How divergence mechanisms influence disassortative mixing property in biology

The duplication–divergence mechanism of network growth has been widely investigated, especially in gene and protein networks. Both the duplication and divergence have a key role in biological network evolution. However, the relative roles of these mechanisms in the influence of disassortative property in protein interaction networks remain to be clarified. It has been shown that duplication can indeed make protein networks evolve towards disassortative networks. To make the relationship between the disassortative property and the duplication–divergence mechanism more clear, we further discuss how the divergence mechanism influences the disassortative property. We tested four different divergence mechanisms, i.e., node deletion, edge deletion, edge addition, and edge rewiring to study their effects on disassortative property. Our study highlights the crucial roles of different divergence evolution mechanisms.     

The average path length for a class of scale-free fractal hierarchical lattices: Rigorous results

With the help of the recurrence relations derived from the self-similar structure, we obtain the closed-form solution for the average path length of a class of scale-free fractal hierarchical lattices (HLs) with a general parameter q, which are simultaneously scale-free, self-similar and disassortative. Our rigorous solution shows that the average path length of the HLs grows logarithmically as in the infinite limit of network size of N_t and that they are not small worlds but grow with a power-law relationship to the number of nodes.     

Influence of the variance of degree distributions on the evolution of cooperation in complex networks

We study how initial network structure affects the evolution of cooperation in a spatial prisoner’s dilemma game. The network structure is characterized by various statistical properties. Among those properties, we focus on the variance of the degree distribution, and inquire how it affects the evolution of cooperation by three methods of imitation. For every method, it was found that a scale-free network does not always promote the evolution of cooperation, and that there exists an appropriate value of the variance, at which cooperation is optimal.     

Diversity of contribution promotes cooperation in public goods games

In most previous studies of public goods game, individuals conventionally donate their contributions equally to the games they participate in. We develop an extended public goods game model, in which individuals distribute their contributions based on the groups’ qualities. Namely, the individuals are allowed to increase their investment to the superior groups at the expense of the nasty ones. The quality of a group is positively correlated with its cooperation level. In numerical simulations, synchronized stochastic strategy updating rule based on pairwise comparison for a fixed noise level is adopted. The results show that the high-quality group preference mechanism can greatly improve cooperation, compared with conventional models. Besides, the system with stronger preference toward high-quality groups performs better. Investigation of wealth distribution at equilibrium reveals that cooperators’ wealth appreciates with the increase of preference degree when cooperators take up the same fraction of the population.     

Cascading failure in Watts-Strogatz small-world networks

In this paper, we study the cascading failure in Watts-Strogatz small-world networks. We find that this network model has a heterogeneous betweenness distribution, although its degree distribution is homogeneous. Further study shows that this small-world network is robust to random attack but fragile to intentional attack, in the cascading failure scenario. With comparison to standard random graph and scale-free networks, our result indicates that the robust yet fragile property in the cascading failure scenario is mainly related to heterogeneous betweenness, rather than the network degree distribution. Thus, it suggests that we have to be very careful when we use terms such as homogeneous network and heterogeneous network, unless the distribution we refer to is specified.     

Reliability evaluation of a revised stochastic flow network with uncertain minimum time

This paper constructs a revised stochastic flow network to model a realistic computer network in which each arc has a lead time and a stochastic capacity. The minimum time to send a specified amount of data through the network is thus uncertain. Hence, this paper mainly proposes an approach for evaluating the system reliability that d units of data can be transmitted through k minimal paths simultaneously within the time threshold T. The idea of lower boundary points for (d,T), the minimal system states satisfying the demand d within the time threshold T, is proposed firstly. All system states meeting the time and demand requirements can be represented as the union of subsets generated from all lower boundary points for (d,T), and thus the system reliability is computed quickly.     

Impact of delays and rewiring on the dynamics of small-world neuronal networks with two types of coupling

We study synchronization transitions and pattern formation on small-world networks consisting of Morris-Lecar excitable neurons in dependence on the information transmission delay and the rewiring probability. In addition, networks formed via gap junctional connections and coupling via chemical synapses are considered separately. For gap-junctionally coupled networks we show that short delays can induce zigzag fronts of excitations, whereas long delays can further detriment synchronization due to a dynamic clustering anti-phase synchronization transition. For the synaptically coupled networks, on the other hand, we find that the clustering anti-phase synchronization can appear as a direct consequence of the prolongation of information transmission delay, without being accompanied by zigzag excitatory fronts. Irrespective of the coupling type, however, we show that an appropriate small-world topology can always restore synchronized activity if only the information transmission delays are short or moderate at most. Long information transmission delays always evoke anti-phase synchronization and clustering, in which case the fine-tuning of the network topology fails to restore the synchronization of neuronal activity.     

STDP-driven networks and the C. elegans neuronal network

We study the dynamics of the structure of a formal neural network wherein the strengths of the synapses are governed by spike-timing-dependent plasticity (STDP). For properly chosen input signals, there exists a steady state with a residual network. We compare the motif profile of such a network with that of a real neural network of C. elegans and identify robust qualitative similarities. In particular, our extensive numerical simulations show that this STDP-driven resulting network is robust under variations of the model parameters.     

Continuous opinion model in small-world directed networks

In the compromise model of continuous opinions proposed by Deffuant et al., the states of two agents in a network can start to converge if they are neighbors and if their opinions are sufficiently close to each other, below a given threshold of tolerance ?. In directed networks, if agent i is a neighbor of agent j,j need not be a neighbor of i. In Watts-Strogatz networks we performed simulations to find the averaged number of final opinions 〈F〉 and their distribution as a function of ? and of the network structural disorder. In directed networks 〈F〉 exhibits a rich structure, being larger than in undirected networks for higher values of ?, and smaller for lower values of ?.     

Motif structure and cooperation in real-world complex networks

Networks of dynamical nodes serve as generic models for real-world systems in many branches of science ranging from mathematics to physics, technology, sociology and biology. Collective behavior of agents interacting over complex networks is important in many applications. The cooperation between selfish individuals is one of the most interesting collective phenomena. In this paper we address the interplay between the motifs’ cooperation properties and their abundance in a number of real-world networks including yeast protein-protein interaction, human brain, protein structure, email communication, dolphins’ social interaction, Zachary karate club and Net-science coauthorship networks. First, the amount of cooperativity for all possible undirected subgraphs with three to six nodes is calculated. To this end, the evolutionary dynamics of the Prisoner’s Dilemma game is considered and the cooperativity of each subgraph is calculated as the percentage of cooperating agents at the end of the simulation time. Then, the three- to six-node motifs are extracted for each network. The significance of the abundance of a motif, represented by a Z-value, is obtained by comparing them with some properly randomized versions of the original network. We found that there is always a group of motifs showing a significant inverse correlation between their cooperativity amount and Z-value, i.e. the more the Z-value the less the amount of cooperativity. This suggests that networks composed of well-structured units do not have good cooperativity properties.