Which-path problem for one and two particles with two degrees of freedom and a relation between transverse spatial structure and group velocity of light

Quantum mechanics, optics and indeed any wave theory exhibits the phenomenon of interference. In this thesis we present two problems investigating interference due to indistinguishable alternatives and a mostly unrelated investigation into the free space propagation speed of light pulses in particular spatial modes. In chapter 1 we introduce the basic properties of the electromagnetic field needed for the subsequent chapters. In chapter 2 we review the properties of interference using the beam splitter and the Mach-Zehnder interferometer. In particular we review what happens when one of the paths of the interferometer is marked in some way so that the particle having traversed it contains information as to which path it went down (to be followed up in chapter 3) and we review Hong-Ou-Mandel interference at a beam splitter (to be followed up in chapter 5). In chapter 3 we present the first of the interference problems. This consists of a nested Mach-Zehnder interferometer in which each of the free space propagation segments are weakly marked by mirrors vibrating at different frequencies [1]. The original experiment drew the conclusions that the photons followed disconnected paths. We partition the description of the light in the interferometer according to the number of paths it contains which-way information about and reinterpret the results reported in [1] in terms of the interference of paths spatially connected from source to detector. In chapter 4 we briefly review optical angular momentum, entanglement and spontaneous parametric down conversion. These concepts feed into chapter 5 in which we present the second of the interference problems namely Hong-Ou-Mandel interference with particles possessing two degrees of freedom. We analyse the problem in terms of exchange symmetry for both boson and fermion pairs and show that the particle statistics at a beam splitter can be controlled for suitably chosen states. We propose an experimental test of these ideas using orbital angular momentum entangled photons. In chapter 6 we look at the effect that the transverse spatial structure of the mode that a pulse of light is excited in has on its group velocity. We show that the resulting group velocity is slower than the speed of light in vacuum for plane waves and that this reduction in the group velocity is related to the spread in the wave vectors required to create the transverse spatial structure. We present experimental results of the measurement of this slowing down using Hong-Ou-Mandel interference.

Antarctic icebergs distributions 1992-2014

Basal melting of floating ice shelves and iceberg calving constitute the two almost equal paths of freshwater flux between the Antarctic ice cap and the Southern Ocean. The largest icebergs (>100 km2) transport most of the ice volume but their basal melting is small compared to their breaking into smaller icebergs that constitute thus the major vector of freshwater. The archives of nine altimeters have been processed to create a database of small icebergs (<8 km2) within open water containing the positions, sizes, and volumes spanning the 1992–2014 period. The intercalibrated monthly ice volumes from the different altimeters have been merged in a homogeneous 23 year climatology. The iceberg size distribution, covering the 0.1–10,000 km2 range, estimated by combining small and large icebergs size measurements follows well a power law of slope −1.52 ± 0.32 close to the −3/2 laws observed and modeled for brittle fragmentation. The global volume of ice and its distribution between the ocean basins present a very strong interannual variability only partially explained by the number of large icebergs. Indeed, vast zones of the Southern Ocean free of large icebergs are largely populated by small iceberg drifting over thousands of kilometers. The correlation between the global small and large icebergs volumes shows that small icebergs are mainly generated by large ones breaking. Drifting and trapping by sea ice can transport small icebergs for long period and distances. Small icebergs act as an ice diffuse process along large icebergs trajectories while sea ice trapping acts as a buffer delaying melting.

Measurement of target single-spin asymmetry in charged kaon electroproduction on a transversely polarized 3He target

