Painting with starlight : optical techniques for the high-contrast imaging of exoplanets

This thesis describes the development and validation of new high-contrast imaging techniques, with the ultimate goal of enabling the next generation of instruments for ELT-class telescopes to directly image Earth-like extra-solar planets orbiting around nearby stars. In particular, we focus on developing new focal-plane wavefront sensing techniques and liquid crystal optics to achieve high-precision adaptive optics control which is capable of stabilising the entire instrument. We demonstrate that one such hybrid optical concept, the coronagraphic Modal Wavefront Sensor (cMWS), is capable of providing real-time, broadband (500-900 nm) control of non-common path aberrations during on-sky observation. We also demonstrate via both realistic simulations and laboratory testing that the focal-plane sensing technique of “Fast and Furious” phase diversity provides a robust, software-only solution to unforeseen, performance-limiting wavefront control issues such as the low-wind effect seen in the SPHERE instrument at the VLT. Lastly, we characterise the extinction profile of the VLT-SPHERE-IRDIS apodised Lyot coronagraph using observations of the minor planet Ceres, and use this to devise a calibration scheme which optimises the accuracy with which polarised signals from the innermost regions of protoplanetary disks may be retrieved.Nederlandse Onderzoekschool Voor Astronomie (NOVA)Stars and planetary system

Spatial and temporal scaling of sub-daily extreme rainfall for data sparse places

Global efforts to upgrade water, drainage, and sanitation services are hampered by hydrometeorological data-scarcity plus uncertainty about climate change. Intensity–duration–frequency (IDF) tables are used routinely to design water infrastructure so offer an entry point for adapting engineering standards. This paper begins with a novel procedure for guiding downscaling predictor variable selection for heavy rainfall simulation using media reports of pluvial flooding. We then present a three-step workflow to: (1) spatially downscale daily rainfall from grid-to-point resolutions; (2) temporally scale from daily series to sub-daily extreme rainfalls and; (3) test methods of temporal scaling of extreme rainfalls within Regional Climate Model (RCM) simulations under changed climate conditions. Critically, we compare the methods of moments and of parameters for temporal scaling annual maximum series of daily rainfall into sub-daily extreme rainfalls, whilst accounting for rainfall intermittency. The methods are applied to Kampala, Uganda and Kisumu, Kenya using the Statistical Downscaling Model (SDSM), two RCM simulations covering East Africa (CP4 and P25), and in hybrid form (RCM-SDSM). We demonstrate that Gumbel parameters (and IDF tables) can be reliably scaled to durations of 3 h within observations and RCMs. Our hybrid RCM-SDSM scaling reduces errors in IDF estimates for the present climate when compared with direct RCM output. Credible parameter scaling relationships are also found within RCM simulations under changed climate conditions. We then discuss the practical aspects of applying such workflows to other city-regions

Spatial linear dark field control and holographic modal wavefront sensing with a vAPP coronagraph on MagAO-X

