Polarisation Coherence Imaging of Electric and Magnetic Fields in Plasmas

Polarisation coherence imaging is a powerful spectroscopic diagnostic for high spatial resolution measurements of strong electric and/or magnetic fields inside high temperature fusion plasmas. The motional Stark effect (MSE) is the principal application for the technique, involving measurement of the Balmer-α polarised emission from high velocity neutral beam atoms subjected to a strong vxB electric field. The research in this thesis examines all aspects of polarisation coherence imaging including: the atomic physics of the Stark-Zeeman split light emission; the optical physics and measurement principles involved in the technique; and experimental measurements on the DIII-D tokamak and H-1 heliac. The polarisation properties of single electron atoms in crossed electric and magnetic fields are revealed to be more complex than previously recognised due to the remaining degeneracy in the Stark-Zeeman energy levels and the absence of a well-defined magnetic quantum number. A linear perturbation theory analysis finds distinct polarisation structures for the σ emission that apply when the fine-structure of the atom and microscopic electric fields are considered. Only the σ±1 polarisation orientation is sensitive to upper-state populations, which are known to be non-statistical for MSE beam-into-gas calibrations, however with appropriate viewing geometries and neutral beam injection directions the effect can be made negligible. Similarly beam-into-gas calibrations of the σ±1:π±3 line intensity ratio are found to be sensitive to upper-state populations and are therefore potentially invalid. Equations for the linear and circular polarisation of each Balmer-α transition are formulated, correct to second order in the Zeeman:Stark splitting ratio, for straightforward interpretation of the Stokes parameters. Calculations reveal the net circular polarisation fraction for the π±3 and π±4 emission is ~20% for typical beam energies. Various imaging polarimeter designs exist and their different advantages and calibration challenges are examined. Some imaging MSE strategies encode the Stark-Zeeman circular polarisation at the same spatial frequency as the linear polarisation, however fortunately it is established that the interferometric delay can be tuned to mitigate the circular polarisation signal without severely reducing the linear polarisation signal. A newly developed non-axial ray model is capable of predicting and characterising additional spatial carriers generated by a sequence of displacer waveplates. An imaging MSE diagnostic was benchmarked against existing conventional MSE polarimeters on DIII-D and delivered new capabilities for measuring the magnetic pitch angle from 2 neutral beams and on the high field side of DIII-D. The imaging measurements from each neutral beam were self-consistent and good agreement was demonstrated with conventional MSE measurements for shots with magnetic field and plasma current in the standard direction, however the agreement is lost for shots with either reversed field or current direction. An analysis of the magnetic axis position independently measured with the conventional MSE, imaging MSE, electron cyclotron emission and magnetics is presented to elucidate differences between the MSE measurements. The ferroelectric liquid crystal waveplate used in the imaging polarimeter was discovered to have spatially non-uniform retardance, hence it is imperative for the illumination of the calibration source to replicate the ray paths of the neutral beam emission through the optical system. A systematic distortion is apparent in the images above and below the midplane, possibly due to remaining uncertainties from the Faraday rotation calibration or the illumination source dependence. Phase resolved imaging on the H-1 heliac revealed a 7MHz temporal oscillation in the light intensity that has the structure of a propagating wave. Using multiple viewing geometries and a magnetic field strength scan it was revealed that the wave characteristics are consistent with electron density perturbations produced by an electromagnetic ion cyclotron wave propagating near the last closed flux surface. The parallel velocity of the observed RF wave is comparable to the electron thermal speed suggesting that Landau damping of the wave energy to electrons drives the edge electron heating on H-1

The Sudbury Neutrino Observatory

The Sudbury Neutrino Observatory is a second generation water Cherenkov detector designed to determine whether the currently observed solar neutrino deficit is a result of neutrino oscillations. The detector is unique in its use of D2O as a detection medium, permitting it to make a solar model-independent test of the neutrino oscillation hypothesis by comparison of the charged- and neutral-current interaction rates. In this paper the physical properties, construction, and preliminary operation of the Sudbury Neutrino Observatory are described. Data and predicted operating parameters are provided whenever possible.Comment: 58 pages, 12 figures, submitted to Nucl. Inst. Meth. Uses elsart and epsf style files. For additional information about SNO see http://www.sno.phy.queensu.ca . This version has some new reference

Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.

