Measuring Hubble's Constant in our Inhomogeneous Universe

Recent observations of Cepheids in the Virgo cluster have bolstered the evidence that supports a Hubble constant in 70-90 km/s/Mpc range. This evidence, by and large, probes the expansion of the Universe within 100 Mpc. We investigate the possibility that the expansion rate within this region is systematically higher than the true expansion rate due to the presence of a local, large underdense region or void. We begin by calculating the expected deviations between the locally measured Hubble constant and the true Hubble constant for a variety of models. We also discuss the expected correlations between these deviations and mass fluctuation for the sample volume. We find that the fluctuations are small for the standard cold dark matter as well as mixed dark matter models but can be substantial in a number of interesting and viable nonstandard scenarios. However, deviations in the Hubble flow for a region of radius 200 Mpc are small for virtually all reasonable models. Therefore, methods based on supernovae or the Sunyaev-Zel'dovich effect, which can probe 200 Mpc scales, will be essential in determining the true Hubble constant. We discuss, in detail, the fluctuations induced in the cosmic background radiation by voids at the last scattering surface. In addition, we discuss the dipole and quadrupole fluctuations one would expect if the void enclosing us is aspherical or if we lie off-center.Comment: 20 pages (58K), 8 Postscript figures (111K compressed); Submitted to MNRAS. Postscript source available at http://astro.queensu.ca/~dursi/preprints

Local Ignition in Carbon/Oxygen White Dwarfs -- I: One-zone Ignition and Spherical Shock Ignition of Detonations

The details of ignition of Type Ia supernovae remain fuzzy, despite the importance of this input for any large-scale model of the final explosion. Here, we begin a process of understanding the ignition of these hotspots by examining the burning of one zone of material, and then investigate the ignition of a detonation due to rapid heating at single point. We numerically measure the ignition delay time for onset of burning in mixtures of degenerate material and provide fitting formula for conditions of relevance in the Type Ia problem. Using the neon abundance as a proxy for the white dwarf metallicity, we then find that ignition times can decrease by ~20% with addition of even 5% of neon by mass. When temperature fluctuations that successfully kindle a region are very rare, such a reduction in ignition time can increase the probability of ignition by orders of magnitude. If the neon comes largely at the expense of carbon, a similar increase in the ignition time can occur. We then consider the ignition of a detonation by an explosive energy input in one localized zone, eg a Sedov blast wave leading to a shock-ignited detonation. Building on previous work on curved detonations, we find that surprisingly large inputs of energy are required to successfully launch a detonation, leading to required matchheads of ~4500 detonation thicknesses - tens of centimeters to hundreds of meters - which is orders of magnitude larger than naive considerations might suggest. This is a very difficult constraint to meet for some pictures of a deflagration-to-detonation transition, such as a Zel'dovich gradient mechanism ignition in the distributed burning regime.Comment: 29 pages; accepted to ApJ. Comments welcome at http://www.cita.utoronto.ca/~ljdursi/thisweek/ . Updated version addressing referee comment

Structure of magnetic fields in intracluster cavities

Observations of clusters of galaxies show ubiquitous presence of X-ray cavities, presumably blown by the AGN jets. We consider magnetic field structures of these cavities. Stability requires that they contain both toroidal and poloidal magnetic fields, while realistic configurations should have vanishing magnetic field on the boundary. For axisymmetric configurations embedded in unmagnetized plasma, the continuity of poloidal and toroidal magnetic field components on the surface of the bubble then requires solving the elliptical Grad-Shafranov equation with both Dirichlet and Neumann boundary conditions. This leads to a double eigenvalue problem, relating the pressure gradients and the toroidal magnetic field to the radius of the bubble. We have found fully analytical stable solutions. This result is confirmed by numerical simulation. We present synthetic X-ray images and synchrotron emission profiles and evaluate the rotation measure for radiation traversing the bubble.Comment: 10 pages, 13 figures, accepted by MNRA

Detecting the orientation of magnetic fields in galaxy clusters

Clusters of galaxies, filled with hot magnetized plasma, are the largest bound objects in existence and an important touchstone in understanding the formation of structures in our Universe. In such clusters, thermal conduction follows field lines, so magnetic fields strongly shape the cluster's thermal history; that some have not since cooled and collapsed is a mystery. In a seemingly unrelated puzzle, recent observations of Virgo cluster spiral galaxies imply ridges of strong, coherent magnetic fields offset from their centre. Here we demonstrate, using three-dimensional magnetohydrodynamical simulations, that such ridges are easily explained by galaxies sweeping up field lines as they orbit inside the cluster. This magnetic drape is then lit up with cosmic rays from the galaxies' stars, generating coherent polarized emission at the galaxies' leading edges. This immediately presents a technique for probing local orientations and characteristic length scales of cluster magnetic fields. The first application of this technique, mapping the field of the Virgo cluster, gives a startling result: outside a central region, the magnetic field is preferentially oriented radially as predicted by the magnetothermal instability. Our results strongly suggest a mechanism for maintaining some clusters in a 'non-cooling-core' state.Comment: 48 pages, 21 figures, revised version to match published article in Nature Physics, high-resolution version available at http://www.cita.utoronto.ca/~pfrommer/Publications/pfrommer-dursi.pd

Magnetohydrodynamic relaxation of AGN ejecta: radio bubbles in the intracluster medium

X-ray images of galaxy clusters often display underdense bubbles which are apparently inflated by AGN outflow. I consider the evolution of the magnetic field inside such a bubble, using a mixture of analytic and numerical methods. It is found that the field relaxes into an equilibrium filling the entire volume of the bubble. The timescale on which this happens depends critically on the magnetisation and helicity of the outflow as well as on properties of the surrounding ICM. If the outflow is strongly magnetised, the magnetic field undergoes reconnection on a short timescale, magnetic energy being converted into heat whilst the characteristic length scale of the field rises; this process stops when a global equilibrium is reached. The strength of the equilibrium field is determined by the magnetic helicity injected into the bubble by the AGN: if the outflow has a consistent net flux and consequently a large helicity then a global equilibrium will be reached on a short timescale, whereas a low-helicity outflow results in no global equilibrium being reached and at the time of observation reconnection will be ongoing. However, localised flux-tube equilibria will form. If, on the other hand, the outflow is very weakly magnetised, no reconnection occurs and the magnetic field inside the bubble remains small-scale and passive. These results have implications for the internal composition of the bubbles, their interaction with ICM -- in particular to explain how bubbles could move a large distance through the ICM without breaking up -- as well as for the cooling flow problem in general. In addition, reconnection sites in a bubble could be a convenient source of energetic particles, circumventing the problem of synchrotron emitters having a shorter lifetime than the age of the bubble they inhabit.Comment: MNRAS accepted. 15 pages, 10 figures

Author Correction: Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Correction to this paper has been published: https://doi.org/10.1038/s41467-020-20128-w

Author Correction:Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples (Nature Communications, (2020), 11, 1, (4748), 10.1038/s41467-020-18151-y)

The original version of this Article omitted from the author list the 9th author Yize Li, who is from the ‘The McDonnell Genome Institute at Washington University, St. Louis, MO 63108, USA and Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO 63108, USA’. This has been corrected in both the PDF and HTML versions of the Article

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.publishedVersio

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts