Design, fabrication and characterization of resonant waveguide grating based optical biosensors

The absence of rapid, low cost and highly sensitive biodetection platform has hindered the implementation of next generation cheap and early stage clinical or home based point-of-care diagnostics. Label-free optical biosensing with high sensitivity, throughput, compactness, and low cost, plays an important role to resolve these diagnostic challenges and pushes the detection limit down to single molecule. Optical nanostructures, specifically the resonant waveguide grating (RWG) and nano-ribbon cavity based biodetection are promising in this context. The main element of this dissertation is design, fabrication and characterization of RWG sensors for different spectral regions (e.g. visible, near infrared) for use in label-free optical biosensing and also to explore different RWG parameters to maximize sensitivity and increase detection accuracy. Design and fabrication of the waveguide embedded resonant nano-cavity are also studied. Multi-parametric analyses were done using customized optical simulator to understand the operational principle of these sensors and more important the relationship between the physical design parameters and sensor sensitivities. Silicon nitride (SixNy) is a useful waveguide material because of its wide transparency across the whole infrared, visible and part of UV spectrum, and comparatively higher refractive index than glass substrate. SixNy based RWGs on glass substrate are designed and fabricated applying both electron beam lithography and low cost nano-imprint lithography techniques. A Chromium hard mask aided nano-fabrication technique is developed for making very high aspect ratio optical nano-structure on glass substrate. An aspect ratio of 10 for very narrow (~60 nm wide) grating lines is achieved which is the highest presented so far. The fabricated RWG sensors are characterized for both bulk (183.3 nm/RIU) and surface sensitivity (0.21nm/nm-layer), and then used for successful detection of Immunoglobulin-G (IgG) antibodies and antigen (~1μg/ml) both in buffer and serum. Widely used optical biosensors like surface plasmon resonance and optical microcavities are limited in the separation of bulk response from the surface binding events which is crucial for ultralow biosensing application with thermal or other perturbations. A RWG based dual resonance approach is proposed and verified by controlled experiments for separating the response of bulk and surface sensitivity. The dual resonance approach gives sensitivity ratio of 9.4 whereas the competitive polarization based approach can offer only 2.5. The improved performance of the dual resonance approach would help reducing probability of false reading in precise bio-assay experiments where thermal variations are probable like portable diagnostics.

Optically injected multi-mode semiconductor lasers

As a device, the laser is an elegant conglomerate of elementary physical theories and state-of-the-art techniques ranging from quantum mechanics, thermal and statistical physics, material growth and non-linear mathematics. The laser has been a commercial success in medicine and telecommunication while driving the development of highly optimised devices specifically designed for a plethora of uses. Due to their low-cost and large-scale predictability many aspects of modern life would not function without the lasers. However, the laser is also a window into a system that is strongly emulated by non-linear mathematical systems and are an exceptional apparatus in the development of non-linear dynamics and is often used in the teaching of non-trivial mathematics. While single-mode semiconductor lasers have been well studied, a unified comparison of single and two-mode lasers is still needed to extend the knowledge of semiconductor lasers, as well as testing the limits of current model. Secondly, this work aims to utilise the optically injected semiconductor laser as a tool so study non-linear phenomena in other fields of study, namely ’Rogue waves’ that have been previously witnessed in oceanography and are suspected as having non-linear origins. The first half of this thesis includes a reliable and fast technique to categorise the dynamical state of optically injected two mode and single mode lasers. Analysis of the experimentally obtained time-traces revealed regions of various dynamics and allowed the automatic identification of their respective stability. The impact of this method is also extended to the detection regions containing bi-stabilities. The second half of the thesis presents an investigation into the origins of Rogue Waves in single mode lasers. After confirming their existence in single mode lasers, their distribution in time and sudden appearance in the time-series is studied to justify their name. An examination is also performed into the existence of paths that make Rogue Waves possible and the impact of noise on their distribution is also studied.

SDN enabled dynamically reconfigurable high capacity optical access architecture for converged services

Dynamically reconfigurable time-division multiplexing (TDM) dense wavelength division multiplexing (DWDM) long-reach passive optical networks (PONs) can support the reduction of nodes and network interfaces by enabling a fully meshed flat optical core. In this paper we demonstrate the flexibility of the TDM-DWDM PON architecture, which can enable the convergence of multiple service types on a single physical layer. Heterogeneous services and modulation formats, i.e. residential 10G PON channels, business 100G dedicated channel and wireless fronthaul, are demonstrated co-existing on the same long reach TDM-DWDM PON system, with up to 100km reach, 512 users and emulated system load of 40 channels, employing amplifier nodes with either erbium doped fiber amplifiers (EDFAs) or semiconductor optical amplifiers (SOAs). For the first time end-to-end software defined networking (SDN) management of the access and core network elements is also implemented and integrated with the PON physical layer in order to demonstrate two service use cases: a fast protection mechanism with end-to-end service restoration in the case of a primary link failure; and dynamic wavelength allocation (DWA) in response to an increased traffic demand.

Stable isotopes, radionuclides, and calculated sea surface temperature of two sediment cores in the Sicily Channel

The Eastern Mediterranean Transient (EMT) occurred in the Aegean Sea from 1988 to 1995 and is the most significant intermediate-to-deep Mediterranean overturning perturbation reported by instrumental records. The EMT was likely caused by accumulation of high salinity waters in the Levantine and enhanced heat loss in the Aegean Sea, coupled with surface water freshening in the Sicily Channel. It is still unknown whether similar transients occurred in the past and, if so, what their forcing processes were. In this study, sediments from the Sicily Channel document surface water freshening (SCFR) at 1910±12, 1812±18, 1725±25 and 1580±30 CE. A regional ocean hindcast links SCFR to enhanced deep-water production and in turn to strengthened Mediterranean thermohaline circulation. Independent evidence collected in the Aegean Sea supports this reconstruction, showing that enhanced bottom water ventilation in the Eastern Mediterranean was associated with each SCFR event. Comparison between the records and multi-decadal atmospheric circulation patterns and climatic external forcings indicates that Mediterranean circulation destabilisation occurs during positive North Atlantic Oscillation (NAO) and negative Atlantic Multidecadal Oscillation (AMO) phases, reduced solar activity and strong tropical volcanic eruptions. They may have recurrently produced favourable deep-water formation conditions, both increasing salinity and reducing temperature on multi-decadal time scales.

Optical properties of chiral thin films and microparticles

In this work I study the optical properties of helical particles and chiral sculptured thin films, using computational modeling (discrete dipole approximation, Berreman calculus), and experimental techniques (glancing angle deposition, ellipsometry, scatterometry, and non-linear optical measurements). The first part of this work focuses on linear optics, namely light scattering from helical microparticles. I study the influence of structural parameters and orientation on the optical properties of particles: circular dichroism (CD) and optical rotation (OR), and show that as a consequence of random orientation, CD and OR can have the opposite sign, compared to that of the oriented particle, potentially resulting in ambiguity of measurement interpretation. Additionally, particles in random orientation scatter light with circular and elliptical polarization states, which implies that in order to study multiple scattering from randomly oriented chiral particles, the polarization state of light cannot be disregarded. To perform experiments and attempt to produce particles, a newly constructed multi stage thin film coating chamber is calibrated. It enables the simultaneous fabrication of multiple sculptured thin film coatings, each with different structure. With it I successfully produce helical thin film coatings with Ti and TiO_{2}. The second part of this work focuses on non-linear optics, with special emphasis on second-harmonic generation. The scientific literature shows extensive experimental and theoretical work on second harmonic generation from chiral thin films. Such films are expected to always show this non-linear effect, due to their lack of inversion symmetry. However no experimental studies report non-linear response of chiral sculptured thin films. In this work I grow films suitable for a second harmonic generation experiment, and report the first measurements of non-linear response.

