Power-law Distributions in the Kauffman Net

We study the properties of the distance between attractors in Random Boolean Networks, a prominent model of genetic regulatory networks. We define three distance measures, upon which attractor distance matrices are constructed and their main statistic parameters are computed. The experimental analysis shows that ordered networks have a very clustered set of attractors, while chaotic networks' attractors are scattered; critical networks show, instead, a pattern with characteri...

Boolean variables are such that they take only values on $ \mathbb{Z}_2 \cong \left\{0, 1 \right\} $. \textit{NK}-Kauffman networks are dynamical deterministic systems of $ N $ Boolean functions that depend only on $ K \leq N $ Boolean variables. They were proposed by Kauffman as a first step to understand cellular behaviour [Kauffman, S.A.; {\rm The Large Scale Structure and Dynamics of Gene Control Circuits: An Ensemble Approach}. {\it J. Theoret. Biol.} {\bf 44} (1974) 167...

A model of cellular metabolism due to S. Kauffman is analyzed. It consists of a network of Boolean gates randomly assembled according to a probability distribution. It is shown that the behavior of the network depends very critically on certain simple algebraic parameters of the distribution. In some cases, the analytic results support conclusions based on simulations of random Boolean networks, but in other cases, they do not.

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 $\...

Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by regulatory rules driving the dynamics that have certain so-called canalizing properties. In this paper, we investigate the dynamics of a random Boolean network with such properties using analytical methods and simulations. From our simulation...

We analyze the synchronization transition for a pair of coupled identical Kauffman networks in the chaotic phase. The annealed model for Kauffman networks shows that synchronization appears through a transcritical bifurcation, and provides an approximate description for the whole dynamics of the coupled networks. We show that these analytical predictions are in good agreement with numerical results for sufficiently large networks, and study finite-size effects in detail. Prel...

We study the dynamics of randomly connected networks composed of binary Boolean elements and those composed of binary majority vote elements. We elucidate their differences in both sparsely and densely connected cases. The quickness of large network dynamics is usually quantified by the length of transient paths, an analytically intractable measure. For discrete-time dynamics of networks of binary elements, we address this dilemma with an alternative unified framework by usin...

In this paper, we show our discovery that state-transition networks in several chaotic dynamical systems are "scale-free networks," with a technique to understand a dynamical system as a whole, which we call the analysis for "Discretized-State Transition" (DST) networks; This scale-free nature is found universally in the logistic map, the sine map, the cubic map, the general symmetric map, the sine-circle map, the Gaussian map, and the delayed logistic map. Our findings prove...

We investigate the influence of a deterministic but non-synchronous update on Random Boolean Networks, with a focus on critical networks. Knowing that ``relevant components'' determine the number and length of attractors, we focus on such relevant components and calculate how the length and number of attractors on these components are modified by delays at one or more nodes. The main findings are that attractors decrease in number when there are more delays, and that periods ...

We undertake a systematic study of the dynamics of Boolean networks to determine the origin of chaos observed in recent experiments. Networks with nodes consisting of ideal logic gates are known to display either steady states, periodic behavior, or an ultraviolet catastrophe where the number of logic-transition events circulating in the network per unit time grows as a power-law. In an experiment, non-ideal behavior of the logic gates prevents the ultraviolet catastrophe and...