The Magellan Extreme Adaptive Optics (MagAO-X) Instrument is an extreme AO system coming online at the end of 2019 that will be operating within the visible and near-IR. With state-of-the-art wavefront sensing and coronagraphy, MagAO-X will be optimized for high-contrast direct exoplanet imaging at challenging visible wavelengths, particularly Hα. To enable high-contrast imaging, the instrument hosts a vector apodizing phase plate (vAPP) coronagraph. The vAPP creates a static region of high contrast next to the star that is referred to as a dark hole; on MagAO-X, the expected dark hole raw contrast is ∼4  ×  10  −  6. The ability to maintain this contrast during observations, however, is limited by the presence of non-common path aberrations (NCPA) and the resulting quasi-static speckles that remain unsensed and uncorrected by the primary AO system. These quasi-static speckles within the dark hole degrade the high contrast achieved by the vAPP and dominate the light from an exoplanet. The aim of our efforts here is to demonstrate two focal plane wavefront sensing (FPWFS) techniques for sensing NCPA and suppressing quasi-static speckles in the final focal plane. To sense NCPA to which the primary AO system is blind, the science image is used as a secondary wavefront sensor. With the vAPP, a static high-contrast dark hole is created on one side of the PSF, leaving the opposite side of the PSF unocculted. In this unobscured region, referred to as the bright field, the relationship between modulations in intensity and low-amplitude pupil plane phase aberrations can be approximated as linear. The bright field can therefore be used as a linear wavefront sensor to detect small NCPA and suppress quasi-static speckles. This technique, known as spatial linear dark field control (LDFC), can monitor the bright field for aberrations that will degrade the high-contrast dark hole. A second form of FPWFS, known as holographic modal wavefront sensing (hMWFS), is also employed with the vAPP. This technique uses hologram-generated PSFs in the science image to monitor the presence of low-order aberrations. With LDFC and the hMWFS, high contrast across the dark hole can be maintained over long observations, thereby allowing planet light to remain visible above the stellar noise over the course of observations on MagAO-X. Here, we present simulations and laboratory demonstrations of both spatial LDFC and the hMWFS with a vAPP coronagraph at the University of Arizona Extreme Wavefront Control Laboratory. We show both in simulation and in the lab that the hMWFS can be used to sense low-order aberrations and reduce the wavefront error (WFE) by a factor of 3  −  4  ×  . We also show in simulation that, in the presence of a temporally evolving pupil plane phase aberration with 27-nm root-mean-square (RMS) WFE, LDFC can reduce the WFE to 18-nm RMS, resulting in factor of 6 to 10 gain in contrast that is kept stable over time. This performance is also verified in the lab, showing that LDFC is capable of returning the dark hole to the average contrast expected under ideal lab conditions. These results demonstrate the power of the hMWFS and spatial LDFC to improve MagAO-X’s high-contrast imaging capabilities for direct exoplanet imaging.Instrumentatio

Vector-apodizing phase plate coronagraph: design, current performance, and future development [Invited]

Instrumentatio

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Painting with starlight : optical techniques for the high-contrast imaging of exoplanets

This thesis describes the development and validation of new high-contrast imaging techniques, with the ultimate goal of enabling the next generation of instruments for ELT-class telescopes to directly image Earth-like extra-solar planets orbiting around nearby stars. In particular, we focus on developing new focal-plane wavefront sensing techniques and liquid crystal optics to achieve high-precision adaptive optics control which is capable of stabilising the entire instrument. We demonstrate that one such hybrid optical concept, the coronagraphic Modal Wavefront Sensor (cMWS), is capable of providing real-time, broadband (500-900 nm) control of non-common path aberrations during on-sky observation. We also demonstrate via both realistic simulations and laboratory testing that the focal-plane sensing technique of “Fast and Furious” phase diversity provides a robust, software-only solution to unforeseen, performance-limiting wavefront control issues such as the low-wind effect seen in the SPHERE instrument at the VLT. Lastly, we characterise the extinction profile of the VLT-SPHERE-IRDIS apodised Lyot coronagraph using observations of the minor planet Ceres, and use this to devise a calibration scheme which optimises the accuracy with which polarised signals from the innermost regions of protoplanetary disks may be retrieved.</p

Changing water temperatures: a surface water archive for England and Wales

The temperature of water in lakes, rivers and streams has a fundamental influence on aquatic organisms, ecological processes and the potency of many pollutants. We expect water temperature in the UK to increase under projected climate change, but rtes and spatial variation of change remain unclear for inland waters. It is also unclear how we might manage land and river flow regimes to modify river temperature where this may be desirable, for example, to protect fish from lethal temperatures. Although water temperature broadly correlates with air temperature, the drivers of surface water temperature involve dynamic heat (energy) exchanges at the water surface and river bed and complex hydrological fluxes. To date, published reports of water temperature change in British rivers have been based on a limited number of sites: these have provided useful monitoring data on the thermal processes of rivers but rather less about the thermal regime of rivers. Our understanding of river thermal spatio-temporal variability and processes remains incomplete. In part, this has been related to a lack of long-term data across a range of different environments. The Environment Agency has recently created a surface water temperature archive for England and Wales based on measurements at over 30 000 sites, with observations extending back to between <5 and 30 years. The archive is being used to assess post-1990 trends in water temperature across England and Wales. Here, we briefly describe the archive and its potential uses. We present preliminary observations of the variation in river water temperature across England and Wales and the changing relationship between water and air temperatures at and between sites. We also illustrate the potential for exploring ecological response to changes in water temperature