Numerical Modelling of Eddy Current Probes for CANDU® Fuel Channel Inspection

Multi-frequency Eddy Current (EC) inspection with a transmit-receive probe (two horizontally offset coils) is used to monitor the Pressure Tube (PT) to Calandria Tube (CT) gap of CANDU® fuel channels. Accurate gap measurements are crucial to ensure fitness of service; however, variations in probe liftoff, PT electrical resistivity, and PT wall thickness can generate systematic measurement errors. Validated mathematical models of the EC probe are very useful for data interpretation, and may improve the gap measurement under inspection conditions where these parameters vary. As a first step, exact solutions for the electromagnetic response of a transmit-receive coil pair situated above two parallel plates separated by an air gap were developed. This model was validated against experimental data with flat-plate samples. Finite element method models revealed that this geometrical approximation could not accurately match experimental data with real tubes, so analytical solutions for the probe in a double-walled pipe (the CANDU® fuel channel geometry) were generated using the Second-Order Vector Potential (SOVP) formalism. All electromagnetic coupling coefficients arising from the probe, and the layered conductors were determined and substituted into Kirchhoff’s circuit equations for the calculation of the pickup coil signal. The flat-plate model was used as a basis for an Inverse Algorithm (IA) to simultaneously extract the relevant experimental parameters from EC data. The IA was validated over a large range of second layer plate resistivities (1.7 to 174 µΩ∙cm), plate wall thickness (~1 to 4.9 mm), probe liftoff (~2 mm to 8 mm), and plate-to plate gap (~0 mm to 13 mm). The IA achieved a relative error of less than 6% for the extracted FP resistivity and an accuracy of ±0.1 mm for the LO measurement. The IA was able to achieve a plate gap measurement with an accuracy of less than ±0.7 mm error over a ~2.4 mm to 7.5 mm probe liftoff and ±0.3 mm at nominal liftoff (2.42±0.05 mm), providing confidence in the general validity of the algorithm. This demonstrates the potential of using an analytical model to extract variable parameters that may affect the gap measurement accuracy.

A randomised controlled trial of calcium channel blockade (CCB) with Amlodipine For the treatment oF subcortical ischaEmic vasCular demenTia (AFFECT): study protocol

BACKGROUND: Vascular dementia is the second most common cause of dementia affecting over seven million people worldwide, yet there are no licensed treatments. There is an urgent need for a clinical trial in this patient group. Subcortical ischaemic vascular dementia is the most common variant of vascular dementia. This randomised trial will investigate whether use of calcium channel blockade with amlodipine, a commonly used agent, can provide the first evidence-based pharmacological treatment for subcortical ischaemic vascular dementia.

METHODS/DESIGN: This is a randomised controlled trial of calcium channel blockade with Amlodipine For the treatment oF subcortical ischaEmic vasCular demenTia (AFFECT) to test the hypothesis that treatment with amlodipine can improve outcomes for these patients in a phase IIb, multi-centre, double-blind, placebo-controlled randomised trial. The primary outcome is the change from baseline to 12 months in the Vascular Dementia Assessment Scale cognitive subscale (VADAS-cog). Secondary outcomes include cognitive function, executive function, clinical global impression of change, change in blood pressure, quantitative evaluation of lesion accrual based on magnetic resonance imaging (MRI), health-related quality of life, activities of daily living, non-cognitive dementia symptoms, care-giver burden and care-giver health-related quality of life, cost-effectiveness and institutionalisation. A total of 588 patients will be randomised in a 1:1 ratio to either amlodipine or placebo, recruited from sites across the UK and enrolled in the trial for 104 weeks.

DISCUSSION: There are no treatments licensed for vascular dementia. The most common subtype is subcortical ischaemic vascular dementia (SIVD). This study is designed to investigate whether amlodipine can produce benefits compared to placebo in established SIVD. It is estimated that the numbers of people with VaD and SIVD will increase globally in the future and the results of this study should inform important treatment decisions.