The subject of quark transverse spin and transverse momentum distribution are two current research frontier in understanding the spin structure of the nucleons. The goal of the research reported in this dissertation is to extract new information on the quark transversity distribution and the novel transverse-momentum-dependent Sivers function in the neutron. A semi-inclusive deep inelastic scattering experiment was performed at the Hall A of the Jefferson laboratory using 5.9 GeV electron beam and a transversely polarized ^{3}He target. The scattered electrons and the produced hadrons (pions, kaons, and protons) were detected in coincidence with two large magnetic spectrometers. By regularly flipping the spin direction of the transversely polarized target, the single-spin-asymmetry (SSA) of the semi-inclusive deep inelastic reaction ^{3}He^{uparrow}(e,e'h^{\pm})X was measured over the kinematic range 0.13 < x < 0.41 and 1.3 < Q^{2} < 3.1 (GeV)^{2}. The SSA contains several different azimuthal angular modulations which are convolutions of quarks distribution functions in the nucleons and the quark fragmentation functions into hadrons. It is from the extraction of the various ``moments'' of these azimuthal angular distributions (Collins moment and Sivers moment) that we obtain information on the quark transversity distribution and the novel T-odd Sivers function. In this dissertation, I first introduced the theoretical background and experimental status of nucleon spins and the physics of SSA. I will then present the experimental setup and data collection of the JLab E06-010 experiment. Details of data analysis will be discussed next with emphasis on the kaon particle identification and the Ring-Imaging Cherenkov detector which are my major responsibilities in this experiment. Finally, results on the kaon Collins and Sivers moments extracted from the Maximum Likelihood method will be presented and interpreted. I will conclude with a discussion on the future prospects for this research.

High alkaline phosphatase activity in phosphate replete waters: The case of two macrotidal estuaries

The occurrence of alkaline phosphatase activity (APA) that hydrolyses organic phosphorus into phosphate (PO4) is commonly related to PO4 deficiency of oceanic, coastal and fresh waters. APA is almost never investigated in PO4-rich estuaries, since very low activities are expected to occur. As a consequence, microbial mineralization of organic phosphorus into PO4 has often been ignored in estuaries. In this study, we examined the importance of potential APA and the associated microbial dynamics in two estuaries, the Aulne and the Elorn (Northwestern France), presenting two different levels of PO4 concentrations. Unexpected high potential APA was observed in both estuaries. Values ranged from 50 to 506 nmol L−1 h−1, which range is usually found in very phosphorus-limited environments. High potential APA values were observed in the oligohaline zone (salinity 5–15) in spring and summer, corresponding to a PO4 peak and a maximum bacterial production of particle-attached bacteria. In all cases, high potential APA was associated with high suspended particulate matter and total particulate phosphorus. The low contribution of the 0.2–1 μm fraction to total APA, the strong correlation between particulate APA and bacterial biomass, and the close relationship between the production of particle-attached bacteria and APA, suggested that high potential APA is mainly due to particle-attached bacteria. These results suggest that the microbial mineralization of organic phosphorus may contribute to an estuarine PO4 production in spring and summer besides physicochemical processes.

Integration of virus-like particle macromolecular bioreceptors in electrochemical biosensors

Rapid, sensitive and selective detection of chemical hazards and biological pathogens has shown growing importance in the fields of homeland security, public safety and personal health. In the past two decades, efforts have been focusing on performing point-of-care chemical and biological detections using miniaturized biosensors. These sensors convert target molecule binding events into measurable electrical signals for quantifying target molecule concentration. However, the low receptor density and the use of complex surface chemistry in receptors immobilization on transducers are common bottlenecks in the current biosensor development, adding to the cost, complexity and time. This dissertation presents the development of selective macromolecular Tobacco mosaic virus-like particle (TMV VLP) biosensing receptor, and the microsystem integration of VLPs in microfabricated electrochemical biosensors for rapid and performance-enhanced chemical and biological sensing. Two constructs of VLPs carrying different receptor peptides targeting at 2,4,6-trinitrotoluene (TNT) explosive or anti-FLAG antibody are successfully bioengineered. The VLP-based TNT electrochemical sensor utilizes unique diffusion modulation method enabled by biological binding between target TNT and receptor VLP. The method avoids the influence from any interfering species and environmental background signals, making it extremely suitable for directly quantifying the TNT level in a sample. It is also a rapid method that does not need any sensor surface functionalization process. For antibody sensing, the VLPs carrying both antibody binding peptides and cysteine residues are assembled onto the gold electrodes of an impedance microsensor. With two-phase immunoassays, the VLP-based impedance sensor is able to quantify antibody concentrations down to 9.1 ng/mL. A capillary microfluidics and impedance sensor integrated microsystem is developed to further accelerate the process of VLP assembly on sensors and improve the sensitivity. Open channel capillary micropumps and stop-valves facilitate localized and evaporation-assisted VLP assembly on sensor electrodes within 6 minutes. The VLP-functionalized impedance sensor is capable of label-free sensing of antibodies with the detection limit of 8.8 ng/mL within 5 minutes after sensor functionalization, demonstrating great potential of VLP-based sensors for rapid and on-demand chemical and biological sensing.

