Automatic analysis of Swift-XRT data

The Swift spacecraft detects and autonomously observes ~100 Gamma Ray Bursts (GRBs) per year, ~96% of which are detected by the X-ray telescope (XRT). GRBs are accompanied by optical transients and the field of ground-based follow-up of GRBs has expanded significantly over the last few years, with rapid response instruments capable of responding to Swift triggers on timescales of minutes. To make the most efficient use of limited telescope time, follow-up astronomers need accurate positions of GRBs as soon as possible after the trigger. Additionally, information such as the X-ray light curve, is of interest when considering observing strategy. The Swift team at Leicester University have developed techniques to improve the accuracy of the GRB positions available from the XRT, and to produce science-grade X-ray light curves of GRBs. These techniques are fully automated, and are executed as soon as data are available.Comment: 4 pages, 2 figures, to appear in the proceedings of ADASS XVII (ASP Conference Series

Spectral evolution and the onset of the X-ray GRB afterglow

Based on light curves from the Swift Burst Analyser, we investigate whether a `dip' feature commonly seen in the early-time hardness ratios of Swift-XRT data could arise from the juxtaposition of the decaying prompt emission and rising afterglow. We are able to model the dip as such a feature, assuming the afterglow rises as predicted by Sari & Piran (1999). Using this model we measure the initial bulk Lorentz factor of the fireball. For a sample of 23 GRBs we find a median value of Gamma_0=225, assuming a constant-density circumburst medium; or Gamma_0=93 if we assume a wind-like medium.Comment: 4 pages, 3 figures. To appear in the proceedings of GRB 2010, Annapolis November 2010. (AIP Conference proceedings

Preconditioning Kernel Matrices

The computational and storage complexity of kernel machines presents the primary barrier to their scaling to large, modern, datasets. A common way to tackle the scalability issue is to use the conjugate gradient algorithm, which relieves the constraints on both storage (the kernel matrix need not be stored) and computation (both stochastic gradients and parallelization can be used). Even so, conjugate gradient is not without its own issues: the conditioning of kernel matrices is often such that conjugate gradients will have poor convergence in practice. Preconditioning is a common approach to alleviating this issue. Here we propose preconditioned conjugate gradients for kernel machines, and develop a broad range of preconditioners particularly useful for kernel matrices. We describe a scalable approach to both solving kernel machines and learning their hyperparameters. We show this approach is exact in the limit of iterations and outperforms state-of-the-art approximations for a given computational budget

A search for thermal X-ray signatures in Gamma-Ray Bursts I: Swift bursts with optical supernovae

The X-ray spectra of Gamma-Ray Bursts can generally be described by an absorbed power law. The landmark discovery of thermal X-ray emission in addition to the power law in the unusual GRB 060218, followed by a similar discovery in GRB 100316D, showed that during the first thousand seconds after trigger the soft X-ray spectra can be complex. Both the origin and prevalence of such spectral components still evade understanding, particularly after the discovery of thermal X-ray emission in the classical GRB 090618. Possibly most importantly, these three objects are all associated with optical supernovae, begging the question of whether the thermal X-ray components could be a result of the GRB-SN connection, possibly in the shock breakout. We therefore performed a search for blackbody components in the early Swift X-ray spectra of 11 GRBs that have or may have associated optical supernovae, accurately recovering the thermal components reported in the literature for GRBs 060218, 090618 and 100316D. We present the discovery of a cooling blackbody in GRB 101219B/SN2010ma, and in four further GRB-SNe we find an improvement in the fit with a blackbody which we deem possible blackbody candidates due to case-specific caveats. All the possible new blackbody components we report lie at the high end of the luminosity and radius distribution. GRB 101219B appears to bridge the gap between the low-luminosity and the classical GRB-SNe with thermal emission, and following the blackbody evolution we derive an expansion velocity for this source of order 0.4c. We discuss potential origins for the thermal X-ray emission in our sample, including a cocoon model which we find can accommodate the more extreme physical parameters implied by many of our model fits.Comment: 16 pages, 6 figures, accepted for MNRA

Black hole hunting in the Andromeda Galaxy

We present a new technique for identifying stellar mass black holes in low mass X-ray binaries (LMXBs), and apply it to XMM-Newton observations of M31. We examine X-ray time series variability seeking power density spectra (PDS) typical of LMXBs accreting at a low accretion rate (which we refer to as Type A PDS); these are very similar for black hole and neutron star LMXBs. Galactic neutron star LMXBs exhibit Type A PDS at low luminosities (~10^36--10^37 erg/s) while black hole LMXBs can exhibit them at luminosities >10^38 erg/s. We propose that Type A PDS are confined to luminosities below a critical fraction of the Eddington limit, $l_c$ that is constant for all LMXBs; we have examined asample of black hole and neutron star LMXBs and find they are all consistent with $l_c$ = 0.10+/-0.04 in the 0.3--10 keV band. We present luminosity and PDS data from 167 observations of X-ray binaries in M31 that provide strong support for our hypothesis. Since the theoretical maximum mass for a neutron star is \~3.1 M_Sun, we therefore assert that any LMXB that exhibits a Type A PDS at a 0.3--10 keV luminosity greater than 4 x 10^37 erg/s is likely to contain a black hole primary. We have found eleven new black hole candidates in M31 using this method. We focus on XMM-Newton observations of RX J0042.4+4112, an X-ray source in M31 and find the mass of the primary to be 7+/-2 M_Sun, if our assumptions are correct. Furthermore, RX J0042.4+4112 is consistently bright in \~40 observations made over 23 years, and is likely to be a persistently bright LMXB; by contrast all known Galactic black hole LMXBs are transient. Hence our method may be used to find black holes in known, persistently bright Galactic LMXBs and also in LMXBs in other galaxies.Comment: 6 Pages, 6 figures. To appear in the conference proceedings of "Interacting Binaries: Accretion, Evolution and Outcomes" (Cefalu, July 4-10 2004

