Non-coding RNAs and a layered architecture of genetic networks

In eukaryotic cells, protein-coding sequences constitute a relatively small part of the genome. The rest of the genome is transcribed to non-coding RNAs (ncRNAs). Such RNAs form the cornerstone of a regulatory network that operates in parallel with the protein network. Their biological functions are based primarily on the ability to pair with and deactivate target messenger RNAs (mRNAs). To clarify the likely role of ncRNAs in complex genetic networks, we present and comprehensively analyze a kinetic model of one of the key counterparts of the network architectures. Specifically, the genes transcribed to ncRNAs are considered to interplay with a hierarchical two-layer set of genes transcribed to mRNAs. The genes forming the bottom layer are regulated from the top and negatively self-regulated. If the former regulation is positive, the dependence of the RNA populations on the governing parameters is found to be often non-monotonous. Specifically, the model predicts bistability. If the regulation is negative, the dependence of the RNA populations on the governing parameters is monotonous. In particular, the population of the mRNAs, corresponding to the genes forming the bottom layer, is nearly constant.     

Interplay of noncoding RNAs,mRNAs, and proteins during the growth of eukaryotic cells

Numerous biological functions of noncoding RNAs (ncRNAs) in eukaryotic cells are based primarily on their ability to pair with target mRNAs and then either to prevent translation or to result in rapid degradation of the mRNA-ncRNA complex. Using a general model describing this scenario, we show that ncRNAs may help to maintain constant mRNA and protein concentrations during the growth of cells. The possibility of observation of this effect on the global scale is briefly discussed.     

Hierarchical genetic networks and noncoding RNAs

In eukaryotic cells, many genes are transcribed into noncoding RNAs. Such RNAs may associate with mRNAs and inhibit their translation and facilitate degradation. To clarify what may happen in this case, we propose a kinetic model describing the effect of noncoding RNAs on a mRNA-protein network with the hierarchical three-layer architecture. For positive regulation of the layers, our model predicts either bistability with a fairly narrow hysteresis loop or a unique steady state. For negative or mixed regulation, the steady state is found to be unique.     

Topological origin of global attractors in gene regulatory networks

Fixed-point attractors with global stability manifest themselves in a number of gene regulatory networks. This property indicates the stability of regulatory networks against small state perturbations and is closely related to other complex dynamics. In this paper, we aim to reveal the core modules in regulatory networks that determine their global attractors and the relationship between these core modules and other motifs. This work has been done via three steps. Firstly, inspired by the signal transmission in the regulation process, we extract the model of chain-like network from regulation networks. We propose a module of “ideal transmission chain(ITC)”, which is proved sufficient and necessary(under certain condition) to form a global fixed-point in the context of chain-like network. Secondly, by examining two well-studied regulatory networks(i.e., the cell-cycle regulatory networks of Budding yeast and Fission yeast), we identify the ideal modules in true regulation networks and demonstrate that the modules have a superior contribution to network stability(quantified by the relative size of the biggest attraction basin). Thirdly, in these two regulation networks, we find that the double negative feedback loops, which are the key motifs of forming bistability in regulation, are connected to these core modules with high network stability. These results have shed new light on the connection between the topological feature and the dynamic property of regulatory networks.     

Exponential synchronization of complex networks with Markovian jump and mixed delays

In this Letter, we investigate the exponential synchronization problem for an array of N linearly coupled complex networks with Markovian jump and mixed time-delays. The complex network consists of m modes and the network switches from one mode to another according to a Markovian chain with known transition probability. The mixed time-delays are composed of discrete and distributed delays, both of which are mode-dependent. The nonlinearities imbedded with the complex networks are assumed to satisfy the sector condition that is more general than the commonly used Lipschitz condition. By making use of the Kronecker product and the stochastic analysis tool, we propose a novel Lyapunov–Krasovskii functional suitable for handling distributed delays and then show that the addressed synchronization problem is solvable if a set of linear matrix inequalities (LMIs) are feasible. Therefore, a unified LMI approach is developed to establish sufficient conditions for the coupled complex network to be globally exponentially synchronized in the mean square. Note that the LMIs can be easily solved by using the Matlab LMI toolbox and no tuning of parameters is required. A simulation example is provided to demonstrate the usefulness of the main results obtained.     