The mutable nature of particle-core excitations with spin in the one-valence-proton nucleus Sb-133

The gamma-ray decay of excited states of the one-valence-proton nucleus Sb-133 has been studied using cold-neutron induced fission of U-235 and Pu-241 targets, during the EXILL campaign at the ILL reactor in Grenoble. By using a highly efficient HPGe array, coincidences between gamma-rays prompt with the fission event and those delayed up to several tens of microseconds were investigated, allowing to observe, for the first time, high-spin excited states above the 16.6 mu s isomer. Lifetimes analysis, performed by fast-timing techniques with LaBr3(Ce) scintillators, revealed a difference of almost two orders of magnitude in B(M1) strength for transitions between positive-parity medium-spin yrast states. The data are interpreted by a newly developed microscopic model which takes into account couplings between core excitations (both collective and non-collective) of the doubly magic nucleus Sn-132 and the valence proton, using Skyrme effective interaction in a consistent way. The results point to a fast change in the nature of particle-core excitations with increasing spin. (C) 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license.

Design of composites for thermal management: Aluminum reinforced with diamond-containing bimodal particle mixtures

A new design route is proposed in order to fabricate aluminum matrix diamond-containing composite materials with optimized values of thermal conductivity (TC) for thermal management applications. The proper size ratio and proportions of particulate diamond–diamond and diamond–SiC bimodal mixtures are selected based on calculations with predictive schemes, which combine two main issues: (i) the volume fraction of the packed particulate mixtures, and (ii) the influence of different types of particulates (with intrinsically different metal/reinforcement interfacial thermal conductances) on the overall thermal conductivity of the composite material. The calculated results are validated by comparison with measurements on composites fabricated by gas pressure infiltration of aluminum into preforms of selected compositions of particle mixtures. Despite the relatively low quality (low price) of the diamond particles used in this work, outstanding values of TC are encountered: a maximum of 770 W/m K for Al/diamond–diamond and values up to 690 W/m K for Al/diamond–SiC.

A new reinforcement learning-based memetic particle swarm optimizer

Developing an effective memetic algorithm that integrates the Particle Swarm Optimization (PSO) algorithm and a local search method is a difficult task. The challenging issues include when the local search method should be called, the frequency of calling the local search method, as well as which particle should undergo the local search operations. Motivated by this challenge, we introduce a new Reinforcement Learning-based Memetic Particle Swarm Optimization (RLMPSO) model. Each particle is subject to five operations under the control of the Reinforcement Learning (RL) algorithm, i.e. exploration, convergence, high-jump, low-jump, and fine-tuning. These operations are executed by the particle according to the action generated by the RL algorithm. The proposed RLMPSO model is evaluated using four uni-modal and multi-modal benchmark problems, six composite benchmark problems, five shifted and rotated benchmark problems, as well as two benchmark application problems. The experimental results show that RLMPSO is useful, and it outperforms a number of state-of-the-art PSO-based algorithms.

Modified CADF and CIPS panel unit root statistics with standard chi-squared and normal limiting distributions

In an influential paper Pesaran ('A simple panel unit root test in presence of cross-section dependence', Journal of Applied Econometrics, Vol. 22, pp. 265-312, 2007) proposes two unit root tests for panels with a common factor structure. These are the CADF and CIPS test statistics, which are amongst the most popular test statistics in the literature. One feature of these statistics is that their limiting distributions are highly non-standard, making for relatively complicated implementation. In this paper, we take this feature as our starting point to develop modified CADF and CIPS test statistics that support standard chi-squared and normal inference.

