Transport optimization on complex networks

We present a comparative study of the application of a recently introduced heuristic algorithm to the optimization of transport on three major types of complex networks. The algorithm balances network traffic iteratively by minimizing the maximum node betweenness with as little path lengthening as possible. We show that by using this optimal routing, a network can sustain significantly higher traffic without jamming than in the case of shortest path routing. A formula is proved that allows quick computation of the average number of hops along the path and of the average travel times once the betweennesses of the nodes are computed. Using this formula, we show that routing optimization preserves the small-world character exhibited by networks under shortest path routing, and that it significantly reduces the average travel time on congested networks with only a negligible increase in the average travel time at low loads. Finally, we study the correlation between the weights of the links in the case of optimal routing and the betweennesses of the nodes connected by them.Comment: 19 pages, 7 figure

Optimal transport on wireless networks

We present a study of the application of a variant of a recently introduced heuristic algorithm for the optimization of transport routes on complex networks to the problem of finding the optimal routes of communication between nodes on wireless networks. Our algorithm iteratively balances network traffic by minimizing the maximum node betweenness on the network. The variant we consider specifically accounts for the broadcast restrictions imposed by wireless communication by using a different betweenness measure. We compare the performance of our algorithm to two other known algorithms and find that our algorithm achieves the highest transport capacity both for minimum node degree geometric networks, which are directed geometric networks that model wireless communication networks, and for configuration model networks that are uncorrelated scale-free networks.Comment: 5 pages, 4 figure

A stochastic spectral analysis of transcriptional regulatory cascades

The past decade has seen great advances in our understanding of the role of noise in gene regulation and the physical limits to signaling in biological networks. Here we introduce the spectral method for computation of the joint probability distribution over all species in a biological network. The spectral method exploits the natural eigenfunctions of the master equation of birth-death processes to solve for the joint distribution of modules within the network, which then inform each other and facilitate calculation of the entire joint distribution. We illustrate the method on a ubiquitous case in nature: linear regulatory cascades. The efficiency of the method makes possible numerical optimization of the input and regulatory parameters, revealing design properties of, e.g., the most informative cascades. We find, for threshold regulation, that a cascade of strong regulations converts a unimodal input to a bimodal output, that multimodal inputs are no more informative than bimodal inputs, and that a chain of up-regulations outperforms a chain of down-regulations. We anticipate that this numerical approach may be useful for modeling noise in a variety of small network topologies in biology

Canalization and Symmetry in Boolean Models for Genetic Regulatory Networks

Canalization of genetic regulatory networks has been argued to be favored by evolutionary processes due to the stability that it can confer to phenotype expression. We explore whether a significant amount of canalization and partial canalization can arise in purely random networks in the absence of evolutionary pressures. We use a mapping of the Boolean functions in the Kauffman N-K model for genetic regulatory networks onto a k-dimensional Ising hypercube to show that the functions can be divided into different classes strictly due to geometrical constraints. The classes can be counted and their properties determined using results from group theory and isomer chemistry. We demonstrate that partially canalized functions completely dominate all possible Boolean functions, particularly for higher k. This indicates that partial canalization is extremely common, even in randomly chosen networks, and has implications for how much information can be obtained in experiments on native state genetic regulatory networks.Comment: 14 pages, 4 figures; version to appear in J. Phys.

Mean-Field Analysis and Monte Carlo Study of an Interacting Two-Species Catalytic Surface Reaction Model

We study the phase diagram and critical behavior of an interacting one dimensional two species monomer-monomer catalytic surface reaction model with a reactive phase as well as two equivalent adsorbing phase where one of the species saturates the system. A mean field analysis including correlations up to triplets of sites fails to reproduce the phase diagram found by Monte Carlo simulations. The three phases coexist at a bicritical point whose critical behavior is described by the even branching annihilating random walk universality class. This work confirms the hypothesis that the conservation modulo 2 of the domain walls under the dynamics at the bicritical point is the essential feature in producing critical behavior different from directed percolation. The interfacial fluctuations show the same universal behavior seen at the bicritical point in a three-species model, supporting the conjecture that these fluctuations are a new universal characteristic of the model.Comment: 11 pages using RevTeX, plus 4 Postscript figures. Uses psfig.st

Interacting Monomer-Dimer Model with Infinitely Many Absorbing States

We study a modified version of the interacting monomer-dimer (IMD) model that has infinitely many absorbing (IMA) states. Unlike all other previously studied models with IMA states, the absorbing states can be divided into two equivalent groups which are dynamically separated infinitely far apart. Monte Carlo simulations show that this model belongs to the directed Ising universality class like the ordinary IMD model with two equivalent absorbing states. This model is the first model with IMA states which does not belong to the directed percolation (DP) universality class. The DP universality class can be restored in two ways, i.e., by connecting the two equivalent groups dynamically or by introducing a symmetry-breaking field between the two groups.Comment: 5 pages, 5 figure

Braided Rivers and Superconducting Vortex Avalanches

Magnetic vortices intermittently flow through preferred channels when they are forced in or out of a superconductor. We study this behavior using a cellular model, and find that the vortex flow can make braided rivers strikingly similar to aerial photographs of braided fluvial rivers, such as the Brahmaputra. By developing an analysis technique suitable for characterizing a self-affine (multi)fractal, the scaling properties of the braided vortex rivers in the model are compared with those of braided fluvial rivers. We suggest that avalanche dynamics leads to braiding in both cases.Comment: 4 pages, 3 figures. To appear in PR

Dynamics-dependent criticality in models with q absorbing states

We study a one-dimensional, nonequilibrium Potts-like model which has $q$ symmetric absorbing states. For $q=2$, as expected, the model belongs to the parity conserving universality class. For $q=3$ the critical behaviour depends on the dynamics of the model. Under a certain dynamics it remains generically in the active phase, which is also the feature of some other models with three absorbing states. However, a modified dynamics induces a parity conserving phase transition. Relations with branching-annihilating random walk models are discussed in order to explain such a behaviour.Comment: 5 pages, 5 eps figures included, Phys.Rev.E (accepted

Damage spreading for one-dimensional, non-equilibrium models with parity conserving phase transitions

The damage spreading (DS) transitions of two one-dimensional stochastic cellular automata suggested by Grassberger (A and B) and the kinetic Ising model of Menyh\'ard (NEKIM) have been investigated on the level of kinks and spins. On the level of spins the parity conservation is not satisfied and therefore studying these models provides a convenient tool to understand the dependence of DS properties on symmetries. For the model B the critical point and the DS transition point is well separated and directed percolation damage spreading transition universality was found for spin damage as well as for kink damage in spite of the conservation of damage variables modulo 2 in the latter case. For the A stochastic cellular automaton, and the NEKIM model the two transition points coincide with drastic effects on the damage of spin and kink variables showing different time dependent behaviours. While the kink DS transition is continuous and shows regular PC class universality, the spin damage exhibits a discontinuous phase transition with compact clusters and PC like dynamical scaling ($\eta^,$), ($\delta_s$) and ($z_s$) exponents whereas the static exponents determined by FSS are consistent with that of the spins of the NEKIM model at the PC transition point. The generalised hyper-scaling law is satisfied.Comment: 11 pages, 20 figures embedded in the text, minor changes in the text, a new table and new references are adde