Protoplanetary disc evolution and dispersal

In this thesis I have studied how discs around young stars evolve and disperse. In particular, I build models which combine viscous evolution with photoevaporation, as previous work suggests that photoevaporation can reproduce the observed disc evolution and dispersal time-scales. The main question this thesis attempts to address is: Can photoevaporation provide a dominant dispersal mechanism for the observed population of young stars? Photoevaporation arises from the heating that high energy (UV and X-ray) photons provide to the surface layers of a disc. Before I started this work, only photoevaporation from a pure EUV radiation field was described within a hydrodynamic framework. Therefore, I start by building a hydrodynamic solution to the pure X-ray photoevaporation problem, and then extend this solution to the entire high energy spectrum. This hydrodynamic model leads me to conclude that it is the X-ray radiation field that sets the mass-loss rates. These mass-loss rates scale linearly with X-ray luminosity, are independent of the underlying disc structure and explicitly independent of stellar mass. I build a radiation-hydrodynamic algorithm, based on previous work, to describe the process of X-ray heating in discs. I then use this algorithm to span the full range of observed parameter space, to fully solve the X-ray photoevaporation problem. I further extend the algorithm to roughly approximate the heating an FUV radiation field would have on the photoevaporative flow, as well as separately testing the effect an EUV radiation field will have. These numerical tests are in agreement with the hydrodynamic model derived. Specifically, it is the X-rays that are driving the photoevaporative flow from the inner disc. Armed with an accurate description of the photoevaporative mass-loss rates from young stars, I consider the evolution of a population of disc-bearing, young ($0.7$\msun) stars, in order to asses photoevaporation's role as a dispersal mechanism. This study shows that the observed spread in X-ray luminosity of young stars is sufficient to drive the dispersal of the entire population of discs, reproducing both the required time-scales and the required spread in observables (disc lifetime, accretion rate). I also show that a large fraction of the observed population of `transition' discs are consistent with being created through photoevaporation. Having shown photoevaporation can provide a dominant dispersal mechanism for a population of discs, I attempt to describe some direct observable consequences of photoevaporation, both through gas tracers and dust emission. During this work, the first direct evidence of a photoevaporative flow emerging from a young star was obtained from TW Hya, in the NeII 12.8$\mu$m line. Therefore, I discuss this result within the framework of the X-ray photoevaporation model. Furthermore, I suggest that emission from the photoevaporative flow is the origin of the unexplained, blue-shifted, OI 6300\AA~ line observed around all young stars that possess discs. I then described the properties of the dust particles that may be entrained within the photoevaporative flow. The total dust mass in the flow is found to be small compared to the disc, although such a region becomes observable once the disc presents as edge-on, obscuring the central star and hot inner disc. I discuss the emission from these regions and compare them to the sample of currently imaged edge-on discs. The presented photoevaporation model reproduces all of the current observations, and I discuss some predictions it makes with regard to future observations. Finally, photoevporation may have some intriguing consequences on planet formation and dust evolution that warrant further investigation

Nonlinear acoustics in a viscothermal boundary layer over an acoustic lining

Sound within aircraft engines can be 120dB-160dB, pushing the validity of linearized governing equations. Moreover, some components of sound within a visco-thermal mean flow boundary layer over an acoustic lining may be amplified by a factor of ~100 (~40dB) in a typical aircraft engine compared with the sound outside the boundary layer, which may be expected to trigger nonlinear effects within the boundary layer. This is in addition to the well-known nonlinear effects within the holes of the perforated lining facing sheet. This paper presents a mathematical investigation into the effects of weak nonlinearity on the acoustics within a thin parallel mean flow boundary layer in flow over an acoustic lining in a cylindrical duct. (This is the first investigation of nonlinear acoustics in a boundary layer flow over a non-rigid surface, to our knowledge.) The analysis combines the effects of sheared mean flow, viscosity, and nonlinearity into an effective impedance boundary condition. In certain cases, a surprisingly large acoustic streaming effect is found that escapes the mean flow boundary layer and pervades well out into the interior of the duct

