Disciplining Innovations

The editors of the 'Disciplining Innovations' issue introduce the theme

The Impact of Accretion Disk Winds on the Optical Spectra of Cataclysmic Variables

Many high-state non-magnetic cataclysmic variables (CVs) exhibit blue-shifted absorption or P-Cygni profiles associated with ultraviolet (UV) resonance lines. These features imply the existence of powerful accretion disk winds in CVs. Here, we use our Monte Carlo ionization and radiative transfer code to investigate whether disk wind models that produce realistic UV line profiles are also likely to generate observationally significant recombination line and continuum emission in the optical waveband. We also test whether outflows may be responsible for the single-peaked emission line profiles often seen in high-state CVs and for the weakness of the Balmer absorption edge (relative to simple models of optically thick accretion disks). We find that a standard disk wind model that is successful in reproducing the UV spectra of CVs also leaves a noticeable imprint on the optical spectrum, particularly for systems viewed at high inclination. The strongest optical wind-formed recombination lines are H$\alpha$ and He II $\lambda4686$. We demonstrate that a higher-density outflow model produces all the expected H and He lines and produces a recombination continuum that can fill in the Balmer jump at high inclinations. This model displays reasonable verisimilitude with the optical spectrum of RW Trianguli. No single-peaked emission is seen, although we observe a narrowing of the double-peaked emission lines from the base of the wind. Finally, we show that even denser models can produce a single-peaked H$\alpha$ line. On the basis of our results, we suggest that winds can modify, and perhaps even dominate, the line and continuum emission from CVs.Comment: 15 pages, 13 figures. Accepted to MNRA

Line-driven Disk Winds in Active Galactic Nuclei: The Critical Importance of Ionization and Radiative Transfer

Accretion disk winds are thought to produce many of the characteristic features seen in the spectra of active galactic nuclei (AGN) and quasi-stellar objects (QSOs). These outflows also represent a natural form of feedback between the central supermassive black hole and its host galaxy. The mechanism for driving this mass loss remains unknown, although radiation pressure mediated by spectral lines is a leading candidate. Here, we calculate the ionization state of, and emergent spectra for, the hydrodynamic simulation of a line-driven disk wind previously presented by Proga & Kallman (2004). To achieve this, we carry out a comprehensive Monte Carlo simulation of the radiative transfer through, and energy exchange within, the predicted outflow. We find that the wind is much more ionized than originally estimated. This is in part because it is much more difficult to shield any wind regions effectively when the outflow itself is allowed to reprocess and redirect ionizing photons. As a result, the calculated spectrum that would be observed from this particular outflow solution would not contain the ultraviolet spectral lines that are observed in many AGN/QSOs. Furthermore, the wind is so highly ionized that line-driving would not actually be efficient. This does not necessarily mean that line-driven winds are not viable. However, our work does illustrate that in order to arrive at a self-consistent model of line-driven disk winds in AGN/QSO, it will be critical to include a more detailed treatment of radiative transfer and ionization in the next generation of hydrodynamic simulations.Comment: 13 pages, 10 figures - Accepted for publication in Ap

Haptic-assisted interactive molecular docking incorporating receptor flexibility

Haptic-assisted interactive docking tools immerse the user in an environment where intuition and knowledge can be used to help guide the docking process. Here we present such a tool where the user “holds” a rigid ligand via a haptic device through which they feel interaction forces with a flexible receptor biomolecule. To ensure forces transmitted through the haptic device are smooth and stable, they must be updated at a rate greater than 500 Hz. Due to this time constraint, the majority of haptic docking tools do not attempt to model the conformational changes that would occur when molecules interact during binding. Our haptic-assisted docking tool, “Haptimol Flexidock”, models a receptor’s conformational response to forces of interaction with a ligand whilst maintaining the required haptic refresh rate. In order to model receptor flexibility we use the method of linear response for which we determine the variance-covariance matrix of atomic fluctuations from the trajectory of an explicit-solvent Molecular Dynamics simulation of the ligand-free receptor molecule. Key to satisfying the time constraint is an eigenvector decomposition of the variance-covariance matrix which enables a good approximation to the conformational response of the receptor to be calculated rapidly. This exploits a feature of protein dynamics whereby most fluctuation occurs within a relatively small subspace. The method is demonstrated on Glutamine Binding Protein in interaction with glutamine, and Maltose Binding Protein in interaction with maltose. For both proteins, the movement that occurs when the ligand is docked near to its binding site matches the experimentally determined movement well. It is thought that this tool will be particularly useful for structure-based drug design

