing the top quark FCNC is the top-charm associated production in \gamma-\gamma collision, which occurs at a much higher rate than e^+ e^- or e^- \gamma collision and can reach the detectable level for a large part of the parameter space.Comment: 12 pages, 12 figs, talk given at APPI2004, Iweta, Japa

H∞ and L2–L∞ filtering for two-dimensional linear parameter-varying systems

This is the post print version of the article. The official published version can be obtained from the link below - Copyright 2007 Wiley-BlackwellIn this paper, the H∞ and l2–l∞ filtering problem is investigated for two-dimensional (2-D) discrete-time linear parameter-varying (LPV) systems. Based on the well-known Fornasini–Marchesini local state-space (FMLSS) model, the mathematical model of 2-D systems under consideration is established by incorporating the parameter-varying phenomenon. The purpose of the problem addressed is to design full-order H∞ and l2–l∞ filters such that the filtering error dynamics is asymptotic stable and the prescribed noise attenuation levels in H∞ and l2–l∞ senses can be achieved, respectively. Sufficient conditions are derived for existence of such filters in terms of parameterized linear matrix inequalities (PLMIs), and the corresponding filter synthesis problem is then transformed into a convex optimization problem that can be efficiently solved by using standard software packages. A simulation example is exploited to demonstrate the usefulness and effectiveness of the proposed design method

Flat histogram simulation of lattice polymer systems

We demonstrate the use of a new algorithm called the Flat Histogram sampling algorithm for the simulation of lattice polymer systems. Thermodynamics properties, such as average energy or entropy and other physical quantities such as end-to-end distance or radius of gyration can be easily calculated using this method. Ground-state energy can also be determined. We also explore the accuracy and limitations of this method. Key words: Monte Carlo algorithms, flat histogram sampling, HP model, lattice polymer systemsComment: 7 RevTeX two-column page