Scaling relation for determining the critical threshold for continuum percolation of overlapping discs of two sizes

We study continuum percolation of overlapping circular discs of two sizes. We propose a phenomenological scaling equation for the increase in the effective size of the larger discs due to the presence of the smaller discs. The critical percolation threshold as a function of the ratio of sizes of discs, for different values of the relative areal densities of two discs, can be described in terms of a scaling function of only one variable. The recent accurate Monte Carlo estimates of critical threshold by Quintanilla and Ziff [Phys. Rev. E, 76 051115 (2007)] are in very good agreement with the proposed scaling relation.Comment: 4 pages, 3 figure

Roughening Transition in a One-Dimensional Growth Process

A class of nonequilibrium models with short-range interactions and sequential updates is presented. The models describe one dimensional growth processes which display a roughening transition between a smooth and a rough phase. This transition is accompanied by spontaneous symmetry breaking, which is described by an order parameter whose dynamics is non-conserving. Some aspects of models in this class are related to directed percolation in 1+1 dimensions, although unlike directed percolation the models have no absorbing states. Scaling relations are derived and compared with Monte Carlo simulations.Comment: 4 pages, 3 Postscript figures, 1 Postscript formula, uses RevTe

Herding model and 1/f noise

We provide evidence that for some values of the parameters a simple agent based model, describing herding behavior, yields signals with 1/f power spectral density. We derive a non-linear stochastic differential equation for the ratio of number of agents and show, that it has the form proposed earlier for modeling of 1/f^beta noise with different exponents beta. The non-linear terms in the transition probabilities, quantifying the herding behavior, are crucial to the appearance of 1/f noise. Thus, the herding dynamics can be seen as a microscopic explanation of the proposed non-linear stochastic differential equations generating signals with 1/f^beta spectrum. We also consider the possible feedback of macroscopic state on microscopic transition probabilities strengthening the non-linearity of equations and providing more opportunities in the modeling of processes exhibiting power-law statistics

Change in physical activity after smoking cessation: the Coronary Artery Risk Development in Young Adults (CARDIA) study.

AIMS: To estimate physical activity trajectories for people who quit smoking, and compare them to what would have been expected had smoking continued. DESIGN, SETTING AND PARTICIPANTS: A total of 5115 participants in the Coronary Artery Risk Development in Young Adults Study (CARDIA) study, a population-based study of African American and European American people recruited at age 18-30 years in 1985/6 and followed over 25 years. MEASUREMENTS: Physical activity was self-reported during clinical examinations at baseline (1985/6) and at years 2, 5, 7, 10, 15, 20 and 25 (2010/11); smoking status was reported each year (at examinations or by telephone, and imputed where missing). We used mixed linear models to estimate trajectories of physical activity under varying smoking conditions, with adjustment for participant characteristics and secular trends. FINDINGS: We found significant interactions by race/sex (P = 0.02 for the interaction with cumulative years of smoking), hence we investigated the subgroups separately. Increasing years of smoking were associated with a decline in physical activity in black and white women and black men [e.g. coefficient for 10 years of smoking: -0.14; 95% confidence interval (CI) = -0.20 to -0.07, P < 0.001 for white women]. An increase in physical activity was associated with years since smoking cessation in white men (coefficient 0.06; 95% CI = 0 to 0.13, P = 0.05). The physical activity trajectory for people who quit diverged progressively towards higher physical activity from the expected trajectory had smoking continued. For example, physical activity was 34% higher (95% CI = 18 to 52%; P < 0.001) for white women 10 years after stopping compared with continuing smoking for those 10 years (P = 0.21 for race/sex differences). CONCLUSIONS: Smokers who quit have progressively higher levels of physical activity in the years after quitting compared with continuing smokers

Roughness of Crack Interfaces in Two-Dimensional Beam Lattices

The roughness of crack interfaces is reported in quasistatic fracture, using an elastic network of beams with random breaking thresholds. For strong disorders we obtain 0.86(3) for the roughness exponent, a result which is very different from the minimum energy surface exponent, i.e., the value 2/3. A cross-over to lower values is observed as the disorder is reduced, the exponent in these cases being strongly dependent on the disorder.Comment: 9 pages, RevTeX, 3 figure

Detecting modules in dense weighted networks with the Potts method

We address the problem of multiresolution module detection in dense weighted networks, where the modular structure is encoded in the weights rather than topology. We discuss a weighted version of the q-state Potts method, which was originally introduced by Reichardt and Bornholdt. This weighted method can be directly applied to dense networks. We discuss the dependence of the resolution of the method on its tuning parameter and network properties, using sparse and dense weighted networks with built-in modules as example cases. Finally, we apply the method to data on stock price correlations, and show that the resulting modules correspond well to known structural properties of this correlation network.Comment: 14 pages, 6 figures. v2: 1 figure added, 1 reference added, minor changes. v3: 3 references added, minor change

miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling

Transcriptome profiling studies have produced staggering numbers of gene co-expression signatures for a variety of biological systems. A significant fraction of these signatures will be partially or fully explained by miRNA-mediated targeted transcript degradation. miRvestigator takes as input lists of co-expressed genes from Caenorhabditis elegans, Drosophila melanogaster, G. gallus, Homo sapiens, Mus musculus or Rattus norvegicus and identifies the specific miRNAs that are likely to bind to 3′ un-translated region (UTR) sequences to mediate the observed co-regulation. The novelty of our approach is the miRvestigator hidden Markov model (HMM) algorithm which systematically computes a similarity P-value for each unique miRNA seed sequence from the miRNA database miRBase to an overrepresented sequence motif identified within the 3′-UTR of the query genes. We have made this miRNA discovery tool accessible to the community by integrating our HMM algorithm with a proven algorithm for de novo discovery of miRNA seed sequences and wrapping these algorithms into a user-friendly interface. Additionally, the miRvestigator web server also produces a list of putative miRNA binding sites within 3′-UTRs of the query transcripts to facilitate the design of validation experiments. The miRvestigator is freely available at http://mirvestigator.systemsbiology.net

Fracture in Three-Dimensional Fuse Networks

We report on large scale numerical simulations of fracture surfaces using random fuse networks for two very different disorders. There are some properties and exponents that are different for the two distributions, but others, notably the roughness exponents, seem universal. For the universal roughness exponent we found a value of zeta = 0.62 +/- 0.05. In contrast to what is observed in two dimensions, this value is lower than that reported in experimental studies of brittle fractures, and rules out the minimal energy surface exponent, 0.41 +/- 0.01.Comment: 4 pages, RevTeX, 5 figures, Postscrip

First Order Phase Transition in Intermediate Energy Heavy Ion Collisions

We model the disassembly of an excited nuclear system formed as a result of a heavy ion collision. We find that, as the beam energy in central collisions in varied, the dissociating system crosses a liquid-gas coexistence curve, resulting in a first-order phase transition. Accessible experimental signatures are identified: a peak in specific heat, a power-law yield for composites, and a maximum in the second moment of the yield distribution