基于区域密度曲线识别网络上的多影响力节点

复杂网络多影响力节点的识别可以帮助理解网络的结构和功能,具有重要的理论意义和应用价值.本文提出一种基于网络区域密度曲线的多影响力节点的识别方法.应用两种不同的传播模型,在不同网络上与其他中心性指标进行了比较.结果表明,基于区域密度曲线的识别方法能够更好地识别网络中的多影响力节点,选中的影响力节点之间的分布较为分散,自身也比较重要.本文所提方法是基于网络的局部信息,计算的时间复杂度较低.     

Feedback arcs and node hierarchy in directed networks

Directed networks such as gene regulation networks and neural networks are connected by arcs(directed links). The nodes in a directed network are often strongly interwound by a huge number of directed cycles, which leads to complex information-processing dynamics in the network and makes it highly challenging to infer the intrinsic direction of information flow. In this theoretical paper, based on the principle of minimum-feedback, we explore the node hierarchy of directed networks and distinguish feedforward and feedback arcs. Nearly optimal node hierarchy solutions, which minimize the number of feedback arcs from lower-level nodes to higher-level nodes, are constructed by belief-propagation and simulated-annealing methods. For real-world networks, we quantify the extent of feedback scarcity by comparison with the ensemble of direction-randomized networks and identify the most important feedback arcs. Our methods are also useful for visualizing directed networks.     

Structural changes in data communication in wireless sensor networks

Wireless sensor networks are an important technology for making distributed autonomous measures in hostile or inaccessible environments. Among the challenges they pose, the way data travel among them is a relevant issue since their structure is quite dynamic. The operational topology of such devices can often be described by complex networks. In this work, we assess the variation of measures commonly employed in the complex networks literature applied to wireless sensor networks. Four data communication strategies were considered: geometric, random, small-world, and scale-free models, along with the shortest path length measure. The sensitivity of this measure was analyzed with respect to the following perturbations: insertion and removal of nodes in the geometric strategy; and insertion, removal and rewiring of links in the other models. The assessment was performed using the normalized Kullback-Leibler divergence and Hellinger distance quantifiers, both deriving from the Information Theory framework. The results reveal that the shortest path length is sensitive to perturbations.     

Tristable and multiple bistable activity in complex random binary networks of two-state units

We study complex networks of stochastic two-state units. Our aim is to model discrete stochastic excitable dynamics with a rest and an excited state. Both states are assumed to possess different waiting time distributions. The rest state is treated as an activation process with an exponentially distributed life time, whereas the latter in the excited state shall have a constant mean which may originate from any distribution. The activation rate of any single unit is determined by its neighbors according to a random complex network structure. In order to treat this problem in an analytical way, we use a heterogeneous mean-field approximation yielding a set of equations generally valid for uncorrelated random networks. Based on this derivation we focus on random binary networks where the network is solely comprised of nodes with either of two degrees. The ratio between the two degrees is shown to be a crucial parameter. Dependent on the composition of the network the steady states show the usual transition from disorder to homogeneously ordered bistability as well as new scenarios that include inhomogeneous ordered and disordered bistability as well as tristability. The various steady states differ in their spiking activity expressed by a state dependent spiking rate. Numerical simulations agree with analytic results of the heterogeneous mean-field approximation.     

Research on Community Detection in Complex Networks Based on Internode Attraction

With the rapid development of computer technology, the research on complex networks has attracted more and more attention. At present, the research directions of cloud computing, big data, internet of vehicles, and distributed systems with very high attention are all based on complex networks. Community structure detection is a very important and meaningful research hotspot in complex networks. It is a difficult task to quickly and accurately divide the community structure and run it on large-scale networks. In this paper, we put forward a new community detection approach based on internode attraction, named IACD. This algorithm starts from the perspective of the important nodes of the complex network and refers to the gravitational relationship between two objects in physics to represent the forces between nodes in the network dataset, and then perform community detection. Through experiments on a large number of real-world datasets and synthetic networks, it is shown that the IACD algorithm can quickly and accurately divide the community structure, and it is superior to some classic algorithms and recently proposed algorithms.     