Physical Layer Security with Threshold-Based Multiuser Scheduling in Multi-antenna Wireless Networks

In this paper, we consider a multiuser downlink wiretap network consisting of one base station (BS) equipped with AA antennas, NB single-antenna legitimate users, and NE single-antenna eavesdroppers over Nakagami-m fading channels. In particular, we introduce a joint secure transmission scheme that adopts transmit antenna selection (TAS) at the BS and explores threshold-based selection diversity (tSD) scheduling over legitimate users to achieve a good secrecy performance while maintaining low implementation complexity. More specifically, in an effort to quantify the secrecy performance of the considered system, two practical scenarios are investigated, i.e., Scenario I: the eavesdropper’s channel state information (CSI) is unavailable at the BS, and Scenario II: the eavesdropper’s CSI is available at the BS. For Scenario I, novel exact closed-form expressions of the secrecy outage probability are derived, which are valid for general networks with an arbitrary number of legitimate users, antenna configurations, number of eavesdroppers, and the switched threshold. For Scenario II, we take into account the ergodic secrecy rate as the principle performance metric, and derive novel closed-form expressions of the exact ergodic secrecy rate. Additionally, we also provide simple and asymptotic expressions for secrecy outage probability and ergodic secrecy rate under two distinct cases, i.e., Case I: the legitimate user is located close to the BS, and Case II: both the legitimate user and eavesdropper are located close to the BS. Our important findings reveal that the secrecy diversity order is AAmA and the slope of secrecy rate is one under Case I, while the secrecy diversity order and the slope of secrecy rate collapse to zero under Case II, where the secrecy performance floor occurs. Finally, when the switched threshold is carefully selected, the considered scheduling scheme outperforms other well known existing schemes in terms of the secrecy performance and complexity tradeoff

Three-dimensional simulations of gravitationally confined detonations compared to observations of SN 1991T

The gravitationally confined detonation (GCD) model has been proposed as a possible explosion mechanism for Type Ia supernovae in the single-degenerate evolution channel. It starts with ignition of a deflagration in a single off-centre bubble in a near-Chandrasekhar-mass white dwarf. Driven by buoyancy, the deflagration flame rises in a narrow cone towards the surface. For the most part, the main component of the flow of the expanding ashes remains radial, but upon reaching the outer, low-pressure layers of the white dwarf, an additional lateral component develops. This causes the deflagration ashes to converge again at the opposite side, where the compression heats fuel and a detonation may be launched. We first performed five three-dimensional hydrodynamic simulations of the deflagration phase in 1.4 M⊙ carbon/oxygen white dwarfs at intermediate-resolution (2563computational zones). We confirm that the closer the initial deflagration is ignited to the centre, the slower the buoyant rise and the longer the deflagration ashes takes to break out and close in on the opposite pole to collide. To test the GCD explosion model, we then performed a high-resolution (5123 computational zones) simulation for a model with an ignition spot offset near the upper limit of what is still justifiable, 200 km. This high-resolution simulation met our deliberately optimistic detonation criteria, and we initiated a detonation. The detonation burned through the white dwarf and led to its complete disruption. For this model, we determined detailed nucleosynthetic yields by post-processing 106 tracer particles with a 384 nuclide reaction network, and we present multi-band light curves and time-dependent optical spectra. We find that our synthetic observables show a prominent viewing-angle sensitivity in ultraviolet and blue wavelength bands, which contradicts observed SNe Ia. The strong dependence on the viewing angle is caused by the asymmetric distribution of the deflagration ashes in the outer ejecta layers. Finally, we compared our model to SN 1991T. The overall flux level of the model is slightly too low, and the model predicts pre-maximum light spectral features due to Ca, S, and Si that are too strong. Furthermore, the model chemical abundance stratification qualitatively disagrees with recent abundance tomography results in two key areas: our model lacks low-velocity stable Fe and instead has copious amounts of high-velocity 56Ni and stable Fe. We therefore do not find good agreement of the model with SN 1991T.

