Apparent horizons in simplicial Brill wave initial data

We construct initial data for a particular class of Brill wave metrics using Regge calculus, and compare the results to a corresponding continuum solution, finding excellent agreement. We then search for trapped surfaces in both sets of initial data, and provide an independent verification of the existence of an apparent horizon once a critical gravitational wave amplitude is passed. Our estimate of this critical value, using both the Regge and continuum solutions, supports other recent findings.Comment: 7 pages, 6 EPS figures, LaTeX 2e. Submitted to Class. Quant. Gra

Connected component identification and cluster update on GPU

Cluster identification tasks occur in a multitude of contexts in physics and engineering such as, for instance, cluster algorithms for simulating spin models, percolation simulations, segmentation problems in image processing, or network analysis. While it has been shown that graphics processing units (GPUs) can result in speedups of two to three orders of magnitude as compared to serial codes on CPUs for the case of local and thus naturally parallelized problems such as single-spin flip update simulations of spin models, the situation is considerably more complicated for the non-local problem of cluster or connected component identification. I discuss the suitability of different approaches of parallelization of cluster labeling and cluster update algorithms for calculations on GPU and compare to the performance of serial implementations.Comment: 15 pages, 14 figures, one table, submitted to PR

Rotating star initial data for a constrained scheme in numerical relativity

A new numerical code for computing stationary axisymmetric rapidly rotating stars in general relativity is presented. The formulation is based on a fully constrained-evolution scheme for 3+1 numerical relativity using the Dirac gauge and maximal slicing. We use both the polytropic and MIT bag model equations of state to demonstrate that the code can construct rapidly rotating neutron star and strange star models. We compare numerical models obtained by our code and a well-established code, which uses a different gauge condition, and show that the two codes agree to high accuracy.Comment: Minor changes and one figure added. Version accepted for publication in Class. Quant. Gra

The constraints as evolution equations for numerical relativity

The Einstein equations have proven surprisingly difficult to solve numerically. A standard diagnostic of the problems which plague the field is the failure of computational schemes to satisfy the constraints, which are known to be mathematically conserved by the evolution equations. We describe a new approach to rewriting the constraints as first-order evolution equations, thereby guaranteeing that they are satisfied to a chosen accuracy by any discretization scheme. This introduces a set of four subsidiary constraints which are far simpler than the standard constraint equations, and which should be more easily conserved in computational applications. We explore the manner in which the momentum constraints are already incorporated in several existing formulations of the Einstein equations, and demonstrate the ease with which our new constraint-conserving approach can be incorporated into these schemes.Comment: 10 pages, updated to match published versio

Reliable estimation of prediction uncertainty for physico-chemical property models

The predictions of parameteric property models and their uncertainties are sensitive to systematic errors such as inconsistent reference data, parametric model assumptions, or inadequate computational methods. Here, we discuss the calibration of property models in the light of bootstrapping, a sampling method akin to Bayesian inference that can be employed for identifying systematic errors and for reliable estimation of the prediction uncertainty. We apply bootstrapping to assess a linear property model linking the 57Fe Moessbauer isomer shift to the contact electron density at the iron nucleus for a diverse set of 44 molecular iron compounds. The contact electron density is calculated with twelve density functionals across Jacob's ladder (PWLDA, BP86, BLYP, PW91, PBE, M06-L, TPSS, B3LYP, B3PW91, PBE0, M06, TPSSh). We provide systematic-error diagnostics and reliable, locally resolved uncertainties for isomer-shift predictions. Pure and hybrid density functionals yield average prediction uncertainties of 0.06-0.08 mm/s and 0.04-0.05 mm/s, respectively, the latter being close to the average experimental uncertainty of 0.02 mm/s. Furthermore, we show that both model parameters and prediction uncertainty depend significantly on the composition and number of reference data points. Accordingly, we suggest that rankings of density functionals based on performance measures (e.g., the coefficient of correlation, r2, or the root-mean-square error, RMSE) should not be inferred from a single data set. This study presents the first statistically rigorous calibration analysis for theoretical Moessbauer spectroscopy, which is of general applicability for physico-chemical property models and not restricted to isomer-shift predictions. We provide the statistically meaningful reference data set MIS39 and a new calibration of the isomer shift based on the PBE0 functional.Comment: 49 pages, 9 figures, 7 table