X-ray and UV observations of V751 Cyg in an optical high state

Aims: The VY Scl system (anti-dwarf nova) V751 Cyg is examined following a claim of a super-soft spectrum in the optical low state. Methods: A serendipitous XMM-Newton X-ray observation and, 21 months later, Swift X-ray and UV observations, have provided the best such data on this source so far. These optical high-state datasets are used to study the flux and spectral variability of V751 Cyg. Results: Both the XMM-Newton and Swift data show evidence for modulation of the X-rays for the first time at the known 3.467 hr orbital period of V751 Cyg. In two Swift observations, taken ten days apart, the mean X-ray flux remained unchanged, while the UV source brightened by half a magnitude. The X-ray spectrum was not super-soft during the optical high state, but rather due to multi-temperature optically thin emission, with significant (10^{21-22} cm^-2) absorption, which was higher in the observation by Swift than that of XMM-Newton. The X-ray flux is harder at orbital minimum, suggesting that the modulation is related to absorption, perhaps linked to the azimuthally asymmetric wind absorption seen previously in H-alpha.Comment: 6 pages, 9 figures, accepted for publication in A&

Implementing vertex dynamics models of cell populations in biology within a consistent computational framework

The dynamic behaviour of epithelial cell sheets plays a central role during development, growth, disease and wound healing. These processes occur as a result of cell adhesion, migration, division, differentiation and death, and involve multiple processes acting at the cellular and molecular level. Computational models offer a useful means by which to investigate and test hypotheses about these processes, and have played a key role in the study of cell–cell interactions. However, the necessarily complex nature of such models means that it is difficult to make accurate comparison between different models, since it is often impossible to distinguish between differences in behaviour that are due to the underlying model assumptions, and those due to differences in the in silico implementation of the model. In this work, an approach is described for the implementation of vertex dynamics models, a discrete approach that represents each cell by a polygon (or polyhedron) whose vertices may move in response to forces. The implementation is undertaken in a consistent manner within a single open source computational framework, Chaste, which comprises fully tested, industrial-grade software that has been developed using an agile approach. This framework allows one to easily change assumptions regarding force generation and cell rearrangement processes within these models. The versatility and generality of this framework is illustrated using a number of biological examples. In each case we provide full details of all technical aspects of our model implementations, and in some cases provide extensions to make the models more generally applicable

Pragmatic Ontology Evolution: Reconciling User Requirements and Application Performance

Increasingly, organizations are adopting ontologies to describe their large catalogues of items. These ontologies need to evolve regularly in response to changes in the domain and the emergence of new requirements. An important step of this process is the selection of candidate concepts to include in the new version of the ontology. This operation needs to take into account a variety of factors and in particular reconcile user requirements and application performance. Current ontology evolution methods focus either on ranking concepts according to their relevance or on preserving compatibility with existing applications. However, they do not take in consideration the impact of the ontology evolution process on the performance of computational tasks – e.g., in this work we focus on instance tagging, similarity computation, generation of recommendations, and data clustering. In this paper, we propose the Pragmatic Ontology Evolution (POE) framework, a novel approach for selecting from a group of candidates a set of concepts able to produce a new version of a given ontology that i) is consistent with the a set of user requirements (e.g., max number of concepts in the ontology), ii) is parametrised with respect to a number of dimensions (e.g., topological considerations), and iii) effectively supports relevant computational tasks. Our approach also supports users in navigating the space of possible solutions by showing how certain choices, such as limiting the number of concepts or privileging trendy concepts rather than historical ones, would reflect on the application performance. An evaluation of POE on the real-world scenario of the evolving Springer Nature taxonomy for editorial classification yielded excellent results, demonstrating a significant improvement over alternative approaches

A-STAR: The All-Sky Transient Astrophysics Reporter

The small mission A-STAR (All-Sky Transient Astrophysics Reporter) aims to locate the X-ray counterparts to ALIGO and other gravitational wave detector sources, to study the poorly-understood low luminosity gamma-ray bursts, and to find a wide variety of transient high-energy source types, A-STAR will survey the entire available sky twice per 24 hours. The payload consists of a coded mask instrument, Owl, operating in the novel low energy band 4-150 keV, and a sensitive wide-field focussing soft X-ray instrument, Lobster, working over 0.15-5 keV. A-STAR will trigger on ~100 GRBs/yr, rapidly distributing their locations.Comment: Accepted for the European Astronomical Society Publications Series: Proceedings of the Fall 2012 Gamma-Ray Burst Symposium held in Marbella, Spain, 8-12 Oct 201