Features and heterogeneities in growing network models

Many complex networks from the World-Wide-Web to biological networks are growing taking into account the heterogeneous features of the nodes. The feature of a node might be a discrete quantity such as a classification of a URL document as personal page, thematic website, news, blog, search engine, social network, ect. or the classification of a gene in a functional module. Moreover the feature of a node can be a continuous variable such as the position of a node in the embedding space. In order to account for these properties, in this paper we provide a generalization of growing network models with preferential attachment that includes the effect of heterogeneous features of the nodes. The main effect of heterogeneity is the emergence of an "effective fitness" for each class of nodes, determining the rate at which nodes acquire new links. The degree distribution exhibits a multiscaling behaviour analogous to the the fitness model. This property is robust with respect to variations in the model, as long as links are assigned through effective preferential attachment. Beyond the degree distribution, in this paper we give a full characterization of the other relevant properties of the model. We evaluate the clustering coefficient and show that it disappears for large network size, a property shared with the Barab\'asi-Albert model. Negative degree correlations are also present in the studied class of models, along with non-trivial mixing patterns among features. We therefore conclude that both small clustering coefficients and disassortative mixing are outcomes of the preferential attachment mechanism in general growing networks.Comment: 16 pages, 6 figures, revte

Static triplet correlations in glass-forming liquids: A molecular dynamics study

We present a numerical evaluation of the three-point static correlations functions of the Kob-Andersen Lennard-Jones binary mixture and of its purely repulsive, Weeks-Chandler-Andersen variant. In the glassy regime, the two models possess a similar pair structure, yet their dynamics differ markedly. The static triplet correlation functions S^(3) indicate that the local ordering is more pronounced in the Lennard-Jones model, an observation consistent with its slower dynamics. A comparison of the direct triplet correlation functions c^(3) reveals that these structural differences are due, to a good extent, to an amplification of the small discrepancies observed at the pair level. We demonstrate the existence of a broad, positive peak at small wave-vectors and angles in c^(3). In this portion of k-space, slight, systematic differences between the models are observed, revealing "genuine" three-body contributions to the triplet structure. The possible role of the low-k features of c^(3) and the implications of our results for dynamic theories of the glass transition are discussed.Comment: 9 pages, 8 figures, contribution to the JCP Special Issue on the Glass Transitio

Spatial correlations in the relaxation of the Kob-Andersen model

We describe spatio-temporal correlations and heterogeneities in a kinetically constrained glassy model, the Kob-Andersen model. The kinetic constraints of the model alone induce the existence of dynamic correlation lengths, that increase as the density $\rho$ increases, in a way compatible with a double-exponential law. We characterize in detail the trapping time correlation length, the cooperativity length, and the distribution of persistent clusters of particles. This last quantity is related to the typical size of blocked clusters that slow down the dynamics for a given density.Comment: 7 pages, 6 figures, published version (title has changed

On the Nature and Shape of Tubulin Trails: Implications on Microtubule Self-Organization

Microtubules, major elements of the cell skeleton are, most of the time, well organized in vivo, but they can also show self-organizing behaviors in time and/or space in purified solutions in vitro. Theoretical studies and models based on the concepts of collective dynamics in complex systems, reaction-diffusion processes and emergent phenomena were proposed to explain some of these behaviors. In the particular case of microtubule spatial self-organization, it has been advanced that microtubules could behave like ants, self-organizing by 'talking to each other' by way of hypothetic (because never observed) concentrated chemical trails of tubulin that are expected to be released by their disassembling ends. Deterministic models based on this idea yielded indeed like-looking spatio-temporal self-organizing behaviors. Nevertheless the question remains of whether microscopic tubulin trails produced by individual or bundles of several microtubules are intense enough to allow microtubule self-organization at a macroscopic level. In the present work, by simulating the diffusion of tubulin in microtubule solutions at the microscopic scale, we measure the shape and intensity of tubulin trails and discuss about the assumption of microtubule self-organization due to the production of chemical trails by disassembling microtubules. We show that the tubulin trails produced by individual microtubules or small microtubule arrays are very weak and not elongated even at very high reactive rates. Although the variations of concentration due to such trails are not significant compared to natural fluctuations of the concentration of tubuline in the chemical environment, the study shows that heterogeneities of biochemical composition can form due to microtubule disassembly. They could become significant when produced by numerous microtubule ends located in the same place. Their possible formation could play a role in certain conditions of reaction. In particular, it gives a mesoscopic basis to explain the collective dynamics observed in excitable microtubule solutions showing the propagation of concentration waves of microtubules at the millimeter scale, although we doubt that individual microtubules or bundles can behave like molecular ants

Localization transition, Lifschitz tails and rare-region effects in network models

Effects of heterogeneity in the suspected-infected-susceptible model on networks are investigated using quenched mean-field theory. The emergence of localization is described by the distributions of the inverse participation ratio and compared with the rare-region effects appearing in simulations and in the Lifschitz tails. The latter, in the linear approximation, is related to the spectral density of the Laplacian matrix and to the time dependent order parameter. I show that these approximations indicate correctly Griffiths Phases both on regular one-dimensional lattices and on small world networks exhibiting purely topological disorder. I discuss the localization transition that occurs on scale-free networks at $\gamma=3$ degree exponent.Comment: 9 pages, 9 figures, accepted version in PR

Seismic scattering and absorption mapping from intermediate-depth earthquakes reveals complex tectonic interactions acting in the Vrancea region and surroundings (Romania)

The present study was performed during a stay at the University of Münster financed by a grant awarded by the German Academic Exchange Service (DAAD) in 2014. Data used in the present study were provided by the National Institute for Earth Physics (Romania) and processed within the National Data Centre in Magurele. Seismic Analysis Code (SAC) (Goldstein and Snoke, 2005) and GMT (Wessel et al., 2013) codes were used. We thank the College of Physical Sciences (University of Aberdeen) and the Santander Mobility Award for providing travel grant to LDS to complete this manuscript. We are grateful as well to the anonymous reviewer for his useful remarks which helped us to improve the paper.Peer reviewedPostprin

Physical Pictures of Transport in Heterogeneous Media: Advection-Dispersion, Random Walk and Fractional Derivative Formulations

The basic conceptual picture and theoretical basis for development of transport equations in porous media are examined. The general form of the governing equations is derived for conservative chemical transport in heterogeneous geological formations, for single realizations and for ensemble averages of the domain. The application of these transport equations is focused on accounting for the appearance of non-Fickian (anomalous) transport behavior. The general ensemble-averaged transport equation is shown to be equivalent to a continuous time random walk (CTRW) and reduces to the conventional forms of the advection-dispersion equation (ADE) under highly restrictive conditions. Fractional derivative formulations of the transport equations, both temporal and spatial, emerge as special cases of the CTRW. In particular, the use in this context of L{\'e}vy flights is critically examined. In order to determine chemical transport in field-scale situations, the CTRW approach is generalized to non-stationary systems. We outline a practical numerical scheme, similar to those used with extended geological models, to account for the often important effects of unresolved heterogeneities.Comment: 14 pages, REVTeX4, accepted to Wat. Res. Res; reference adde