Protein annotation and modelling servers at University College London

The UCL Bioinformatics Group web portal offers several high quality protein structure prediction and function annotation algorithms including PSIPRED, pGenTHREADER, pDomTHREADER, MEMSAT, MetSite, DISOPRED2, DomPred and FFPred for the prediction of secondary structure, protein fold, protein structural domain, transmembrane helix topology, metal binding sites, regions of protein disorder, protein domain boundaries and protein function, respectively. We also now offer a fully automated 3D modelling pipeline: BioSerf, which performed well in CASP8 and uses a fragment-assembly approach which placed it in the top five servers in the de novo modelling category. The servers are available via the group web site at http://bioinf.cs.ucl.ac.uk/

Chandra and FUSE spectroscopy of the hot bare stellar core H1504+65

H1504+65 is an extremely hot hydrogen-deficient white dwarf with an effective temperature close to 200,000 K. We present new FUV and soft X-ray spectra obtained with FUSE and Chandra, which confirm that H1504+65 has an atmosphere primarily composed of carbon and oxygen. The Chandra LETG spectrum (60-160 Angstroem) shows a wealth of photospheric absorption lines from highly ionized oxygen, neon, and - for the first time identified in this star - magnesium and suggests relatively high Ne and Mg abundances. This corroborates an earlier suggestion that H1504+65 represents a naked C/O stellar core or even the C/O envelope of an O-Ne-Mg white dwarf.Comment: 15 pages, 10 figures, accepted for publication in A&

Prospect of Studying Hard X- and Gamma-Rays from Type Ia Supernovae

We perform multi-dimensional, time-dependent radiation transfer simulations for hard X-ray and gamma-ray emissions, following radioactive decays of 56Ni and 56Co, for two-dimensional delayed detonation models of Type Ia supernovae (SNe Ia). The synthetic spectra and light curves are compared with the sensitivities of current and future observatories for an exposure time of 10^6 seconds. The non-detection of the gamma-ray signal from SN 2011fe at 6.4 Mpc by SPI on board INTEGRAL places an upper limit for the mass of 56Ni of \lesssim 1.0 Msun, independently from observations in any other wavelengths. Signals from the newly formed radioactive species have not been convincingly measured yet from any SN Ia, but the future X-ray and gamma-ray missions are expected to deepen the observable horizon to provide the high energy emission data for a significant SN Ia sample. We predict that the hard X-ray detectors on board NuStar (launched in 2012) or ASTRO-H (scheduled for launch in 2014) will reach to SNe Ia at \sim15 Mpc, i.e., one SN every few years. Furthermore, according to the present results, the soft gamma-ray detector on board ASTRO-H will be able to detect the 158 keV line emission up to \sim25 Mpc, i.e., a few SNe Ia per year. Proposed next generation gamma-ray missions, e.g., GRIPS, could reach to SNe Ia at \sim20 - 35 Mpc by MeV observations. Those would provide new diagnostics and strong constraints on explosion models, detecting rather directly the main energy source of supernova light.Comment: 14 pages, 7 figures, 1 table, accepted for publication in Ap

SDWFS-MT-1: A Self-Obscured Luminous Supernova at z~0.2

We report the discovery of a six-month-long mid-infrared transient, SDWFS-MT-1 (aka SN 2007va), in the Spitzer Deep, Wide-Field Survey of the NOAO Deep Wide-Field Survey Bootes field. The transient, located in a z=0.19 low luminosity (M_[4.5]~-18.6 mag, L/L_MilkyWay~0.01) metal-poor (12+log(O/H)~7.8) irregular galaxy, peaked at a mid-infrared absolute magnitude of M_[4.5]~-24.2 in the 4.5 micron Spitzer/IRAC band and emitted a total energy of at least 10^51 ergs. The optical emission was likely fainter than the mid-infrared, although our constraints on the optical emission are poor because the transient peaked when the source was "behind" the Sun. The Spitzer data are consistent with emission by a modified black body with a temperature of ~1350 K. We rule out a number of scenarios for the origin of the transient such as a Galactic star, AGN activity, GRB, tidal disruption of a star by a black hole and gravitational lensing. The most plausible scenario is a supernova exploding inside a massive, optically thick circumstellar medium, composed of multiple shells of previously ejected material. If the proposed scenario is correct, then a significant fraction (~10%) of the most luminous supernova may be self-enshrouded by dust not only before but also after the supernova occurs. The spectral energy distribution of the progenitor of such a supernova would be a slightly cooler version of eta Carina, peaking at 20-30 microns.Comment: 26 pages, 5 figures, 1 table, accepted for publication in Ap

