Edge usage, motifs and regulatory logic for cell cycling genetic networks

The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression patterns? We tackle this question in silico by examining the ensemble of all regulatory networks which satisfy the constraint of producing a given sequence of gene expressions. We focus on three cell cycle profiles coming from baker's yeast, fission yeast and mammals. First, we show that the networks in each of the ensembles use just a few interactions that are repeatedly reused as building blocks. Second, we find an enrichment in network motifs that is similar in the two yeast cell cycle systems investigated. These motifs do not have autonomous functions, but nevertheless they reveal a regulatory logic for cell cycling based on a feed-forward cascade of activating interactions.Comment: 9 pages, 9 figures, to be published in Phys. Rev.

Adaptive networks of trading agents

Multi-agent models have been used in many contexts to study generic collective behavior. Similarly, complex networks have become very popular because of the diversity of growth rules giving rise to scale-free behavior. Here we study adaptive networks where the agents trade ``wealth'' when they are linked together while links can appear and disappear according to the wealth of the corresponding agents; thus the agents influence the network dynamics and vice-versa. Our framework generalizes a multi-agent model of Bouchand and Mezard, and leads to a steady state with fluctuating connectivities. The system spontaneously self-organizes into a critical state where the wealth distribution has a fat tail and the network is scale-free; in addition, network heterogeneities lead to enhanced wealth condensation.Comment: 7 figure

Network of inherent structures in spin glasses: scaling and scale-free distributions

The local minima (inherent structures) of a system and their associated transition links give rise to a network. Here we consider the topological and distance properties of such a network in the context of spin glasses. We use steepest descent dynamics, determining for each disorder sample the transition links appearing within a given barrier height. We find that differences between linked inherent structures are typically associated with local clusters of spins; we interpret this within a framework based on droplets in which the characteristic ``length scale'' grows with the barrier height. We also consider the network connectivity and the degrees of its nodes. Interestingly, for spin glasses based on random graphs, the degree distribution of the network of inherent structures exhibits a non-trivial scale-free tail.Comment: minor changes and references adde

From simple to complex networks: inherent structures, barriers and valleys in the context of spin glasses

Given discrete degrees of freedom (spins) on a graph interacting via an energy function, what can be said about the energy local minima and associated inherent structures? Using the lid algorithm in the context of a spin glass energy function, we investigate the properties of the energy landscape for a variety of graph topologies. First, we find that the multiplicity Ns of the inherent structures generically has a lognormal distribution. In addition, the large volume limit of ln/ differs from unity, except for the Sherrington-Kirkpatrick model. Second, we find simple scaling laws for the growth of the height of the energy barrier between the two degenerate ground states and the size of the associated valleys. For finite connectivity models, changing the topology of the underlying graph does not modify qualitatively the energy landscape, but at the quantitative level the models can differ substantially.Comment: 10 pages, 9 figs, slightly improved presentation, more references, accepted for publication in Phys Rev

Grand-Canonical Ensemble of Random Surfaces with Four Species of Ising Spins

The grand-canonical ensemble of dynamically triangulated surfaces coupled to four species of Ising spins (c=2) is simulated on a computer. The effective string susceptibility exponent for lattices with up to 1000 vertices is found to be $\gamma = - 0.195(58)$. A specific scenario for $c > 1$ models is conjectured.Comment: LaTeX, 11 pages + 1 postscript figure appended, preprint LPTHE-Orsay 94/1

Energy consumption and capacity utilization of galvanizing furnaces

An explicit equation leading to a method for improving furnace efficiency is presented. This equation is dimensionless and can be applied to furnaces of any size and fuel type for the purposes of comparison. The implications for current furnace design are discussed. Currently the technique most commonly used to reduce energy consumption in galvanizing furnaces is to increase burner turndown. This is shown by the analysis presented here actually to worsen the thermal efficiency of the furnace, particularly at low levels of capacity utilization. Galvanizing furnaces are different to many furnaces used within industry, as a quantity of material (in this case zinc) is kept molten within the furnace at all times, even outside production periods. The dimensionless analysis can, however, be applied to furnaces with the same operational function as a galvanizing furnace, such as some furnaces utilized within the glass industry. © IMechE 2004

On the microscopic dynamics of DCC formation

The dynamics of the pion field after a quench is studied in the framework of the linear sigma model. Our aim is to determine to what extent the amplified pion field resembles the DCC picture originally proposed in the early '90s. We present the result of a computer experiment where, among other things, we study in detail the correlation between isospin orientations of the distinct modes of the field. We show that this correlation is absent. In a sense, the distinct modes behave as distinct DCCs. The implications of this observation are discussed.Comment: 19 pages, Latex2e, 7 figures in EPS, uses (included) boldgreek.sty and standard epsf package

A Remark on the Renormalization Group Equation for the Penner Model

It is possible to extract values for critical couplings and gamma_string in matrix models by deriving a renormalization group equation for the variation of the of the free energy as the size N of the matrices in the theory is varied. In this paper we derive a ``renormalization group equation'' for the Penner model by direct differentiation of the partition function and show that it reproduces the correct values of the critical coupling and gamma_string and is consistent with the logarithmic corrections present for g=0,1.Comment: LaTeX, 5 pages, LPTHE-Orsay-94-5

Local charge compensation from colour preconfinement as a key to the dynamics of hadronization

If, as is commonly accepted, the colour-singlet, `preconfined', perturbative clusters are the primary units of hadronization, then the electric charge is necessarily compensated locally at the scale of the typical cluster mass. As a result, the minijet electric charge is suppressed at scales that are greater than the cluster mass. We hence argue, and demonstrate by means of Monte Carlo simulations using HERWIG, that the scale at which charge compensation is violated is close to the mass of the clusters involved in hadronization, and its measurement would provide a clue to resolving the nature of the dynamics. We repeat the calculation using PYTHIA and find that the numbers produced by the two generators are similar. The cluster mass distribution is sensitive to soft emission that is considered unresolved in the parton shower phase. We discuss how the description of the splitting of large clusters in terms of unresolved emission modifies the algorithm of HERWIG, and relate the findings to the yet unknown underlying nonperturbative mechanism. In particular, we propose a form of $\alpha_S$ that follows from a power-enhanced beta function, and discuss how this $\alpha_S$ that governs unresolved emission may be related to power corrections. Our findings are in agreement with experimental data.Comment: 37 pages, 20 figure