Unsupervised categorisation and cross-classification in humans and rats

This thesis examines how stimulus similarity structure and the statistical properties of the environment influence human and nonhuman animal categorisation. Two aspects of categorisation behaviour are explored: unsupervised (spontaneous) categorisation and stimulus cross-classification. In my General Introduction, I raise the issue of the respective roles of similarity and the classifier in determining categorisation behaviour. In Chapter 1, I review previous laboratory-based unsupervised categorisation research, which shows an overwhelming bias for unsupervised classification based on a single feature. Given the prominent role of overall similarity (family resemblance) in theories of human conceptual structure, I argue that this bias for unidimensional classification is likely an artefact. One factor in producing this artefact, I suggest, are the biases that exist within the similarity structure of laboratory stimuli. Consequently, Chapter 2 examines if it is possible to predict unidimensional versus multidimensional classification based solely on abstract similarity structure. Results show that abstract similarity structure commands a strong influence over participants' unsupervised classification behaviour (although not always in the manner predicted), and a bias for multidimensional unsupervised classification is reported. In Chapter 3, I examine unsupervised categorisation more broadly, by investigating how stimulus similarity structure influences spontaneous classification in both humans and rats. In this way, evidence is sought for human-like spontaneous classification behaviour in rats. Results show that humans and rats show qualitatively different patterns of behaviour following incidental stimulus exposure that should encourage spontaneous classification. In Chapter 4,1 investigate whether rats exhibit another important aspect of human categorisation namely, stimulus cross-classification. Results show that the statistical properties of the environment can engender such cognitively flexible behaviour in rats. Overall, the results of this thesis document the important influence of stimulus similarity structure and the statistical properties of the environment on human and nonhuman animal behaviour

Combining stage specificity and metabolomic profiling to advance antimalarial drug discovery

We report detailed susceptibility profiling of asexual blood stages of the malaria parasite Plasmodium falciparum to clinical and experimental antimalarials, combined with metabolomic fingerprinting. Results revealed a variety of stage-specific and metabolic profiles that differentiated the modes of action of clinical antimalarials including chloroquine, piperaquine, lumefantrine, and mefloquine, and identified late trophozoite-specific peak activity and stage-specific biphasic dose-responses for the mitochondrial inhibitors DSM265 and atovaquone. We also identified experimental antimalarials hitting previously unexplored druggable pathways as reflected by their unique stage specificity and/or metabolic profiles. These included several ring-active compounds, ones affecting hemoglobin catabolism through distinct pathways, and mitochondrial inhibitors with lower propensities for resistance than either DSM265 or atovaquone. This approach, also applicable to other microbes that undergo multiple differentiation steps, provides an effective tool to prioritize compounds for further development within the context of combination therapies

Development of a novel antimicrobial-releasing glass ionomer cement functionalized with chlorhexidine hexametaphosphate nanoparticles

BACKGROUND: Glass ionomer cements (GICs) are a class of dental biomaterials. They have a wide range of uses including permanent restorations (fillings), cavity linings, fissure sealants and adhesives. One of the most common reasons for replacing a dental restoration is recurrent bacterial tooth decay around the margins of the biomaterial. Therefore, a dental biomaterial which creates a sustained antimicrobial environment around the restoration would be of considerable clinical benefit. In this manuscript, the formulation of a GIC containing novel antimicrobial nanoparticles composed of chlorhexidine hexametaphosphate at 1, 2, 5, 10 and 20% powder substitution by mass is reported. The aim is to create GICs which contain chlorhexidine-hexametaphosphate nanoparticles and characterize the nanoparticle size, morphology and charge and the release of chlorhexidine and fluoride, tensile strength and morphology of the GICs. RESULTS: The GICs released chlorhexidine, which is a broad spectrum antimicrobial agent effective against a wide range of oral bacteria, over the duration of the experiment in a dose-dependent manner. This was not at the expense of other properties; fluoride release was not significantly affected by the substitution of antimicrobial nanoparticles in most formulations and internal structure appeared unaffected up to and including 10% substitution. Diametral tensile strength decreased numerically with substitutions of 10 and 20% nanoparticles but this difference was not statistically significant. CONCLUSION: A series of GICs functionalized with chlorhexidine-hexametaphosphate nanoparticles were created for the first time. These released chlorhexidine in a dose-dependent manner. These materials may find application in the development of a new generation of antimicrobial dental nanomaterials

Upward revision of global fossil fuel methane emissions based on isotope database

Methane has the second-largest global radiative forcing impact of anthropogenic greenhouse gases after carbon dioxide, but our understanding of the global atmospheric methane budget is incomplete. The global fossil fuel industry (production and usage of natural gas, oil and coal) is thought to contribute 15 to 22 per cent of methane emissions to the total atmospheric methane budget. However, questions remain regarding methane emission trends as a result of fossil fuel industrial activity and the contribution to total methane emissions of sources from the fossil fuel industry and from natural geological seepage, which are often co-located. Here we re-evaluate the global methane budget and the contribution of the fossil fuel industry to methane emissions based on long-term global methane and methane carbon isotope records. We compile the largest isotopic methane source signature database so far, including fossil fuel, microbial and biomass-burning methane emission sources. We find that total fossil fuel methane emissions (fossil fuel industry plus natural geological seepage) are not increasing over time, but are 60 to 110 per cent greater than current estimates owing to large revisions in isotope source signatures. We show that this is consistent with the observed global latitudinal methane gradient. After accounting for natural geological methane seepage, we find that methane emissions from natural gas, oil and coal production and their usage are 20 to 60 per cent greater than inventories. Our findings imply a greater potential for the fossil fuel industry to mitigate anthropogenic climate forcing, but we also find that methane emissions from natural gas as a fraction of production have declined from approximately 8 per cent to approximately 2 per cent over the past three decades.Published88-916A. Geochimica per l'ambienteJCR Journa