PTF11kx: A Type-Ia Supernova with a Symbiotic Nova Progenitor

There is a consensus that Type-Ia supernovae (SNe Ia) arise from the thermonuclear explosion of white dwarf stars that accrete matter from a binary companion. However, direct observation of SN Ia progenitors is lacking, and the precise nature of the binary companion remains uncertain. A temporal series of high-resolution optical spectra of the SN Ia PTF 11kx reveals a complex circumstellar environment that provides an unprecedentedly detailed view of the progenitor system. Multiple shells of circumsteller are detected and the SN ejecta are seen to interact with circumstellar material (CSM) starting 59 days after the explosion. These features are best described by a symbiotic nova progenitor, similar to RS Ophiuchi.Comment: 27 pages, 5 figures. In pres

The surface science of quasicrystals

The surfaces of quasicrystals have been extensively studied since about 1990. In this paper we review work on the structure and morphology of clean surfaces, and their electronic and phonon structure. We also describe progress in adsorption and epitaxy studies. The paper is illustrated throughout with examples from the literature. We offer some reflections on the wider impact of this body of work and anticipate areas for future development. (Some figures in this article are in colour only in the electronic version

ASCR/HEP Exascale Requirements Review Report

This draft report summarizes and details the findings, results, and recommendations derived from the ASCR/HEP Exascale Requirements Review meeting held in June, 2015. The main conclusions are as follows. 1) Larger, more capable computing and data facilities are needed to support HEP science goals in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of the demand at the 2025 timescale is at least two orders of magnitude -- and in some cases greater -- than that available currently. 2) The growth rate of data produced by simulations is overwhelming the current ability, of both facilities and researchers, to store and analyze it. Additional resources and new techniques for data analysis are urgently needed. 3) Data rates and volumes from HEP experimental facilities are also straining the ability to store and analyze large and complex data volumes. Appropriately configured leadership-class facilities can play a transformational role in enabling scientific discovery from these datasets. 4) A close integration of HPC simulation and data analysis will aid greatly in interpreting results from HEP experiments. Such an integration will minimize data movement and facilitate interdependent workflows. 5) Long-range planning between HEP and ASCR will be required to meet HEP's research needs. To best use ASCR HPC resources the experimental HEP program needs a) an established long-term plan for access to ASCR computational and data resources, b) an ability to map workflows onto HPC resources, c) the ability for ASCR facilities to accommodate workflows run by collaborations that can have thousands of individual members, d) to transition codes to the next-generation HPC platforms that will be available at ASCR facilities, e) to build up and train a workforce capable of developing and using simulations and analysis to support HEP scientific research on next-generation systems.Comment: 77 pages, 13 Figures; draft report, subject to further revisio

Tycho Brahe's 1572 supernova as a standard type Ia explosion revealed from its light echo spectrum

Type Ia supernovae (SNe Ia) are thermonuclear explosions of white dwarf stars in close binary systems. They play an important role as cosmological distance indicators and have led to the discovery of the accelerated expansion of the Universe. Among the most important unsolved questions are how the explosion actually proceeds and whether accretion occurs from a companion or via the merging of two white dwarfs. Tycho Brahe's supernova of 1572 (SN 1572) is thought to be one of the best candidates for a SN Ia in the Milky Way. The proximity of the SN 1572 remnant has allowed detailed studies, such as the possible identification of the binary companion, and provides a unique opportunity to test theories of the explosion mechanism and the nature of the progenitor. The determination of the yet unknown exact spectroscopic type of SN 1572 is crucial to relate these results to the diverse population of SNe Ia. Here we report an optical spectrum of Tycho Brahe's supernova near maximum brightness, obtained from a scattered-light echo more than four centuries after the direct light of the explosion swept past Earth. We find that SN 1572 belongs to the majority class of normal SNe Ia. The presence of a strong Ca II IR feature at velocities exceeding 20,000 km/s, which is similar to the previously observed polarized features in other SNe Ia, suggests asphericity in SN 1572.Comment: 15 pages, 3 figures - accepted for publication in Natur

