Abstract:
Fixed points are fundamental states in any dynamical system. In the case of gene regulatory networks (GRNs) they correspond to stable genes profiles associated to the various cell types. We use Kauffman's approach to model GRNs with random Boolean networks (RBNs). We start this paper by proving that, if we fix the values of the source nodes (nodes with in-degree 0), the expected number of fixed points of any RBN is one (independently of the topology we choose). For finding such fixed points we use the {\alpha}-asynchronous dynamics (where every node is updated independently with probability 0 < {\alpha} < 1). In fact, it is well-known that asynchrony avoids the cycle attractors into which parallel dynamics tends to fall. We perform simulations and we show the remarkable property that, if for a given RBN with scale-free topology and {\alpha}-asynchronous dynamics an initial configuration reaches a fixed point, then every configuration also reaches a fixed point. By contrast, in the parallel regime, the percentage of initial configurations reaching a fixed point (for the same networks) is dramatically smaller. We contrast the results of the simulations on scale-free networks with the classical Erdos-Renyi model of random networks. Everything indicates that scale-free networks are extremely robust. Finally, we study the mean and maximum time/work needed to reach a fixed point when starting from randomly chosen initial configurations.

Abstract:
We study the intrinsic properties of attractors in the Boolean dynamics in complex network with scale-free topology, comparing with those of the so-called random Kauffman networks. We have numerically investigated the frozen and relevant nodes for each attractor, and the robustness of the attractors to the perturbation that flips the state of a single node of attractors in the relatively small network ($N=30 \sim 200$). It is shown that the rate of frozen nodes in the complex networks with scale-free topology is larger than that in the random Kauffman model. Furthermore, we have found that in the complex scale-free networks with fluctuations of in-degree number the attractors are more sensitive to the state flip of a highly connected node than to the state flip of a less connected node.

Abstract:
We investigate how scale-free (SF) and Erdos-Renyi (ER) topologies affect the interplay between evolvability and robustness of model gene regulatory networks with Boolean threshold dynamics. In agreement with Oikonomou and Cluzel (2006) we find that networks with SFin topologies, that is SF topology for incoming nodes and ER topology for outgoing nodes, are significantly more evolvable towards specific oscillatory targets than networks with ER topology for both incoming and outgoing nodes. Similar results are found for networks with SFboth and SFout topologies. The functionality of the SFout topology, which most closely resembles the structure of biological gene networks (Babu et al., 2004), is compared to the ER topology in further detail through an extension to multiple target outputs, with either an oscillatory or a non-oscillatory nature. For multiple oscillatory targets of the same length, the differences between SFout and ER networks are enhanced, but for non-oscillatory targets both types of networks show fairly similar evolvability. We find that SF networks generate oscillations much more easily than ER networks do, and this may explain why SF networks are more evolvable than ER networks are for oscillatory phenotypes. In spite of their greater evolvability, we find that networks with SFout topologies are also more robust to mutations than ER networks. Furthermore, the SFout topologies are more robust to changes in initial conditions (environmental robustness). For both topologies, we find that once a population of networks has reached the target state, further neutral evolution can lead to an increase in both the mutational robustness and the environmental robustness to changes in initial conditions.

Abstract:
We investigate analytically and numerically the critical line in undirected random Boolean networks with arbitrary degree distributions, including scale-free topology of connections $P(k)\sim k^{-\gamma}$. We show that in infinite scale-free networks the transition between frozen and chaotic phase occurs for $3<\gamma < 3.5$. The observation is interesting for two reasons. First, since most of critical phenomena in scale-free networks reveal their non-trivial character for $\gamma<3$, the position of the critical line in Kauffman model seems to be an important exception from the rule. Second, since gene regulatory networks are characterized by scale-free topology with $\gamma<3$, the observation that in finite-size networks the mentioned transition moves towards smaller $\gamma$ is an argument for Kauffman model as a good starting point to model real systems. We also explain that the unattainability of the critical line in numerical simulations of classical random graphs is due to percolation phenomena.

Abstract:
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.

Abstract:
Inspired by the local minority game, we propose a network Boolean game and investigate its dynamical properties on scale-free networks. The system can self-organize to a stable state with better performance than random choice game, although only the local information is available to the agent. By introducing the heterogeneity of local interactions, we find the system has the best performance when each agent's interaction frequency is linear correlated with its information capacity. Generally, the agents with more information gain more than those with less information, while in the optimal case, each agent almost has the same average profit. In addition, we investigate the role of irrational factor and find an interesting symmetrical behavior.

Abstract:
Scale-free networks with topology-dependent interactions are studied. It is shown that the universality classes of critical behavior, which conventionally depend only on topology, can also be explored by tuning the interactions. A mapping, $\gamma' = (\gamma - \mu)/(1-\mu)$, describes how a shift of the standard exponent $\gamma$ of the degree distribution $P(q)$ can absorb the effect of degree-dependent pair interactions $J_{ij} \propto (q_iq_j)^{-\mu}$. Replica technique, cavity method and Monte Carlo simulation support the physical picture suggested by Landau theory for the critical exponents and by the Bethe-Peierls approximation for the critical temperature. The equivalence of topology and interaction holds for equilibrium and non-equilibrium systems, and is illustrated with interdisciplinary applications.

Abstract:
Different weighted scale-free networks show weights-topology correlations indicated by the non linear scaling of the node strength with node connectivity. In this paper we show that networks with and without weight-topology correlations can emerge from the same simple growth dynamics of the node connectivities and of the link weights. A weighted fitness network is introduced in which both nodes and links are assigned intrinsic fitness. This model can show a local dependence of the weight-topology correlations and can undergo a phase transition to a state in which the network is dominated by few links which acquire a finite fraction of the total weight of the network.

Abstract:
We study a recently introduced class of scale-free networks showing a high clustering coefficient and non-trivial connectivity correlations. We find that the connectivity probability distribution strongly depends on the fine details of the model. We solve exactly the case of low average connectivity, providing also exact expressions for the clustering and degree correlation functions. The model also exhibits a lack of small world properties in the whole parameters range. We discuss the physical properties of these networks in the light of the present detailed analysis.

Abstract:
We study two types of simplified Boolean dynamics over scale-free networks, both with synchronous update. Assigning only Boolean functions AND and XOR to the nodes with probability $1-p$ and $p$, respectively, we are able to analyze the density of 1's and the Hamming distance on the network by numerical simulations and by a mean-field approximation (annealed approximation). We show that the behavior is quite different if the node always enters in the dynamic as its own input (self-regulation) or not. The same conclusion holds for the Kauffman KN model. Moreover, the simulation results and the mean-field ones (i) agree well when there is no self-regulation, and (ii) disagree for small $p$ when self-regulation is present in the model.