Towards optical polarization control of laser-driven proton acceleration in foils undergoing relativistic transparency

Control of the collective response of plasma particles to intense laser light is intrinsic to relativistic optics, the development of compact laser-driven particle and radiation sources, as well as investigations of some laboratory astrophysics phenomena. We recently demonstrated that a relativistic plasma aperture produced in an ultra-thin foil at the focus of intense laser radiation can induce diffraction, enabling polarization-based control of the collective motion of plasma electrons. Here we show that under these conditions the electron dynamics are mapped into the beam of protons accelerated via strong charge-separation-induced electrostatic fields. It is demonstrated experimentally and numerically via 3D particle-in-cell simulations that the degree of ellipticity of the laser polarization strongly influences the spatial-intensity distribution of the beam of multi-MeV protons. The influence on both sheath-accelerated and radiation pressure-accelerated protons is investigated. This approach opens up a potential new route to control laser-driven ion sources.

Filamentation in Air and Water and Nonlinear Optical Characterization of Biopolymer Using Ultrashort Laser Pulses

Important issues related to femtosecond (fs) pulses and its relevance to this thesis are discussed. A fundamental characteristic, like the timebandwidth product for fs pulses is decribed in detail. A brief review of generation of ultrashort pulses and its propagation through an optically transparent media are presented. Interaction of strong pulses with matter and different ionization processes are also described. An overview of the thesis is presented at the end

The High-Redshift Quasar Luminosity Function from Multi-Epoch Imaging Surveys

Thesis (Ph.D.)--University of Washington, 2016-08

Évaluation de la modélisation de la taille de grain de neige du modèle multi-couches thermodynamique SNOWPACK: implication dans l'évaluation des risques d'avalanches

Résumé: L’Institut pour l'étude de la neige et des avalanches en Suisse (SLF) a développé SNOWPACK, un modèle thermodynamique multi-couches de neige permettant de simuler les propriétés géophysiques du manteau neigeux (densité, température, taille de grain, teneur en eau, etc.) à partir desquelles un indice de stabilité est calculé. Il a été démontré qu’un ajustement de la microstructure serait nécessaire pour une implantation au Canada. L'objectif principal de la présente étude est de permettre au modèle SNOWPACK de modéliser de manière plus réaliste la taille de grain de neige et ainsi obtenir une prédiction plus précise de la stabilité du manteau neigeux à l’aide de l’indice basé sur la taille de grain, le Structural Stability Index (SSI). Pour ce faire, l’erreur modélisée (biais) par le modèle a été analysée à l’aide de données précises sur le terrain de la taille de grain à l’aide de l’instrument IRIS (InfraRed Integrated Sphere). Les données ont été recueillies durant l’hiver 2014 à deux sites différents au Canada : parc National des Glaciers, en Colombie-Britannique ainsi qu’au parc National de Jasper. Le site de Fidelity était généralement soumis à un métamorphisme à l'équilibre tandis que celui de Jasper à un métamorphisme cinétique plus prononcé. Sur chacun des sites, la stratigraphie des profils de densités ainsi des profils de taille de grain (IRIS) ont été complétés. Les profils de Fidelity ont été complétés avec des mesures de micropénétromètre (SMP). L’analyse des profils de densité a démontré une bonne concordance avec les densités modélisées (R[indice supérieur 2]=0.76) et donc la résistance simulée pour le SSI a été jugée adéquate. Les couches d’instabilités prédites par SNOWPACK ont été identifiées à l’aide de la variation de la résistance dans les mesures de SMP. L’analyse de la taille de grain optique a révélé une surestimation systématique du modèle ce qui est en accord avec la littérature. L’erreur de taille de grain optique dans un environnement à l’équilibre était assez constante tandis que l’erreur en milieux cinétique était plus variable. Finalement, une approche orientée sur le type de climat représenterait le meilleur moyen pour effectuer une correction de la taille de grain pour une évaluation de la stabilité au Canada.

Optical and Spin Properties of Defect-Bound Excitons in Semiconductors

Thesis (Ph.D.)--University of Washington, 2016-08