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THE EFFECT OF COUPLED FEEDBACK ON NOISE FILTERING IN SIGNAL TRANSDUCTION NETWORKS

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Journal of Systems Science & Complexity 2010年第5期23卷 942-950页

作者： Dengyu liu Xiao CHANG zengrong liu Luonan CHEN Ruiqi WANG Institute of Systems Biology Shanghai University Shanghai 200444 China College of Physics and Mathematics Jinggangshan University Ji'an 343009 China Institute of Systems Biology Shanghai University Shanghai 200444 China Key Laboratory of Systems Biology SIBS-Novo Nordisk Translational Research Centre for PreDiabetes Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Many interacting biomolecular components in cells form different positive or negative feedback loops. When biological signals transduce through cascades consisting of various loops they will be affected or even distorted. Especially, how to process various signals buried in various intrinsic and extrinsic noises is an important issue. This paper analyzes how the response time influences noise filtering ability and how to enhance the ability by coupling different feedback loops. A parameter to measure the response time of the signal transduction, i.e., τ0.9, and its relationship between the response time and noise filtering will be discussed. The authors show clearly that the longer the response time is, the better the ability to filter noises will be. Therefore, to enhance the ability to filter noises, the authors can prolong the response time by coupling different positive or negative feedback loops. The results provide a possible approach to enhance the ability to filter noises in larger biomolecular networks.

关键词： Coupled feedback filtering noises response time signal cycle.

Yeast protein-protein interaction network model based on biological experimental data

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Applied Mathematics and Mechanics(English Edition) 2015年第6期36卷 827-834页

作者： Chunhong WANG Shuiming CAI zengrong liu Youwen CHEN Department of Mathematics Shanghai University Faculty of Science Jiangsu University Institute of Systems Biology Shanghai University

Duplication and divergence have been widely recognized as the two domi- nant evolutionary forces in shaping biological networks, e.g., gene regulatory networks and protein-protein interaction （PPI） networks. It has been shown that the network growth models constructed on the principle of duplication and divergence can recapture the topo- logical properties of real PPI networks. However, such network models only consider the evolution processes. How to select the model parameters with the real biological experi- mental data has not been presented. Therefore, based on the real PPI network statistical data, a yeast PPI network model is constructed. The simulation results indicate that the topological characteristics of the constructed network model are well consistent with those of real PPI networks, especially on sparseness, scale-free, small-world, hierarchical modularity, and disassortativity.

关键词： yeast duplication-divergence protein-protein interaction (PPI) network,disassortativity

Distributed coordinated adaptive tracking in networked redundant robotic systems with a dynamic leader

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Science China(Technological Sciences) 2014年第5期57卷 905-913页

作者： ZHOU Jin WU XingJie liu zengrong Shanghai Institute of Applied Mathematics and Mechanics Shanghai Key Laboratory of Mechanics in Energy Engineering Shanghai University School of Mathematics and Statistics Hefei Normal University Institute of System Biology Shanghai University

Distributed coordinated control of networked robotic systems formulated by Lagrange dynamics has recently been a subject of considerable interest within science and technology communities due to its broad engineering applications involving complex and integrated production processes,where high flexibility,manipulability,and maneuverability are desirable *** this paper,we investigate the distributed coordinated adaptive tracking problem of networked redundant robotic systems with a dynamic *** provide an analysis procedure for the controlled synchronization of such systems with uncertain *** also find that the proposed control strategy does not require computing positional inverse kinematics and does not impose any restriction on the self-motion of the manipulators;therefore,the extra degrees of freedom are applicable for other sophisticated *** with some existing work,a distinctive feature of the designed distributed control algorithm is that only a subset of followers needs to access the position information of the dynamic leader in the task space,where the underlying directed graph has a spanning ***,we present a simulation example to verify the effectiveness of the proposed algorithms.

关键词： networked Lagrange system redundant robot distributed adaptive control tracking synchronization algorithm

Bogdanov-Takens bifurcation with codimension three of a predator-prey system suffering the additive Allee effect

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International Journal of Biomathematics 2017年第3期10卷 261-284页

作者： Yanwei liu zengrong liu Ruiqi Wang College of MathemaLics and Information Science Zhengzhou University of Light Industry Zhengzhou 450002 P. R. China Department of Mathematics Shanghai University Shanghai 200444 P. R. China

In the present work, research efforts have focused on investigating codimension two and three Bogdanov-Takens bifurcations of a predator-prey system with additive Allee effect. According to the existence conditions of Bogdanov-Takens bifurcation, we give the associated generic unfolding, and derive the dynamical classification in the perturbation parameter plane using some smooth parameter-dependent transformations of coordinate. Moreover, some numerical examples and simulations are performed to complete and illustrate our results.

