Partitioning Complex Networks via Size-constrained Clustering

The most commonly used method to tackle the graph partitioning problem in practice is the multilevel approach. During a coarsening phase, a multilevel graph partitioning algorithm reduces the graph size by iteratively contracting nodes and edges until the graph is small enough to be partitioned by some other algorithm. A partition of the input graph is then constructed by successively transferring the solution to the next finer graph and applying a local search algorithm to improve the current solution. In this paper, we describe a novel approach to partition graphs effectively especially if the networks have a highly irregular structure. More precisely, our algorithm provides graph coarsening by iteratively contracting size-constrained clusterings that are computed using a label propagation algorithm. The same algorithm that provides the size-constrained clusterings can also be used during uncoarsening as a fast and simple local search algorithm. Depending on the algorithm's configuration, we are able to compute partitions of very high quality outperforming all competitors, or partitions that are comparable to the best competitor in terms of quality, hMetis, while being nearly an order of magnitude faster on average. The fastest configuration partitions the largest graph available to us with 3.3 billion edges using a single machine in about ten minutes while cutting less than half of the edges than the fastest competitor, kMetis

Escherichia coli low-copy-number plasmid R1 centromere parC forms a U-shaped complex with its binding protein ParR

The Escherichia coli low-copy-number plasmid R1 contains a segregation machinery composed of parC, ParR and parM. The R1 centromere-like site parC contains two separate sets of repeats. By atomic force microscopy (AFM) we show here that ParR molecules bind to each of the 5-fold repeated iterons separately with the intervening sequence unbound by ParR. The two ParR protein complexes on parC do not complex with each other. ParR binds with a stoichiometry of about one ParR dimer per each single iteron. The measured DNA fragment lengths agreed with B-form DNA and each of the two parC 5-fold interon DNA stretches adopts a linear path in its complex with ParR. However, the overall parC/ParR complex with both iteron repeats bound by ParR forms an overall U-shaped structure: the DNA folds back on itself nearly completely, including an angle of ∼150°. Analysing linear DNA fragments, we never observed dimerized ParR complexes on one parC DNA molecule (intramolecular) nor a dimerization between ParR complexes bound to two different parC DNA molecules (intermolecular). This bacterial segrosome is compared to other bacterial segregation complexes. We speculate that partition complexes might have a similar overall structural organization and, at least in part, common functional properties

Multilevel mesh partitioning for optimising domain shape

Multilevel algorithms are a successful class of optimisation techniques which address the mesh partitioning problem for mapping meshes onto parallel computers. They usually combine a graph contraction algorithm together with a local optimisation method which refines the partition at each graph level. To date these algorithms have been used almost exclusively to minimise the cut-edge weight in the graph with the aim of minimising the parallel communication overhead. However it has been shown that for certain classes of problem, the convergence of the underlying solution algorithm is strongly influenced by the shape or aspect ratio of the subdomains. In this paper therefore, we modify the multilevel algorithms in order to optimise a cost function based on aspect ratio. Several variants of the algorithms are tested and shown to provide excellent results

Experimental pig-to-pig transmission dynamics for African swine fever virus, Georgia 2007/1 strain

African swine fever virus (ASFV) continues to cause outbreaks in domestic pigs and wild boar in Eastern European countries. To gain insights into its transmission dynamics, we estimated the pig-to-pig basic reproduction number (R 0) for the Georgia 2007/1 ASFV strain using a stochastic susceptible-exposed-infectious-recovered (SEIR) model with parameters estimated from transmission experiments. Models showed that R 0 is 2·8 [95% confidence interval (CI) 1·3–4·8] within a pen and 1·4 (95% CI 0·6–2·4) between pens. The results furthermore suggest that ASFV genome detection in oronasal samples is an effective diagnostic tool for early detection of infection. This study provides quantitative information on transmission parameters for ASFV in domestic pigs, which are required to more effectively assess the potential impact of strategies for the control of between-farm epidemic spread in European countries.ISSN:0950-2688ISSN:1469-440

