Rotating Boson Stars and Q-Balls

We consider axially symmetric, rotating boson stars. Their flat space limits represent spinning Q-balls. We discuss their properties and determine their domain of existence. Q-balls and boson stars are stationary solutions and exist only in a limited frequency range. The coupling to gravity gives rise to a spiral-like frequency dependence of the boson stars. We address the flat space limit and the limit of strong gravitational coupling. For comparison we also determine the properties of spherically symmetric Q-balls and boson stars.Comment: 22 pages, 18 figure

MTR-Viewer: Identifying regions within genes under purifying selection

Advances in genomic sequencing have enormous potential to revolutionise personalised medicine, however distinguishing disease-causing from benign variants remains a challenge. The increasing number of human genome and exome sequences available has revealed areas where unfavourable variation is removed through purifying selection. Here we present the MTR-Viewer, a web-server enabling easy visualisation at the gene or variant level of the Missense Tolerance Ratio (MTR), a measure of regional intolerance to missense variation calculated using variation from 220,000 exome and genome sequences. The MTR-Viewer enables exploration of MTR calculations, using different sliding windows, for over 18,000 human protein-coding genes and 85,000 alternative transcripts. Users can also view MTR scores calculated for specific ethnicities, to enable easy exploration of regions that may be under different selective pressure. The spatial distribution of population and known disease variants is also displayed on the protein’s domain structure. Intolerant regions were found to be highly enriched for ClinVar pathogenic and COSMIC somatic missense variants (Mann-Whitney U test p < 2.2x10-16). As the MTR is not biased by known domains and protein features, it can highlight functionally important regions within genes overlooked or inaccessible by traditional methods. MTR-Viewer is freely available via a user friendly web-server at http://biosig.unimelb.edu.au/mtr-viewer/.M.S. was supported by the Australian Government Research Training Program. S.P. was supported by an NHMRC R.D. Wright Career Development Fellowship (1126877). S.P. is an employee of AstraZeneca. D.B.A. was supported by the Jack Brockhoff Foundation [JBF 4186, 2016], a Newton Fund RCUK-CONFAP Grant awarded by The Medical Research Council (MRC) [MR/M026302/1]; the National Health and Medical Research Council of Australia [APP1072476]; and the Department of Biochemistry and Molecular Biology, University of Melbourne

Sharp interface limits of phase-field models

The use of continuum phase-field models to describe the motion of well-defined interfaces is discussed for a class of phenomena, that includes order/disorder transitions, spinodal decomposition and Ostwald ripening, dendritic growth, and the solidification of eutectic alloys. The projection operator method is used to extract the ``sharp interface limit'' from phase field models which have interfaces that are diffuse on a length scale $\xi$. In particular,phase-field equations are mapped onto sharp interface equations in the limits $\xi \kappa \ll 1$ and $\xi v/D \ll 1$, where $\kappa$ and $v$ are respectively the interface curvature and velocity and $D$ is the diffusion constant in the bulk. The calculations provide one general set of sharp interface equations that incorporate the Gibbs-Thomson condition, the Allen-Cahn equation and the Kardar-Parisi-Zhang equation.Comment: 17 pages, 9 figure

Geodesic motion in the space-time of a cosmic string

We study the geodesic equation in the space-time of an Abelian-Higgs string and discuss the motion of massless and massive test particles. The geodesics can be classified according to the particles energy, angular momentum and linear momentum along the string axis. We observe that bound orbits of massive particles are only possible if the Higgs boson mass is smaller than the gauge boson mass, while massless particles always move on escape orbits. Moreover, neither massive nor massless particles can ever reach the string axis for non-vanishing angular momentum. We also discuss the dependence of light deflection by a cosmic string as well as the perihelion shift of bound orbits of massive particles on the ratio between Higgs and gauge boson mass and the ratio between symmetry breaking scale and Planck mass, respectively.Comment: 20 pages including 14 figures; v2: references added, discussion on null geodesics extended, numerical results adde

