Universal core modules govern the dynamics of cellular regulatory networks
This paper contains some immature results. It have been withdrawn.
q-bio.MN↗
arXiv subjects
Jie Ren
Publications and source records attributed to Jie Ren.
Memory-Based Snowdrift Game on Networks
We present a memory-based snowdrift game (MBSG) taking place on networks. We found that, when a lattice is taken to be the underlying structure, the transition of spatial patterns at some critical values of the payoff parameter is observable for both 4 and 8-neighbor lattices. The transition points as well as the styles of spatial patterns can be explained by local stability analysis. In sharp contrast to previously reported results, cooperation is promoted by the spatial structure in the MBSG. Interestingly, we found that the frequency of cooperation of the MBSG on a scale-free network peaks at a specific value of the payoff parameter. This phenomenon indicates that properly encouraging selfish behaviors can optimally enhance the cooperation. The memory effects of individuals are discussed in detail and some non-monotonous phenomena are observed on both lattices and scale-free networks. Our work may shed some new light on the study of evolutionary games over networks.
physics.soc-ph↗
Naming Game on small-world networks: the role of clustering structure
Naming Game is a recently proposed model for describing how a multi-agent system can converge towards a consensus state in a self-organized way. In this paper, we investigate this model on the so-called homogeneous small-world networks and focus on the influence of the triangular topology on the dynamics. Of all the topological quantities, the clustering coefficient is found to play a significant role in the dynamics of the Naming Game. On the one hand, it affects the maximum memory of each agent; on the other hand, it inhibits the growing of clusters in which agents share a common word, i.e., a larger clustering coefficient will cause a slower convergence of the system. We also find a quantitative relationship between clustering coefficient and the maximum memory.
physics.data-an↗
Interplay between evolutionary game and network structure: the coevolution of social net, cooperation and wealth
We study the interplay between evolutionary game and network structure and show how the dynamics of the game affect the growth pattern of the network and how the evolution of the network influence the cooperative behavior in the game. Simulation results show that the payoff-based preferential attachment mechanism leads to the emergence of a scale-free structural property, $P(k)\sim k^{-γ}$. Moreover, we investigate the average path length and the assortative mixing features. The obtained results indicate that the network has small-world and positive assortative behaviors, which are consistent with the observations of some real social networks. In parallel, we found that the evolution of the underlying network structure effectively promotes the cooperation level of the game. We also investigate the wealth distribution obtained by our model, which is consistent with the Pareto law in the real observation. In addition, the analysis of the generated scale-free network structure is provided for better understanding the evolutionary dynamics of our model.
physics.soc-ph↗
Better synchronizability predicted by a new coupling method
In this paper, inspired by the idea that the hub nodes of a highly heterogeneous network are not only the bottlenecks, but also effective controllers in the network synchronizing process, we bring forward an asymmetrical coupling method where the coupling strength of each node depends on its neighbors' degrees. Compared with the uniform coupled method and the recently proposed Motter-Zhou-Kurth method, the synchronizability of scale-free networks can be remarkably enhanced by using the present coupled method.
cond-mat.stat-mech↗
Epidemic spreading on heterogeneous networks with identical infectivity
In this paper, we propose a modified susceptible-infected-recovered (SIR) model, in which each node is assigned with an identical capability of active contacts, $A$, at each time step. In contrast to the previous studies, we find that on scale-free networks, the density of the recovered individuals in the present model shows a threshold behavior. We obtain the analytical results using the mean-field theory and find that the threshold value equals 1/A, indicating that the threshold value is independent of the topology of the underlying network. The simulations agree well with the analytic results. Furthermore, we study the time behavior of the epidemic propagation and find a hierarchical dynamics with three plateaus. Once the highly connected hubs are reached, the infection pervades almost the whole network in a progressive cascade across smaller degree classes. Then, after the previously infected hubs are recovered, the disease can only propagate to the class of smallest degree till the infected individuals are all recovered. The present results could be of practical importance in the setup of dynamic control strategies.
physics.soc-ph↗
Analysis to the entangled states from an extended Chaplygin gas model
With considerations of the recently released WMAP year three and supernova legacy survey (SNLS) data set analysis that favors models similar to the $% ΛCDM$ model by possibly mild fluctuations around the vacuum energy or the cosmological constant, we extend the original Chaplygin Gas model (ECG) via modifying the Chaplygin Gas equation of state by two parameters to describe an entangled mixture state from an available matter and the rest component (which can take the cosmological constant or dark energy as in the current cosmic stage, or `curvature-like' term, or radiation component in the early epoch, as various phases) coexistence. At low redshifts, the connection of the ECG model and the Born-infeld field is set up. As paradigms, we use the data coming from the recently released SNLS for the first year and also the famous 157 type Ia supernova (Ia SNe) gold dataset to constrain the model parameters. The restricted results demonstrate clearly how large the entangled degree or the ratio between the energy density parameters of the two entangled phases being. The fact that the ECG models are consistent with the observations of Ia SNe is obtained through the redshift-luminosity distance diagram, hence the ECG can be regarded possible candidates for mimicking the current speed-up expansion of our universe.