In-silico optimisation of two-dimensional high performance liquid chromatography for the determination of Australian methamphetamine seizure samples

In-silico optimisation of a two-dimensional high performance liquid chromatography (2D-HPLC) separation protocol has been developed for the interogation of methamphetamine samples including model, real world seizure, and laboratory synthesised samples. The protocol used Drylab® software to rapidly identify the optimum separation conditions from a library of chromatography columns. The optimum separation space was provided by the Phenomonex Kinetex PFP column (first dimension) and an Agilent Poroshell 120 EC-C18 column (second dimension). To facilitate a rapid 2D-HPLC analysis the particle packed C18 column was replaced with a Phenomenex Onyx Monolithic C18 withought sacrificing separation performance. The Drylab® optimised and experimental separations matched very closely, highlighting the robust nature of HPLC simulations. The chemical information gained from an intermediate methamphetamine sample was significant and complimented that generated from a pure seizure sample. The influence of the two-dimensional separation on the analytical figures of merit was also investigated. The limits of detection for key analytes in the second dimension determined for methamphetamine (4.59 × 10-⁴ M), pseudoephedrine (4.03 × 10-4 M), caffeine (5.16 × 10-⁴ M), aspirin (9.32 × 10-4 M), paracetamol (5.93 × 10-4 M) and procaine (2.02 × 10-3 M).

Investigations of Cloud Microphysical Response to Mixing Using Digital Holography

Cloud edge mixing plays an important role in the life cycle and development of clouds. Entrainment of subsaturated air affects the cloud at the microscale, altering the number density and size distribution of its droplets. The resulting effect is determined by two timescales: the time required for the mixing event to complete, and the time required for the droplets to adjust to their new environment. If mixing is rapid, evaporation of droplets is uniform and said to be homogeneous in nature. In contrast, slow mixing (compared to the adjustment timescale) results in the droplets adjusting to the transient state of the mixture, producing an inhomogeneous result. Studying this process in real clouds involves the use of airborne optical instruments capable of measuring clouds at the `single particle' level. Single particle resolution allows for direct measurement of the droplet size distribution. This is in contrast to other `bulk' methods (i.e. hot-wire probes, lidar, radar) which measure a higher order moment of the distribution and require assumptions about the distribution shape to compute a size distribution. The sampling strategy of current optical instruments requires them to integrate over a path tens to hundreds of meters to form a single size distribution. This is much larger than typical mixing scales (which can extend down to the order of centimeters), resulting in difficulties resolving mixing signatures. The Holodec is an optical particle instrument that uses digital holography to record discrete, local volumes of droplets. This method allows for statistically significant size distributions to be calculated for centimeter scale volumes, allowing for full resolution at the scales important to the mixing process. The hologram also records the three dimensional position of all particles within the volume, allowing for the spatial structure of the cloud volume to be studied. Both of these features represent a new and unique view into the mixing problem. In this dissertation, holographic data recorded during two different field projects is analyzed to study the mixing structure of cumulus clouds. Using Holodec data, it is shown that mixing at cloud top can produce regions of clear but humid air that can subside down along the edge of the cloud as a narrow shell, or advect down shear as a `humid halo'. This air is then entrained into the cloud at lower levels, producing mixing that appears to be very inhomogeneous. This inhomogeneous-like mixing is shown to be well correlated with regions containing elevated concentrations of large droplets. This is used to argue in favor of the hypothesis that dilution can lead to enhanced droplet growth rates. I also make observations on the microscale spatial structure of observed cloud volumes recorded by the Holodec.

Characterization of protection afforded by a bivalent virus-like particle vaccine against bluetongue virus serotypes 1 and 4 in sheep

BACKGROUND Bluetongue virus (BTV) is an economically important, arthropod borne, emerging pathogen in Europe, causing disease mainly in sheep and cattle. Routine vaccination for bluetongue would require the ability to distinguish between vaccinated and infected individuals (DIVA). Current vaccines are effective but are not DIVA. Virus-like particles (VLPs) are highly immunogenic structural mimics of virus particles, that only contain a subset of the proteins present in a natural infection. VLPs therefore offer the potential for the development of DIVA compatible bluetongue vaccines. METHODOLOGY/PRINCIPAL FINDINGS Merino sheep were vaccinated with either monovalent BTV-1 VLPs or a bivalent mixture of BTV-1 VLPs and BTV-4 VLPs, and challenged with virulent BTV-1 or BTV-4. Animals were monitored for clinical signs, antibody responses, and viral RNA. 19/20 animals vaccinated with BTV-1 VLPs either alone or in combination with BTV-4 VLPs developed neutralizing antibodies to BTV-1, and group specific antibodies to BTV VP7. The one animal that showed no detectable neutralizing antibodies, or group specific antibodies, had detectable viral RNA following challenge but did not display any clinical signs on challenge with virulent BTV-1. In contrast, all control animals' demonstrated classical clinical signs for bluetongue on challenge with the same virus. Six animals were vaccinated with bivalent vaccine and challenged with virulent BTV-4, two of these animals had detectable viral levels of viral RNA, and one of these showed clinical signs consistent with BTV infection and died. CONCLUSIONS There is good evidence that BTV-1 VLPs delivered as monovalent or bivalent immunogen protect from bluetongue disease on challenge with virulent BTV-1. However, it is possible that there is some interference in protective response for BTV-4 in the bivalent BTV-1 and BTV-4 VLP vaccine. This raises the question of whether all combinations of bivalent BTV vaccines are possible, or if immunodominance of particular serotypes could interfere with vaccine efficacy.