Accelerating slip rates on the Puente Hills blind thrust fault system beneath metropolitan Los Angeles, California, USA

Slip rates represent the average displacement across a fault over time and are essential to estimating earthquake recurrence for probabilistic seismic hazard assessments. We demonstrate that the slip rate on the western segment of the Puente Hills blind thrust fault system, which is beneath downtown Los Angeles, California (USA), has accelerated from ∼0.22 mm/yr in the late Pleistocene to ∼1.33 mm/yr in the Holocene. Our analysis is based on syntectonic strata derived from the Los Angeles River, which has continuously buried a fold scarp above the blind thrust. Slip on the fault beneath our field site began during the late-middle Pleistocene and progressively increased into the Holocene. This increase in rate implies that the magnitudes and/or the frequency of earthquakes on this fault segment have increased over time. This challenges the characteristic earthquake model and presents an evolving and potentially increasing seismic hazard to metropolitan Los Angeles

Teagasc submission made in response to the Consultation Paper on Interim Review of Ireland’s Nitrates Derogation 2019

Teagasc SubmissionSubmission to governmentThis submission was made in response to the consultation process run jointly by the Department of Housing, Planning, Community and Local Government (DHPCLG) and the Department of Agriculture, Food and the Marine (DAFM) inviting views and comments on proposals for the Interim Review of Ireland’s Nitrates Derogation Programme in 2019. It has been prepared by Teagasc’s Water Quality Working Group in consultation with the Gaseous Emissions Working Group. These working groups have members drawn from both the Knowledge Transfer and Research Directorates of Teagasc. It was prepared following consultation with colleagues across Teagasc using their collective knowledge and expertise in agri-environmental science and practice and the implementation of the Good Agricultural Practice (GAP) and Nitrates Derogation Regulations.https://www.teagasc.ie/publications/2019/teagasc-submission-made-in-response-to-the-consultation-paper-on-interim-review-of-irelands-nitrates-derogation-2019.ph

The Multi-Object, Fiber-Fed Spectrographs for SDSS and the Baryon Oscillation Spectroscopic Survey

We present the design and performance of the multi-object fiber spectrographs for the Sloan Digital Sky Survey (SDSS) and their upgrade for the Baryon Oscillation Spectroscopic Survey (BOSS). Originally commissioned in Fall 1999 on the 2.5-m aperture Sloan Telescope at Apache Point Observatory, the spectrographs produced more than 1.5 million spectra for the SDSS and SDSS-II surveys, enabling a wide variety of Galactic and extra-galactic science including the first observation of baryon acoustic oscillations in 2005. The spectrographs were upgraded in 2009 and are currently in use for BOSS, the flagship survey of the third-generation SDSS-III project. BOSS will measure redshifts of 1.35 million massive galaxies to redshift 0.7 and Lyman-alpha absorption of 160,000 high redshift quasars over 10,000 square degrees of sky, making percent level measurements of the absolute cosmic distance scale of the Universe and placing tight constraints on the equation of state of dark energy. The twin multi-object fiber spectrographs utilize a simple optical layout with reflective collimators, gratings, all-refractive cameras, and state-of-the-art CCD detectors to produce hundreds of spectra simultaneously in two channels over a bandpass covering the near ultraviolet to the near infrared, with a resolving power R = \lambda/FWHM ~ 2000. Building on proven heritage, the spectrographs were upgraded for BOSS with volume-phase holographic gratings and modern CCD detectors, improving the peak throughput by nearly a factor of two, extending the bandpass to cover 360 < \lambda < 1000 nm, and increasing the number of fibers from 640 to 1000 per exposure. In this paper we describe the original SDSS spectrograph design and the upgrades implemented for BOSS, and document the predicted and measured performances.Comment: 43 pages, 42 figures, revised according to referee report and accepted by AJ. Provides background for the instrument responsible for SDSS and BOSS spectra. 4th in a series of survey technical papers released in Summer 2012, including arXiv:1207.7137 (DR9), arXiv:1207.7326 (Spectral Classification), and arXiv:1208.0022 (BOSS Overview