astro-ph↗
Dynamical Coarse Graining of Large Scale-Free Boolean networks
We present a renormalization-grouplike method performed in the state space for detecting the dynamical behaviors of large scale-free Boolean networks, especially for the chaotic regime as well as the edge of chaos. Numerical simulations with different coarse-graining level show that the state space networks of scale-free Boolean networks follow universal power-law distributions of in and out strength, in and out degree, as well as weight. These interesting results indicate scale-free Boolean networks still possess self-organized mechanism near the edge of chaos in the chaotic regime. The number of state nodes as a function of biased parameter for distinct coarse-graining level also demonstrates that the power-law behaviors are not the artifact of coarse-graining procedure. Our work may also shed some light on the investigation of brain dynamics.
cond-mat.dis-nn↗
Emergence of cooperation induced by preferential learning
The evolutionary Prisoner's Dilemma Game (PDG) and the Snowdrift Game (SG) with preferential learning mechanism are studied in the Barabási-Albert network. Simulation results demonstrate that the preferential learning of individuals remarkably promotes the cooperative behavior for both two games over a wide range of payoffs. To understand the effect of preferential learning on the evolution of the systems, we investigate the time series of the cooperator density for different preferential strength and payoffs. It is found that in some specific cases two games both show the $1/f$-scaling behaviors, which indicate the existence of long range correlation. We also figure out that when the large degree nodes have high probability to be selected, the PDG displays a punctuated equilibrium-type behavior. On the contrary, the SG exhibits a sudden increase feature. These temporary instable behaviors are ascribed to the strategy shift of the large degree nodes.
physics.soc-ph↗
Diffusion-limited-aggregation on a directed small world network
For real world systems, nonuniform medium is ubiquitous. Therefore, we investigate the diffusion-limited-aggregation process on a two dimensional directed small-world network instead of regular lattice. The network structure is established by rewiring connections on the two dimensional directed lattice. Those rewired edges are controlled by two parameters $θ$ and $m$, which characterize the spatial length and the density of the long-range connections, respectively. Simulations show that there exists a maximum value of the fractal dimension when $θ$ equals zero. Interestingly, we find that the symmetry of the aggregation pattern is broken when rewired connections are long enough, which may be an explanation for the formation of asymmetrical fractal in nature. Then, we perform multifractal analysis on the patterns further.
physics.comp-ph↗
Cosmology with extended Chaplygin gas media and $w=-1$ crossing
In this paper the accelerating expansion of our universe at the late cosmic evolution time in a generally modified (extended) \emph{Chaplygin gas} (Dark Fluid) model is detailed, which is characterized by two parameters ($m$, $α$). Different choices to the parameters $m$ and $α$ divide this model into two main kinds of situation by different properties with cosmological interests. With proper choices of parameters, we find that this extended model can realize the phantom divide $w=-1$ (Equation Of State parameter) crossing phenomenon with interesting ranges of the scale factor value $a(t)$ corresponding to $w=-1$ and present value of state parameter $w$. Additionally, through Taylor series expansion of the function $A(a)$ in the extended Chaplygin gas model, a specific Equation of State is gained. Under the framework of Friedman-Robertson-Walker cosmic model, it can successfully explain the accelerating expansion of our universe. However, the value of $w$ in this case is large than -1, that is, indicating it like a quintessence fluid and no $w=-1$ crossing occurs.
astro-ph↗
Friedmann cosmology with a generalized equation of state and bulk viscosity
The universe media is considered as a non-perfect fluid with bulk viscosity and described by a more general equation of state. We assume the bulk viscosity is a linear combination of the two terms: one is constant, and the other is proportional to the scalar expansion $θ=3\dot{a}/a$. The equation of state is described as $p=(γ-1)ρ+p_0$, where $p_0$ is a parameter. This model can be used to explain the dark energy dominated universe. Different choices of the parameters may lead to three kinds of fates of the cosmological evolution: no future singularity, big rip, or Type III singularity of Ref. [S. Nojiri, S.D. Odintsov, and S. Tsujikawa, Phys. Rev. D \textbf{71}, 063004 (2005)].
astro-ph↗