The Empirical Low Energy Ion Flux Model for the Terrestrial Magnetosphere

This document includes a viewgraph presentation plus the full paper presented at the conference. The Living With a Star Ion Flux Model (IFM) is a radiation environment risk mitigation tool that provides magnetospheric ion flux values for varying geomagnetic disturbance levels in the geospace environment. IFM incorporates flux observations from the Polar and Geotail spacecraft in a single statistical flux model. IFM is an engineering environment model which predicts the proton flux not only in the magnetosphere, but also in the solar wind and magnetosheath phenomenological regions. This paper describes the ion flux databases that allows for IFM output to be correlated with the geomagnetic activity level, as represented by the Kp index

Behavior of susceptible-infected-susceptible epidemics on heterogeneous networks with saturation

We investigate saturation effects in susceptible-infected-susceptible (SIS) models of the spread of epidemics in heterogeneous populations. The structure of interactions in the population is represented by networks with connectivity distribution $P(k)$,including scale-free(SF) networks with power law distributions $P(k)\sim k^{-\gamma}$. Considering cases where the transmission of infection between nodes depends on their connectivity, we introduce a saturation function $C(k)$ which reduces the infection transmission rate $\lambda$ across an edge going from a node with high connectivity $k$. A mean field approximation with the neglect of degree-degree correlation then leads to a finite threshold $\lambda_{c}>0$ for SF networks with $2<\gamma \leq 3$. We also find, in this approximation, the fraction of infected individuals among those with degree $k$ for $\lambda$ close to $\lambda_{c}$. We investigate via computer simulation the contact process on a heterogeneous regular lattice and compare the results with those obtained from mean field theory with and without neglect of degree-degree correlations.Comment: 6 figure

Numerical study of the scaling properties of SU(2) lattice gauge theory in Palumbo non-compact regularization

In the framework of a non-compact lattice regularization of nonabelian gauge theories we look, in the SU(2) case, for the scaling window through the analysis of the ratio of two masses of hadronic states. In the two-dimensional parameter space of the theory we find the region where the ratio is constant, and equal to the one in the Wilson regularization. In the scaling region we calculate the lattice spacing, finding it at least 20% larger than in the Wilson case; therefore the simulated physical volume is larger.Comment: 24 pages, 7 figure

Analog phase lock between two lasers at LISA power levels

This paper presents the implementation of an analog optical phase-locked-loop with an offset frequency of about 20 MHz between two lasers, where the detected light powers were of the order of 31 pW and 200 mu W. The goal of this setup was the design and characterization of a photodiode transimpedance amplifier for application in LISA. By application of a transimpedance amplifier designed to have low noise and low power consumption, the phase noise between the two lasers was a factor of two above the shot noise limit down to 60 mHz. The achievable phase sensitivity depends ultimately on the available power of the highly attenuated master laser and on the input current noise of the transimpedance amplifier of the photodetector. The limiting noise source below 60 mHz was the analog phase measurement system that was used in this experiment. A digital phase measurement system that is currently under development at the AEI will be used in the near future. Its application should improve the sensitivity

The lifespan method as a tool to study criticality in absorbing-state phase transitions

In a recent work, a new numerical method (the lifespan method) has been introduced to study the critical properties of epidemic processes on complex networks [Phys. Rev. Lett. \textbf{111}, 068701 (2013)]. Here, we present a detailed analysis of the viability of this method for the study of the critical properties of generic absorbing-state phase transitions in lattices. Focusing on the well understood case of the contact process, we develop a finite-size scaling theory to measure the critical point and its associated critical exponents. We show the validity of the method by studying numerically the contact process on a one-dimensional lattice and comparing the findings of the lifespan method with the standard quasi-stationary method. We find that the lifespan method gives results that are perfectly compatible with those of quasi-stationary simulations and with analytical results. Our observations confirm that the lifespan method is a fully legitimate tool for the study of the critical properties of absorbing phase transitions in regular lattices