Orbits in the Field of a Gravitating Magnetic Monopole

Orbits of test particles and light rays are an important tool to study the properties of space-time metrics. Here we systematically study the properties of the gravitational field of a globally regular magnetic monopole in terms of the geodesics of test particles and light. The gravitational field depends on two dimensionless parameters, defined as ratios of the characteristic mass scales present. For critical values of these parameters the resulting metric coefficients develop a singular behavior, which has profound influence on the properties of the resulting space-time and which is clearly reflected in the orbits of the test particles and light rays.Comment: 24 pages, 15 figures. Accepted for publication in GR

Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation

Gene panel and exome sequencing have revealed a high rate of molecular diagnoses among diseases where the genetic architecture has proven suitable for sequencing approaches, with a large number of distinct and highly penetrant causal variants identified among a growing list of disease genes. The challenge is, given the DNA sequence of a new patient, to distinguish disease-causing from benign variants. Large samples of human standing variation data highlight regional variation in the tolerance to missense variation within the protein-coding sequence of genes. This information is not well captured by existing bioinformatic tools, but is effective in improving variant interpretation. To address this limitation in existing tools, we introduce the missense tolerance ratio (MTR), which summarizes available human standing variation data within genes to encapsulate population level genetic variation. We find that patient-ascertained pathogenic variants preferentially cluster in low MTR regions (P < 0.005) of well-informed genes. By evaluating 20 publicly available predictive tools across genes linked to epilepsy, we also highlight the importance of understanding the empirical null distribution of existing prediction tools, as these vary across genes. Subsequently integrating the MTR with the empirically selected bioinformatic tools in a gene-specific approach demonstrates a clear improvement in the ability to predict pathogenic missense variants from background missense variation in disease genes. Among an independent test sample of case and control missense variants, case variants (0.83 median score) consistently achieve higher pathogenicity prediction probabilities than control variants (0.02 median score; Mann-Whitney U test, P < 1 × 10(-16)). We focus on the application to epilepsy genes; however, the framework is applicable to disease genes beyond epilepsy

Precision Mass Measurements of 129-131Cd and Their Impact on Stellar Nucleosynthesis via the Rapid Neutron Capture Process

Masses adjacent to the classical waiting-point nuclide 130Cd have been measured by using the Penning- trap spectrometer ISOLTRAP at ISOLDE/CERN. We find a significant deviation of over 400 keV from earlier values evaluated by using nuclear beta-decay data. The new measurements show the reduction of the N = 82 shell gap below the doubly magic 132Sn. The nucleosynthesis associated with the ejected wind from type-II supernovae as well as from compact object binary mergers is studied, by using state-of-the-art hydrodynamic simulations. We find a consistent and direct impact of the newly measured masses on the calculated abundances in the A = 128 - 132 region and a reduction of the uncertainties from the precision mass input data

Fourier-Space Crystallography as Group Cohomology

We reformulate Fourier-space crystallography in the language of cohomology of groups. Once the problem is understood as a classification of linear functions on the lattice, restricted by a particular group relation, and identified by gauge transformation, the cohomological description becomes natural. We review Fourier-space crystallography and group cohomology, quote the fact that cohomology is dual to homology, and exhibit several results, previously established for special cases or by intricate calculation, that fall immediately out of the formalism. In particular, we prove that {\it two phase functions are gauge equivalent if and only if they agree on all their gauge-invariant integral linear combinations} and show how to find all these linear combinations systematically.Comment: plain tex, 14 pages (replaced 5/8/01 to include archive preprint number for reference 22

Probing the N = 32 shell closure below the magic proton number Z = 20: Mass measurements of the exotic isotopes 52,53K

The recently confirmed neutron-shell closure at N = 32 has been investigated for the first time below the magic proton number Z = 20 with mass measurements of the exotic isotopes 52,53K, the latter being the shortest-lived nuclide investigated at the online mass spectrometer ISOLTRAP. The resulting two-neutron separation energies reveal a 3 MeV shell gap at N = 32, slightly lower than for 52Ca, highlighting the doubly-magic nature of this nuclide. Skyrme-Hartree-Fock-Boguliubov and ab initio Gorkov-Green function calculations are challenged by the new measurements but reproduce qualitatively the observed shell effect.Comment: 5 pages, 5 figure