Probing Kilonova Ejecta Properties Using a Catalog of Short Gamma-Ray Burst Observations

The discovery of GW170817 and GRB 170817A in tandem with AT 2017gfo cemented the connection between neutron star mergers, short gamma-ray bursts (GRBs), and kilonovae. To investigate short GRB observations in the context of diverse kilonova behavior, we present a comprehensive optical and near-infrared (NIR) catalog of 85 bursts discovered over 2005-2020 on timescales of $\lesssim12$ days. The sample includes previously unpublished observations of 23 bursts, and encompasses both detections and deep upper limits. We identify 11.8% and 15.3% of short GRBs in our catalog with upper limits that probe luminosities lower than those of AT 2017gfo and a fiducial NSBH kilonovae model (for pole-on orientations), respectively. We quantify the ejecta masses allowed by the deepest limits in our catalog, constraining blue and `extremely blue' kilonova components of 14.1% of bursts to $M_{\rm ej}\lesssim0.01-0.1 M_{\odot}$. The sample of short GRBs is not particularly constraining for red kilonova components. Motivated by the large catalog as well as model predictions of diverse kilonova behavior, we investigate altered search strategies for future follow-up to short GRBs. We find that ground-based optical and NIR observations on timescales of $\gtrsim 2$ days can play a significant role in constraining more diverse outcomes. We expect future short GRB follow up efforts, such as from the {\it James Webb Space Telescope}, to expand the reach of kilonova detectability to redshifts of $z\approx 1$.Comment: 33 pages, 7 figures, 3 tables. Submitted to Ap

The Broad-band Counterpart of the Short GRB 200522A at z=0.5536z=0.5536:A Luminous Kilonova or a Collimated Outflow with a Reverse Shock?

We present the discovery of the radio afterglow and near-infrared (NIR) counterpart of the Swift short GRB 200522A, located at a small projected offset of $\approx 1$ kpc from the center of a young, star-forming host galaxy at $z=0.5536$. The radio and X-ray luminosities of the afterglow are consistent with those of on-axis cosmological short GRBs. The NIR counterpart, revealed by our HST observations at a rest-frame time of $\approx2.3$ days, has a luminosity of $\approx (1.3-1.7) \times 10^{42}$ erg s$^{-1}$. This is substantially lower than on-axis short GRB afterglow detections, but is a factor of $\approx 8$-$17$ more luminous than the kilonova of GW170817, and significantly more luminous than any kilonova candidate for which comparable observations exist. The combination of the counterpart's color ($i-y = -0.08\pm 0.21$; rest-frame) and luminosity cannot be explained by standard radioactive heating alone. We present two scenarios to interpret the broad-band behavior of GRB 200522A: a synchrotron forward shock with a luminous kilonova (potentially boosted by magnetar energy deposition), or forward and reverse shocks from a $\approx14^{\circ}$, relativistic ($\Gamma_0 \gtrsim 80$) jet. Models which include a combination of enhanced radioactive heating rates, low-lanthanide mass fractions, or additional sources of heating from late-time central engine activity may provide viable alternate explanations. If a stable magnetar was indeed produced in GRB 200522A, we predict that late-time radio emission will be detectable starting $\approx 0.3$-$6$ years after the burst for a deposited energy of $\approx 10^{53}$ erg. Counterparts of similar luminosity to GRB 200522A associated with gravitational wave events will be detectable with current optical searches to $\approx\!250$ Mpc