Reproducible sequence generation in random neural ensembles

Little is known about the conditions that neural circuits have to satisfy to generate reproducible sequences. Evidently, the genetic code cannot control all the details of the complex circuits in the brain. In this Letter, we give the conditions on the connectivity degree that lead to reproducible and robust sequences in a neural population of randomly coupled excitatory and inhibitory neurons. In contrast to the traditional theoretical view we show that the sequences do not need to be learned. In the framework proposed here just the averaged characteristics of the random circuits have to be under genetic control. We found that rhythmic sequences can be generated if random networks are in the vicinity of an excitatory-inhibitory synaptic balance. Reproducible transient sequences, on the other hand, are found far from a synaptic balance.     

Topological structures enhance the presence of dynamical regimes in synthetic networks

Genetic and protein networks, through their underlying dynamical behavior, characterize structural and functional cellular processes, and are thus regarded as "driving forces" of all living systems. Understanding the rhythm generation mechanisms that emerge from such complex networks has benefited in recent years by synthetic approaches, through which simpler network modules (e.g., switches and oscillators) have been built. In this manner, a significant attention to date has been focused on the dynamical behavior of these isolated synthetic circuits, and the occurrence of unifying rhythms in systems of globally coupled genetic units. In contrast to this, we address here the question: Could topologically distinct structures enhance the presence of various dynamical regimes in synthetic networks? We show that an intercellular mechanism, engineered to operate on a local scale, will inevitably lead to multirhythmicity, and to the appearance of several coexisting (complex) dynamical regimes, if certain preconditions regarding the dynamical structure of the synthetic circuits are met. Moreover, we discuss the importance of regime enhancement in synthetic structures in terms of memory storage and computation capabilities.     

Evolutionary design of oscillatory genetic networks

The present study is devoted to the design and statistical investigations of dynamical gene expression networks. In our model problem, we aim to design genetic networks which would exhibit stable periodic oscillations with a prescribed temporal period. While no rational solution of this problem is available, we show that it can be effectively solved by running a computer evolution of the network models. In this process, structural rewiring mutations are applied to the networks with inhibitory interactions between genes and the evolving networks are selected depending on whether, after a mutation, they closer approach the targeted dynamics. We show that, by using this method, networks with required oscillation periods, varying by up to three orders of magnitude, can be constructed by changing the architecture of regulatory connections between the genes. Statistical properties of designed networks, including motif distributions and Laplacian spectra, are considered.     

Traffic dynamics on layered complex networks

To minimize traffic congestion, understanding how traffic dynamics depend on network structure is necessary. Many real-world complex systems can be described as multilayer structures. In this paper, we introduce the idea of layers to establish a traffic model of two-layer complex networks. By comparing different two-layer complex networks based on random and scale-free networks, we find that the physical layer is much more important to the network capacity of two-layer complex networks than the logical layer. Two-layer complex networks with a homogeneous physical topology are found to be more tolerant to congestion. Moreover, simulation results show that the heterogeneity of logical and physical topologies makes the packet-delivery process of two-layer networks more efficient in the free-flow state, without the occurrence of traffic congestion.     

Distributed wireless quantum communication networks with partially entangled pairs

Wireless quantum communication networks transfer quantum state by teleportation. Existing research focuses on maximal entangled pairs. In this paper, we analyse the distributed wireless quantum communication networks with partially entangled pairs. A quantum routing scheme with multi-hop teleportation is proposed. With the proposed scheme, is not necessary for the quantum path to be consistent with the classical path. The quantum path and its associated classical path are established in a distributed way. Direct multi-hop teleportation is conducted on the selected path to transfer a quantum state from the source to the destination. Based on the feature of multi-hop teleportation using partially entangled pairs, if the node number of the quantum path is even, the destination node will add another teleportation at itself. We simulated the performance of distributed wireless quantum communication networks with a partially entangled state. The probability of transferring the quantum state successfully is statistically analyzed. Our work shows that multi-hop teleportation on distributed wireless quantum networks with partially entangled pairs is feasible.