High quality rendering of protein dynamics in space filling mode

Producing high quality depictions of molecular structures has been an area of academic interest for years, with visualisation tools such as UCSF Chimera, Yasara and PyMol providing a huge number of different rendering modes and lighting effects. However, no visualisation program supports per-pixel lighting effects with shadows whilst rendering a molecular trajectory in space filling mode. In this paper, a new approach to rendering high quality visualisations of molecular trajectories is presented. To enhance depth, ambient occlusion is included within the render. Shadows are also included to help the user perceive relative motions of parts of the protein as they move based on their trajectories. Our approach requires a regular grid to be constructed every time the molecular structure deforms allowing per-pixel lighting effects and ambient occlusion to be rendered every frame, at interactive refresh rates. Two different regular grids are investigated, a fixed grid and a memory efficient compact grid. The algorithms used allow trajectories of proteins comprising of up to 300,000 atoms in size to be rendered at ninety frames per second on a desktop computer using the GPU for general purpose computations. Regular grid construction was found to only take up a small proportion of the total time to render a frame. It was found that despite being slower to construct, the memory efficient compact grid outperformed the theoretically faster fixed grid when the protein being rendered is large, owing to its more efficient memory access patterns. The techniques described could be implemented in other molecular rendering software

Camouflage assessment:Machine and human

A vision model is designed using low-level vision principles so that it can perform as a human observer model for camouflage assessment. In a camouflaged-object assessment task, using military patterns in an outdoor environment, human performance at detection and recognition is compared with the human observer model. This involved field data acquisition and subsequent image calibration, a human experiment, and the design of the vision model. Human and machine performance, at recognition and detection, of military patterns in two environments was found to correlate highly. Our model offers an inexpensive, automated, and objective method for the assessment of camouflage where it is impractical, or too expensive, to use human observers to evaluate the conspicuity of a large number of candidate patterns. Furthermore, the method should generalize to the assessment of visual conspicuity in non-military contexts.</p

The luminosity dependence of thermally-driven disc winds in low-mass X-ray binaries

We have carried out radiation-hydrodynamic simulations of thermally-driven accretion disc winds in low-mass X-ray binaries. Our main goal is to study the luminosity dependence of these outflows and compare with observations. The simulations span the range $\rm{0.04 \leq L_{acc}/L_{Edd} \leq 1.0}$ and therefore cover most of the parameter space in which disc winds have been observed. Using a detailed Monte Carlo treatment of ionization and radiative transfer, we confirm two key results found in earlier simulations that were carried out in the optically thin limit: (i) the wind velocity -- and hence the maximum blueshift seen in wind-formed absorption lines -- increases with luminosity; (ii) the large-scale wind geometry is quasi-spherical, but observable absorption features are preferentially produced along high-column equatorial sightlines. In addition, we find that (iii) the wind efficiency always remains approximately constant at $\rm{\dot{M}_{wind}/\dot{M}_{acc} \simeq 2}$, a behaviour that is consistent with observations. We also present synthetic Fe XXV and Fe XXVI absorption line profiles for our simulated disc winds in order to illustrate the observational implications of our results.Comment: Accepted for publication in MNRA

Mining social media to identify heat waves

Heat waves are one of the deadliest of natural hazards and their frequency and intensity will likely increase as the climate continues to warm. A challenge in studying these phenomena is the lack of a universally accepted quantitative definition that captures both temperature anomalies and associated mortality. We test the hypothesis that social media mining can be used to identify heat wave mortality. Applying the approach to India, we find that the number of heat-related tweets correlates with heat-related mortality much better than traditional climate-based indicators, especially at larger scales, which identify many heat wave days that do not lead to excess mortality. We conclude that social media based heat wave identification can complement climatic data and can be used to: (1) study heat wave impacts at large scales or in developing countries, where mortality data are difficult to obtain and uncertain, and (2) to track dangerous heat wave events in real time

The Effectiveness of the KiVa Bullying Prevention Program in Wales, UK: Results from a Pragmatic Cluster Randomized Controlled Trial

AbstractThe study evaluated the implementation fidelity and effectiveness of KiVa, an evidence-based program that aims to prevent and address bullying in schools, with a particular emphasis on changing the role of bystanders. The study was a two-arm waitlist control cluster randomized controlled trial in which 22 primary schools (clusters) (N = 3214 students aged 7–11) were allocated using a 1:1 ratio to intervention (KiVa; 11 clusters, n = 1588 students) and a waitlist control (usual school provision; 11 clusters, n = 1892 children)). The trial statistician (but not schools or researchers) remained blind to allocation status. The outcomes were as follows: student-reported victimization (primary outcome) and bullying perpetration; teacher-reported child behavior and emotional well-being; and school absenteeism (administrative records). Implementation fidelity was measured using teacher-completed online records (for class lessons) and independent researcher observations (for school-wide elements). Outcome analyses involved 11 intervention schools (n = 1578 children) and 10 control schools (n = 1636 children). There was no statistically significant effect on the primary outcome of child-reported victimization (adjusted intervention/control OR 0.76; 95% CI 0.55 to 1.06; p = 0.11) or on the secondary outcomes. The impact on victimization was not moderated by child gender, age, or victimization status at baseline. Lesson adherence was good but exposure (lesson length) was lower than the recommended amount, and there was considerable variability in the implementation of whole school elements. The trial found insufficient evidence to conclude that KiVa had an effect on the primary outcome. A larger trial of KiVa in the UK is warranted, however, with attention to issues regarding implementation fidelity. Trial registration: Current Controlled Trials ISRCTN23999021 Date 10-6-13</jats:p