FROM GENES TO GENOMES: LOCAL ADAPTATION AND ADAPTIVE POTENTIAL IN TWO ARCTIC SEABIRDS

By investigating the mechanisms underlying the evolution and the maintenance of local adaptations we can help predict how species will adapt to future environmental change. In this thesis I investigate local adaptation and adaptive potential in thick-billed and common murres (Uria lomvia and U. aalge), two arctic seabirds of international conservation concern. Thanks to the recent development of new genomic methods, I address three major themes that are relevant for both the development of evolutionary theory and conservation: 1) the role of gene flow in the origin and maintenance of adaptation; 2) levels and distribution of standing genetic variation, and their contribution to adaptive potential; and 3) the genomic mechanisms maintaining an adaptive dimorphism within a single interbreeding population. First, I review the literature on genomics of local adaptation with gene flow and find that adaptation can be maintained despite gene flow, that gene flow itself can promote adaptation, and that genetic architecture is important in the origin and maintenance of local adaptations. Second, I genotype genome-wide markers and toll-like receptor genes (TLRs) to investigate local adaptation and adaptive potential in thick-billed murres. Thick-billed murres do not show signatures of local adaptation to their breeding grounds, but outlier loci group birds according to their non-breeding distributions, suggesting that selection and/or demographic connectivity in the winter may explain patterns of differentiation in this species. Genetic variation at TLRs does not decrease with increasing latitude as predicted, but tests of selection and measures of genetic diversity suggest differences in local selective regimes at most genes. Thick-billed murres show high levels of standing genetic variation and their adaptive potential will mostly depend on rate and magnitude of environmental change. Finally, I improve and annotate the assembly of the highly heterozygous genome of the thick-billed murre. Using this assembly as a reference, I perform whole genome analyses to investigate the genomic basis of an adaptive dimorphism in Atlantic common murres. I show for the first time that a 60 kb complex copy number variant in a non-coding region maintains differences in plumage and cold adaptation despite high gene flow.

An alternative methodology for fitting selectivity curves to pre-defined distributions

A non-linear least-squares methodology for simultaneously estimating parameters of selectivity curves with a pre-defined functional form, across size classes and mesh sizes, using catch size frequency distributions, was developed based on the model of Kirkwood and Walker [Kirkwood, G.P., Walker, T.L, 1986. Gill net selectivities for gummy shark, Mustelus antarcticus Gunther, taken in south-eastern Australian waters. Aust. J. Mar. Freshw. Res. 37, 689-697] and [Wulff, A., 1986. Mathematical model for selectivity of gill nets. Arch. Fish Wiss. 37, 101-106]. Observed catches of fish of size class I in mesh m are modeled as a function of the estimated numbers of fish of that size class in the population and the corresponding selectivities. A comparison was made with the maximum likelihood methodology of [Kirkwood, G.P., Walker, T.I., 1986. Gill net selectivities for gummy shark, Mustelus antarcticus Gunther, taken in south-eastern Australian waters. Aust. J. Mar. Freshw. Res. 37, 689-697] and [Wulff, A., 1986. Mathematical model for selectivity of gill nets. Arch. Fish Wiss; 37, 101-106], using simulated catch data with known selectivity curve parameters, and two published data sets. The estimated parameters and selectivity curves were generally consistent for both methods, with smaller standard errors for parameters estimated by non-linear least-squares. The proposed methodology is a useful and accessible alternative which can be used to model selectivity in situations where the parameters of a pre-defined model can be assumed to be functions of gear size; facilitating statistical evaluation of different models and of goodness of fit. (C) 1998 Elsevier Science B.V.