关键词： Bogdanov-Takens bifurcation Allee effect universal unfolding

Oscillatory behavior of p53-Mdm2 system driven by transcriptional and translational time delays

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International Journal of Biomathematics 2020年第5期13卷 63-95页

作者： Chunyan Gao Haihong liu zengrong liu Yuan Zhang Fang Yan Department of Mathematics Yunnan Norrmal University No.768Juxian StreetChenggong District KunmingP.R.China School of Mathermatics and Information Technology Yuci Norrmal University No.134Fenghuang Road Yuxi CityYunnan ProvinceP.R.China

Biological experiments clarify that p53-Mdm2 module is the core of tumor network and p53 oscillation plays an important role in determining the tumor cell *** this paper,we investigate the effect of time delay on the oscillatory behavior induced by Hopf bifurcation in p53-Mdm2 ***,the stability of the unique positive equilibriurm point and the existence of Hopf bifurcation are investigated by using the time delay as the bifurcation parameter and by applying the bifurcation ***,the explicit criteria determining the direction of Hopf bifurcation and the stability of bifurcating periodic solutions are developed based on the normal form theory and the center manifold *** addition,the combination of numerical simulation results and theoretical calculation results indicates that time delays in p53-Mdm2 system are critical for p53 *** results may help us to better understand the biological functions of p53 pathway and provide clues for treatment of cancer.

关键词： Time delays stability Hopf bifurcation p53-Mdm2 pathway

A model of calcium signaling and degranulation dynamics induced by laser irradiation in mast cells

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Chinese Science Bulletin 2008年第15期53卷 2315-2325页

作者： SHI XiaoMin ZHENG YuFan liu zengrong YANG WenZhong Institute of Systems Science Shanghai University Shanghai 200444 China Institute of Systems Biology Shanghai University Shanghai 200444 China Department of Physics Fudan University Shanghai 200433 China

Recent experiments show that calcium signaling and degranulation dynamics induced by low power laser irradiation in mast cells must rely on extracellular Ca2+ influx. An analytical expression of Ca2+ flux through TRPV4 cation channel in response to interaction of laser photon energy and extracellular Ca2+ is deduced, and a model characterizing dynamics of calcium signaling and degranulation activated by laser irradiation in mast cells is established. The model indicates that the characteristics of calcium signaling and degranulation dynamics are determined by interaction between laser photon energy and Ca2+ influx. Extracellular Ca2+ concentration is so high that even small photon energy can activate mast cells, thus avoiding the possible injury caused by laser irradiation with shorter wavelengths. The model predicts that there exists a narrow parameter domain of photon energy and extracellular Ca2+ concen-tration of which results in cytosolic Ca2+ limit cycle oscillations, and shows that PKC activity is in direct proportion to the frequency of Ca2+ oscillations. With the model it is found that sustained and stable maximum plateau of cytosolic Ca2+ concentration can get optimal degranulation rate. Furthermore, the idea of introducing the realistic physical energy into model is applicable to modeling other physical signal transduction systems.

关键词：激光钙肥大细胞 TRPV4渠道动态模式

An efficient range-free localization algorithm for wireless sensor networks

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Science China(Technological Sciences) 2011年第5期54卷 1053-1060页

作者： HE QinBin CHEN FangYue CAI ShuiMing HAO JunJun liu zengrong Institute of System Biology Shanghai University Shanghai 200444 China Department of Mathematics Taizhou University Linhai 317000 China School of Science Hangzhou Dianzi University Hangzhou 310018 China

Node positioning is a fundamental problem in applications of wireless sensor networks (WSNs). In this paper, a new range-free algorithm, called spring swarm localization algorithm (SSLA), is proposed for positioning WSNs. To determine the locations of sensor nodes, the proposed algorithm uses network topology information and a small fraction of sensor nodes which know their locations. Numerical simulations show that high positioning accuracy can be obtained by using the algorithm. Some examples are given to illustrate the effectiveness of the algorithm.

关键词： wireless sensor networks localization spring swarm localization algorithm range-based range-free node-link structure

Reduction of the vector fields preserving n-form and the study of their in terrelated problems

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Chinese Science Bulletin 1998年第9期43卷 788-789页

作者： Debin Huang Xiaohua Zhao zengrong liu Department of Mathematics Shanghai University Jiading China Department of Mathematics Yunnan University Kunming China

System approaches reveal the molecular networks involved in neural stem cell differentiation

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Protein & Cell 2012年第3期3卷 213-224页

作者： Kai Wang Haifeng Wang Jiao Wang Yuqiong Xie Jun Chen Huang Yan zengrong liu Tieqiao Wen Laboratory of Molecular Neurobiology School of Life SciencesShanghai UniversityShanghai 200444China School of Communication and Information Engineering Shanghai UniversityShanghai 200444China College of Life Science Wuhan UniversityWuhan 430072China College of Chemical Engineering and Technology Wuhan University of Science and TechnologyWuhan 430081China Institute of Systems Biology Shanghai UniversityShanghai 200444China􀀍

The self-renewal and multipotent potentials in neural stem cells(NSCs)maintain the normal physiological functions of central nervous system(CNS).The ab-normal differentiation of NSCs would lead to CNS ***,the mechanisms of how NSCs differentiate into astrocytes,oligodendrocytes(OLs)and neurons are still unclear,which is mainly due to the complexity of differentiation processes and the limita-tion of the cell separation *** this study,we modeled the dynamics of neural cell interactions in a systemic approach by mining the high-throughput genomic and proteomic data,and identified 8615 genes that are involved in various biological processes and functions with significant changes during the differentiation processes.A total of 1559 genes are specifically expressed in neural cells,in which 242 genes are NSC specific,215 are astrocyte specific,551 are OL specific,and 563 are neuron *** addition,we proposed 57 transcriptional regulators specifically expressed in NSCs may play essential roles in the development *** findings provide more comprehensive analysis for better understanding the endogenous mechanisms of NSC fate determination.

关键词： neural stem cell cell differentiation mo-lecular networks