Accuracy Issues for Numerical Waveforms

We study the convergence properties of our implementation of the 'moving punctures' approach at very high resolutions for an equal-mass, non-spinning, black-hole binary. We find convergence of the Hamiltonian constraint on the horizons and the L2 norm of the Hamiltonian constraint in the bulk for sixth and eighth-order finite difference implementations. The momentum constraint is more sensitive, and its L2 norm shows clear convergence for a system with consistent sixth-order finite differencing, while the momentum and BSSN constraints on the horizons show convergence for both sixth and eighth-order systems. We analyze the gravitational waveform error from the late-inspiral, merger, and ringdown. We find that using several lower-order techniques for increasing the speed of numerical relativity simulations actually lead to apparently non-convergent errors. Even when using standard high-accuracy techniques, rather than seeing clean convergence, where the waveform phase is a monotonic function of grid resolution, we find that the phase tends to oscillate with resolution, possibly due to stochastic errors induced by grid refinement boundaries. Our results seem to indicate that one can obtain gravitational waveform phases to within 0.05 rad. (and possibly as small as 0.015 rad.), while the amplitude error can be reduced to 0.1%. We then compare with the waveforms obtained using the cZ4 formalism. We find that the cZ4 waveforms have larger truncation errors for a given resolution, but the Richardson extrapolation phase of the cZ4 and BSSN waveforms agree to within 0.01 rad., even during the ringdown.Comment: version accepted to PR

(2479) Proposal to conserve the name Marattia kaulfussii (Eupodium kaulfussii) against M. raddiana (Marattiaceae)

Proposal to conserve the name Marattia kaulfussii (Eupodium kaulfussii)against M. raddiana (Marattiaceae). Unless this proposal is accepted, the epithet raddiana will need to be combined under Eupodium and this will become the correctname of what is universally known as E. kaulfussii. Conservation of M. kaulfussii against M. raddiana is therefore seen as the best solution in the interest of nomenclatural stability.Fil: Arana, Marcelo Daniel. Universidad Nacional de Río Cuarto. Facultad de Ciencias Exactas, Fisicoquímicas y Naturales. Departamento de Ciencias Naturales; ArgentinaFil: Christenhusz, MaartenJ.M.. Royal Botanic Gardens; Reino UnidoFil: Ponce, Marta Monica. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Botánica Darwinion. Academia Nacional de Ciencias Exactas, Físicas y Naturales. Instituto de Botánica Darwinion; Argentin

RACS: Rapid Analysis of ChIP-Seq data for contig based genomes

Background: Chromatin immunoprecipitation coupled to next generation sequencing (ChIP-Seq) is a widely used technique to investigate the function of chromatin-related proteins in a genome-wide manner. ChIP-Seq generates large quantities of data which can be difficult to process and analyse, particularly for organisms with contig based genomes. Contig-based genomes often have poor annotations for cis-elements, for example enhancers, that are important for gene expression. Poorly annotated genomes make a comprehensive analysis of ChIP-Seq data difficult and as such standardized analysis pipelines are lacking. Methods: We report a computational pipeline that utilizes traditional High-Performance Computing techniques and open source tools for processing and analysing data obtained from ChIP-Seq. We applied our computational pipeline "Rapid Analysis of ChIP-Seq data" (RACS) to ChIP-Seq data that was generated in the model organism Tetrahymena thermophila, an example of an organism with a genome that is available in contigs. Results: To test the performance and efficiency of RACs, we performed control ChIP-Seq experiments allowing us to rapidly eliminate false positives when analyzing our previously published data set. Our pipeline segregates the found read accumulations between genic and intergenic regions and is highly efficient for rapid downstream analyses. Conclusions: Altogether, the computational pipeline presented in this report is an efficient and highly reliable tool to analyze genome-wide ChIP-Seq data generated in model organisms with contig-based genomes. RACS is an open source computational pipeline available to download from: https://bitbucket.org/mjponce/racs --or-- https://gitrepos.scinet.utoronto.ca/public/?a=summary&p=RACSComment: Submitted to BMC Bioinformatics. Computational pipeline available at https://bitbucket.org/mjponce/rac

Event horizons, gravitational waves and astrophysical kicks in black-hole spacetimes

In this thesis we use computational techniques (numerical simulations) to study different stages of black hole mergers. A first project describes topological properties of the main performer of this play, the black hole and its event horizon. We investigate three configurations: a continuum ring singularity, a \u27discretized\u27 ring (black holes arranged on a ring), and a linear distribution of black holes. We evolve each of the corresponding spacetimes forward and then backwards in time, searching for the respective event horizons. We find some evidence, based on configurations of multiple BHs arranged in a ring, that this configuration leads to singular limit where the horizon width has zero size, possibly indicating the presence of a naked singularity, when the radius of the ring is sufficiently large. In a second project, we study the dynamics of a hydrodynamical accretion disk around a recoiling black hole, which models the behavior of an accretion disk around a binary just after the merger, using \u27smoothed-particle hydrodynamics\u27 techniques. We simulated different recoil angles between the accretion disk and the recoil velocity of the black hole. We find that for more vertical kicks (angles \u3c 30 degrees) a gap remains present in the inner disk, while for more oblique kicks (angles \u3e 45 degrees), matter rapidly accretes toward the black hole. There is a systematic trend for higher potential luminosities for more oblique kick angles for a given black hole mass, disk mass and kick velocity, and we find large amplitude oscillations in time in the case of a kick oriented 60 degrees from the vertical

Consistent discretizations: the Gowdy spacetimes

We apply the consistent discretization scheme to general relativity particularized to the Gowdy space-times. This is the first time the framework has been applied in detail in a non-linear generally-covariant gravitational situation with local degrees of freedom. We show that the scheme can be correctly used to numerically evolve the space-times. We show that the resulting numerical schemes are convergent and preserve approximately the constraints as expected.Comment: 10 pages, 8 figure