The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here, we investigate just how prevalent is the few articles - many proteins phenomenon. We examine the experimentally validated annotation of proteins provided by several groups in the GO Consortium, and show that the distribution of proteins per published study is exponential, with 0.14% of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation. Since each of the dominant articles describes the use of an assay that can find only one function or a small group of functions, this leads to substantial biases in what we know about the function of many proteins. Mass-spectrometry, microscopy and RNAi experiments dominate high throughput experiments. Consequently, the functional information derived from these experiments is mostly of the subcellular location of proteins, and of the participation of proteins in embryonic developmental pathways. For some organisms, the information provided by different studies overlap by a large amount. We also show that the information provided by high throughput experiments is less specific than those provided by low throughput experiments. Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable. Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation data to plan experiments

Validation of collection and anaerobic fermentation techniques for measuring prebiotic impact on gut microbiota

Background: Defining the ability of prebiotic dietary carbohydrates to influence the composition and metabolism of the gut microbiota is central to defining their health impact in diverse individuals. Many clinical trials are using indirect methods. This study aimed to validate collection and fermentation methods enabling their use in the context of clinical studies. Methods and Results: Parameters tested included stool sample acquisition, storage, and growth conditions. Stool from 3 infants and 3 adults was collected and stored under varying conditions. Samples were cultured anaerobically for two days in the presence of prebiotics, whereupon optical density and pH were measured across time. Whole genome shotgun sequencing and NMR metabolomics were performed. Neither the type of collection vial (standard vial and two different BD anaerobic collection vials) nor cryopreservation (-80 °C or 4 °C) significantly influenced either microbial composition at 16 h of anaerobic culture or the principal components of the metabolome at 8 or 16 h. Metagenomic differences were driven primarily by subject, while metabolomic differences were driven by fermentation sugar (2’-fucosyllactose or dextrose). Conclusions: These data identified a feasible and valid approach for prebiotic fermentation analysis of individual samples in large clinical studies: collection of stool microbiota using standard vials; cryopreservation prior to testing; and collecting fermentation read-out at 8 and 16 hr. Thus, fermentation analysis can be a valid technique for testing the effects of prebiotics on human fecal microbiota

Motional Stark effect diagnostics for KSTAR

The motional Stark effect (MSE) diagnostic is used to measure the radial magnetic pitch-angle profile in neutral-beam-heated plasmas. The diagnostic relies upon the measurement of the polarization direction of Stark-split D-alpha emission from injected fast neutral atoms in a magnetic field. Measurements of the magnetic pitch angle are used with magnetic equilibrium reconstruction codes such as EFIT to calculate the safety factor in shaped plasmas. The MSE diagnostic is important for determining the shape of the q profile to optimize confinement and stability, and it has become a key element in high-performance tokamaks. For the purpose of achieving the high-performance operating region in the Korea Superconducting Tokamak Advanced Research KSTAR device, two types of methods are being studied. In KSTAR, a multichord PEM (photo-elastic modulator)-based MSE system is being developed, and an imaging MSE polarimetry system using the coherence imaging technique has been showing promising initial results during the last two KSTAR experimental campaigns in 2012 and 2013, respectively. In this paper, we describe the progress of the KSTAR MSE diagnostics

DIII-D research towards establishing the scientific basis for future fusion reactors

DIII-D research is addressing critical challenges in preparation for ITER and the next generation of fusion devices through focusing on plasma physics fundamentals that underpin key fusion goals, understanding the interaction of disparate core and boundary plasma physics, and developing integrated scenarios for achieving high performance fusion regimes. Fundamental investigations into fusion energy science find that anomalous dissipation of runaway electrons (RE) that arise following a disruption is likely due to interactions with RE-driven kinetic instabilities, some of which have been directly observed, opening a new avenue for RE energy dissipation using naturally excited waves. Dimensionless parameter scaling of intrinsic rotation and gyrokinetic simulations give a predicted ITER rotation profile with significant turbulence stabilization. Coherence imaging spectroscopy confirms near sonic flow throughout the divertor towards the target, which may account for the convectiondominated parallel heat flux. Core-boundary integration studies show that the small angle slot divertor achieves detachment at lower density and extends plasma cooling across the divertor target plate, which is essential for controlling heat flux and erosion. The Super H-mode regime has been extended to high plasma current (2.0 MA) and density to achieve very high pedestal pressures (~30 kPa) and stored energy (3.2 MJ) with H98y2 ≈ 1.6–2.4. In scenario work, the ITER baseline Q = 10 scenario with zero injected torque is found to have a fusion gain metric βτE independent of current between q95 = 2.8–3.7, and a lower limit of pedestal rotation for RMP ELM suppression has been found. In the wide pedestal QH-mode regime that exhibits improved performance and no ELMs, the start-up counter torque has been eliminated so that the entire discharge uses ≈0 injected torque and the operating space is more ITER-relevant. Finally, the high-βN (⩽3.8) hybrid scenario has been extended to the high-density levels necessary for radiating divertor operation, achieving ~40% divertor heat flux reduction using either argon or neon with Ptot up to 15 MW.This material is based upon work supported by the U.S. Department of Energy, Office of Science, Office of Fusion Energy Sciences, using the DIII-D National Fusion Facility, a DOE Office of Science user facility, under Awards DE-FC02- 04ER54698. DIII-D data shown in this paper can be obtained in digital format by following the links at https://fusion.gat. com/global/D3D_DMP