A fully (3+1)-D Regge calculus model of the Kasner cosmology

We describe the first discrete-time 4-dimensional numerical application of Regge calculus. The spacetime is represented as a complex of 4-dimensional simplices, and the geometry interior to each 4-simplex is flat Minkowski spacetime. This simplicial spacetime is constructed so as to be foliated with a one parameter family of spacelike hypersurfaces built of tetrahedra. We implement a novel two-surface initial-data prescription for Regge calculus, and provide the first fully 4-dimensional application of an implicit decoupled evolution scheme (the ``Sorkin evolution scheme''). We benchmark this code on the Kasner cosmology --- a cosmology which embodies generic features of the collapse of many cosmological models. We (1) reproduce the continuum solution with a fractional error in the 3-volume of 10^{-5} after 10000 evolution steps, (2) demonstrate stable evolution, (3) preserve the standard deviation of spatial homogeneity to less than 10^{-10} and (4) explicitly display the existence of diffeomorphism freedom in Regge calculus. We also present the second-order convergence properties of the solution to the continuum.Comment: 22 pages, 5 eps figures, LaTeX. Updated and expanded versio

Measuring degree-degree association in networks

The Pearson correlation coefficient is commonly used for quantifying the global level of degree-degree association in complex networks. Here, we use a probabilistic representation of the underlying network structure for assessing the applicability of different association measures to heavy-tailed degree distributions. Theoretical arguments together with our numerical study indicate that Pearson's coefficient often depends on the size of networks with equal association structure, impeding a systematic comparison of real-world networks. In contrast, Kendall-Gibbons' $\tau_{b}$ is a considerably more robust measure of the degree-degree association

Components of multifractality in the Central England Temperature anomaly series

We study the multifractal nature of the Central England Temperature (CET) anomaly, a time series that spans more than 200 years. The series is analyzed as a complete data set and considering a sliding window of 11 years. In both cases, we quantify the broadness of the multifractal spectrum as well as its components defined by the deviations from the Gaussian distribution and the influence of the dependence between measurements. The results show that the chief contribution to the multifractal structure comes from the dynamical dependencies, mainly the weak ones, followed by a residual contribution of the deviations from Gaussianity. However, using the sliding window, we verify that the spikes in the non-Gaussian contribution occur at very close dates associated with climate changes determined in previous works by component analysis methods. Moreover, the strong non-Gaussian contribution found in the multifractal measures from the 1960s onwards is in agreement with global results very recently proposed in the literature.Comment: 21 pages, 10 figure

Whole Genome Sequencing for Public Health Surveillance of Shiga Toxin-Producing Escherichia coli Other than Serogroup O157

Shiga toxin-producing Escherichia coli (STEC) are considered to be a significant threat to public health due to the severity of gastrointestinal symptoms associated with human infection. In England STEC O157 is the most commonly detected STEC serogroup, however, the implementation of PCR at local hospital laboartories has resulted in an increase in the detection of STEC other than serogroup O157 (non-O157 STEC). The aim of this study was to evaluate the use of whole genome sequencing (WGS) for routine public health surveillance of non-O157 STEC by comparing this approach to phenotypic serotyping and PCR for subtyping the stx-encoding genes. Of the 102 isolates where phenotypic and genotypic serotyping could be compared, 98 gave fully concordant results. The most common non-O157 STEC serogroups detected were O146 (22) and O26 (18). All but one of the 38 isolates that could not be phenotypically serotyped (designated O unidentifiable or O rough) were serotyped using the WGS data. Of the 73 isolates where a flagella type was available by traditional phenotypic typing, all results matched the H-type derived from the WGS data. Of the 140 sequenced non-O157 isolates, 52 (37.1%) harboured stx1 only, 42 (30.0%) had stx2 only, 46 (32.9%) carried stx1 and stx2. Of these, stx subtyping PCR results were available for 131 isolates and 121 of these had concordant results with the stx subtype derived from the WGS data. Non-specific primer binding during PCR amplification, due to the similarity of the stx2 subtype gene sequences was the most likely cause. The results of this study showed WGS provided a reliable and robust one-step process for characterisation of STEC. Deriving the full serotype from WGS data in real time has enabled us to report a higher level of strain discrimination while stx subtyping provides data on the pathogenic potential of each isolate, enabling us to predict clinical outcome of each case and to monitor the emergence of hyper-virulent strains