Distributions of gaps and end-to-end correlations in random transverse-field Ising spin chains

A previously introduced real space renormalization-group treatment of the random transverse-field Ising spin chain is extended to provide detailed information on the distribution of the energy gap and the end-to-end correlation function for long chains with free boundary conditions. Numerical data, using the mapping of the problem to free fermions, are found to be in good agreement with the analytic finite size scaling predictions.Comment: 12 pages revtex, 10 figures, submitted to Phys. Rev.

Stability of Elastic Glass Phases in Random Field XY Magnets and Vortex Lattices in Type II Superconductors

A description of a dislocation-free elastic glass phase in terms of domain walls is developed and used as the basis of a renormalization group analysis of the energetics of dislocation loops added to the system. It is found that even after optimizing over possible paths of large dislocation loops, their energy is still very likely to be positive when the dislocation core energy is large. This implies the existence of an equilibrium elastic glass phase in three dimensional random field X-Y magnets, and a dislocation free, bond-orientationally ordered ``Bragg glass'' phase of vortices in dirty Type II superconductors.Comment: 12 pages, Revtex, no figures, submitted to Phys Rev Letter

The viscous slowing down of supercooled liquids as a temperature-controlled superArrhenius activated process: a description in terms of frustration-limited domains

We propose that the salient feature to be explained about the glass transition of supercooled liquids is the temperature-controlled superArrhenius activated nature of the viscous slowing down, more strikingly seen in weakly-bonded, fragile systems. In the light of this observation, the relevance of simple models of spherically interacting particles and that of models based on free-volume congested dynamics are questioned. Finally, we discuss how the main aspects of the phenomenology of supercooled liquids, including the crossover from Arrhenius to superArrhenius activated behavior and the heterogeneous character of the $\alpha$ relaxation, can be described by an approach based on frustration-limited domains.Comment: 13 pages, 4 figures, accepted in J. Phys.: Condensed Matter, proceedings of the Trieste workshop on "Unifying Concepts in Glass Physics

Random Walks, Reaction-Diffusion, and Nonequilibrium Dynamics of Spin Chains in One-dimensional Random Environments

Sinai's model of diffusion in one-dimension with random local bias is studied by a real space renormalization group which yields asymptotically exact long time results. The distribution of the position of a particle and the probability of it not returning to the origin are obtained, as well as the two-time distribution which exhibits "aging" with $\frac{\ln t}{\ln t'}$ scaling and a singularity at $\ln t =\ln t'$. The effects of a small uniform force are also studied. Extension to motion of many domain walls yields non-equilibrium time dependent correlations for the 1D random field Ising model with Glauber dynamics and "persistence" exponents of 1D reaction-diffusion models with random forces.Comment: 5 pages, 1 figures, RevTe

Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects

Funding: R.A.F. was funded by the Natural Environment Research Council (NERC). D.A.H. and M.C.F. were supported by the Wellcome Trust. No additional external funding received for this study.Peer reviewedPublisher PD

Vortex Glass Phase and Universal Susceptibility Variations in Planar Array of Flux Lines

Some of the properties of the low temperature vortex-glass phase of randomly-pinned flux lines in 1+1 dimensions are studied. The flux arrays are found to be sensitive to small changes in external parameters such as the magnetic field or temperature. These effects are captured by the variations in the magnetic response and noise, which have universal statistics and should provide an unambiguous signature of the glass phase.Comment: 11 pages and no figures; revtex 3.

Nonequilibrium dynamics of random field Ising spin chains: exact results via real space RG

Non-equilibrium dynamics of classical random Ising spin chains are studied using asymptotically exact real space renormalization group. Specifically the random field Ising model with and without an applied field (and the Ising spin glass (SG) in a field), in the universal regime of a large Imry Ma length so that coarsening of domains after a quench occurs over large scales. Two types of domain walls diffuse in opposite Sinai random potentials and mutually annihilate. The domain walls converge rapidly to a set of system-specific time-dependent positions {\it independent of the initial conditions}. We obtain the time dependent energy, magnetization and domain size distribution (statistically independent). The equilibrium limits agree with known exact results. We obtain exact scaling forms for two-point equal time correlation and two-time autocorrelations. We also compute the persistence properties of a single spin, of local magnetization, and of domains. The analogous quantities for the spin glass are obtained. We compute the two-point two-time correlation which can be measured by experiments on spin-glass like systems. Thermal fluctuations are found to be dominated by rare events; all moments of truncated correlations are computed. The response to a small field applied after waiting time $t_w$, as measured in aging experiments, and the fluctuation-dissipation ratio $X(t,t_w)$ are computed. For $(t-t_w) \sim t_w^{\hat{\alpha}}$, $\hat{\alpha} <1$, it equals its equilibrium value X=1, though time translational invariance fails. It exhibits for $t-t_w \sim t_w$ aging regime with non-trivial $X=X(t/t_w) \neq 1$, different from mean field.Comment: 55 pages, 9 figures, revte

Microevolutionary traits and comparative population genomics of the emerging pathogenic fungus Cryptococcus gattii

Emerging fungal pathogens cause an expanding burden of disease across the animal kingdom, including a rise in morbidity and mortality in humans. Yet, we currently have only a limited repertoire of available therapeutic interventions. A greater understanding of the mechanisms of fungal virulence and of the emergence of hypervirulence within species is therefore needed for new treatments and mitigation efforts. For example, over the past decade, an unusual lineage of Cryptococcus gattii, which was first detected on Vancouver Island, has spread to the Canadian mainland and the Pacific Northwest infecting otherwise healthy individuals. The molecular changes that led to the development of this hypervirulent cryptococcal lineage remain unclear. To explore this, we traced the history of similar microevolutionary events that can lead to changes in host range and pathogenicity. Here, we detail fine-resolution mapping of genetic differences between two highly related Cryptococcus gattii VGIIc isolates that differ in their virulence traits (phagocytosis, vomocytosis, macrophage death, mitochondrial tubularization and intracellular proliferation). We identified a small number of single site variants within coding regions that potentially contribute to variations in virulence. We then extended our methods across multiple lineages of C. gattii to study how selection is acting on key virulence genes within different lineages. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’

Bounding biomass in the Fisher equation

The FKPP equation with a variable growth rate and advection by an incompressible velocity field is considered as a model for plankton dispersed by ocean currents. If the average growth rate is negative then the model has a survival-extinction transition; the location of this transition in the parameter space is constrained using variational arguments and delimited by simulations. The statistical steady state reached when the system is in the survival region of parameter space is characterized by integral constraints and upper and lower bounds on the biomass and productivity that follow from variational arguments and direct inequalities. In the limit of zero-decorrelation time the velocity field is shown to act as Fickian diffusion with an eddy diffusivity much larger than the molecular diffusivity and this allows a one-dimensional model to predict the biomass, productivity and extinction transitions. All results are illustrated with a simple growth and stirring model.Comment: 32 Pages, 13 Figure

Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity

This project was funded by the UK Natural Environmental Research Council (NERC) grant NE/E006701/1, the European Research Council (ERC) grant 260801-BIG_IDEA, the Swiss National Science Foundation grant 31-125099 and the Biodiversa project RACE: Risk Assessment of Chytridiomycosis to European Amphibian Biodiversity (http://www.bd-maps.eu). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD