The design of curved optical waveguides : analytical and numerical analysis

A model for understanding the formation and propagation of modes in curved optical waveguides is developed. A numerical method for the calculation of curved waveguide mode profiles and propagation constants in two dimensional waveguides is developed, implemented and tested. A numerical method for the analysis of propagation of modes in three dimensional curved optical waveguides is developed, implemented and tested. A technique for the design of curved waveguides with reduced transition loss is presented. A scheme for drawing these new waveguides and ensuring that they have constant width is also provided. Claims about the waveguide design technique are substantiated through numerical simulations.

Visualising ribosome profiling and using it for reading frame detection and exploration of eukaryotic translation initiation

Ribosome profiling (ribo-seq) is a recently developed technique that provides genomewide information on protein synthesis (GWIPS) in vivo. The high resolution of ribo-seq is one of the exciting properties of this technique. In Chapter 2, I present a computational method that utilises the sub-codon precision and triplet periodicity of ribosome profiling data to detect transitions in the translated reading frame. Application of this method to ribosome profiling data generated for human HeLa cells allowed us to detect several human genes where the same genomic segment is translated in more than one reading frame. Since the initial publication of the ribosome profiling technique in 2009, there has been a proliferation of studies that have used the technique to explore various questions with respect to translation. A review of the many uses and adaptations of the technique is provided in Chapter 1. Indeed, owing to the increasing popularity of the technique and the growing number of published ribosome profiling datasets, we have developed GWIPS-viz (http://gwips.ucc.ie), a ribo-seq dedicated genome browser. Details on the development of the browser and its usage are provided in Chapter 3. One of the surprising findings of ribosome profiling of initiating ribosomes carried out in 3 independent studies, was the widespread use of non-AUG codons as translation initiation start sites in mammals. Although initiation at non-AUG codons in mammals has been documented for some time, the extent of non-AUG initiation reported by these ribo-seq studies was unexpected. In Chapter 4, I present an approach for estimating the strength of initiating codons based on the leaky scanning model of translation initiation. Application of this approach to ribo-seq data illustrates that initiation at non-AUG codons is inefficient compared to initiation at AUG codons. In addition, our approach provides a probability of initiation score for each start site that allows its strength of initiation to be evaluated.

Fabrication and characterisation of semiconductor nanowires and metal interconnects

One-dimensional semiconductor nanowires are considered to be promising materials for future nanoelectronic applications. However, before these nanowires can be integrated into such applications, a thorough understanding of their growth behaviour is necessary. In particular, methods that allow the control over nanowire growth are deemed especially important as it is these methods that will enable the control of nanowire dimensions such as length and diameter (high aspect ratios). The production of nanowires with high-aspect ratios is vital in order to take advantage of the unique properties experienced at the nanoscale, thus allowing us to maximise their use in devices. Additionally, the development of low-resistivity interconnects is desirable in order to connect such nanowires in multi-nanowire components. Consequently, this thesis aims to discuss the synthesis and characterisation of germanium (Ge) nanowires and platinum (Pt) interconnects. Particular emphasis is placed on manipulating the nanowire growth kinetics to produce high aspect ratio structures. The discussion of Pt interconnects focuses on the development of low-resistivity devices and the electrical and structural analysis of those devices. Chapter 1 reviews the most critical aspects of Ge nanowire growth which must be understood before they can be integrated into future nanodevices. These features include the synthetic methods employed to grow Ge nanowires, the kinetic and thermodynamic aspects of their growth and nanowire morphology control. Chapter 2 outlines the experimental methods used to synthesise and characterise Ge nanowires as well as the methods used to fabricate and analyse Pt interconnects. Chapter 3 discusses the control of Ge nanowire growth kinetics via the manipulation of the supersaturation of Ge in the Au/Ge binary alloy system. This is accomplished through the use of bi-layer films, which pre-form Au/Ge alloy catalysts before the introduction of the Ge precursor. The growth from these catalysts is then compared with Ge nanowire growth from standard elemental Au seeds. Nanowires grown from pre-formed Au/Ge alloy seeds demonstrate longer lengths and higher growth rates than those grown from standard Au seeds. In-situ TEM heating on the Au/Ge bi-layer films is used to support the growth characteristics observed. Chapter 4 extends the work of chapter 3 by utilising Au/Ag/Ge tri-layer films to enhance the growth rates and lengths of Ge nanowires. These nanowires are grown from Au/Ag/Ge ternary alloy catalysts. Once again, the supersaturation is influenced, only this time it is through the simultaneous manipulation of both the solute concentration and equilibrium concentration of Ge in the Au/Ag/Ge ternary alloy system. The introduction of Ag to the Au/Ge binary alloy lowers the equilibrium concentration, thus increasing the nanowire growth rate and length. Nanowires with uniform diameters were obtained via synthesis from AuxAg1-x alloy nanoparticles. Manifestation of the Gibbs-Thomson effect, resulting from the dependence of the mean nanowire length as a function of diameter, was observed for all of the nanowires grown from the AuxAg1-x nanoparticles. Finally, in-situ TEM heating was used to support the nanowire growth characteristics. Chapter 5 details the fabrication and characterisation of Pt interconnects deposited by electron beam induced deposition of two different precursors. The fabrication is conducted inside a dual beam FIB. The electrical and structural characteristics of interconnects deposited from a standard organometallic precursor and a novel carbon-free precursor are compared. The electrical performance of the carbon-free interconnects is shown to be superior to that of the organometallic devices and this is correlated to the structural composition of both interconnects via in-situ TEM heating and HAADF-STEM analysis. Annealing of the interconnects is carried out under two different atmospheres in order to reduce the electrical resistivity even further. Finally, chapter 6 presents some important conclusions and summarises each of the previous chapters.

Investigation of toll-like receptor tolerance in the regulation of inflammation

Inflammation is a complex and highly organised immune response to microbes and tissue injury. Recognition of noxious stimuli by pathogen recognition receptor families including Toll-like receptors results in the expression of hundreds of genes that encode cytokines, chemokines, antimicrobials and regulators of inflammation. Regulation of TLR activation responses is controlled by TLR tolerance which induces a global change in the cellular transcriptional expression profile resulting in gene specific suppression and induction of transcription. In this thesis the plasticity of TLR receptor tolerance is investigated using an in vivo, transcriptomics and functional approach to determine the plasticity of TLR tolerance in the regulation of inflammation. Firstly, using mice deficient in the negative regulator of TLR gene transcription, Bcl-3 (Bcl-3-/-) in a model of intestinal inflammation, we investigated the role of Bcl-3 in the regulation of intestinal inflammatory responses. Our data revealed a novel role for Bcl-3 in the regulation of epithelial cell proliferation and regeneration during intestinal inflammation. Furthermore this data revealed that increased Bcl-3 expression contributes to the development of inflammatory bowel disease (IBD). Secondly, we demonstrate that lipopolysaccharide tolerance is transient and recovery from LPS tolerance results in polarisation of macrophages to a previously un-described hybrid state (RM). In addition, we identified that RM cells have a unique transcriptional profile with suppression and induction of genes specific to this polarisation state. Furthermore, using a functional approach to characterise the outcomes of TLR tolerance plasticity, we demonstrate that cytokine transcription is uncoupled from cytokine secretion in macrophages following recovery from LPS tolerance. Here we demonstrate a novel mechanism of regulation of TLR tolerance through suppression of cytokine secretion in macrophages. We show that TNF-α is alternatively trafficked towards a degradative intracellular compartment. These studies demonstrate that TLR tolerance is a complex immunological response with the plasticity of this state playing an important role in the regulation of inflammation.

Genetic analysis of bacteriophages from clinical and environmental samples

Bacteriophages, viruses infecting bacteria, are uniformly present in any location where there are high numbers of bacteria, both in the external environment and the human body. Knowledge of their diversity is limited by the difficulty to culture the host species and by the lack of the universal marker gene present in all viruses. Metagenomics is a powerful tool that can be used to analyse viral communities in their natural environments. The aim of this study was to investigate diverse populations of uncultured viruses from clinical (a sputum of patient with cystic fibrosis, CF) and environmental samples (a sludge from a dairy food wastewater treatment plant) containing rich bacterial populations using genetic and metagenomic analyses. Metagenomic sequencing of viruses obtained from these samples revealed that the majority of the metagenomic reads (97-99%) were novel when compared to the NCBI protein database using BLAST. A large proportion of assembled contigs were assignable as novel phages or uncharacterised prophages, the next largest assignable group being single-stranded eukaryotic virus genomes. Sputum from a cystic fibrosis patient contained DNA typical of phages of bacteria that are traditionally involved in CF lung infections and other bacteria that are part of the normal oral flora. The only eukaryotic virus detected in the CF sputum was Torque Teno virus (TTV). A substantial number of assigned sequences from dairy wastewater could be affiliated with phages of bacteria that are typically found in the soil and aquatic environments, including wastewater. Eukaryotic viral sequences were dominated by plant pathogens from the Geminiviridae and Nanoviridae families, and animal pathogens from the Circoviridae family. Antibiotic resistance genes were detected in both metagenomes suggesting phages could be a source for transmissible antimicrobial resistance. Overall, diversity of viruses in the CF sputum was low, with 89 distinct viral genotypes predicted, and higher (409 genotypes) in the wastewater. Function-based screening of a metagenomic library constructed from DNA extracted from dairy food wastewater viruses revealed candidate promoter sequences that have ability to drive expression of GFP in a promoter-trap vector in Escherichia coli. The majority of the cloned DNA sequences selected by the assay were related to ssDNA circular eukaryotic viruses and phages which formed a minority of the metagenome assembly, and many lacked any significant homology to known database sequences. Natural diversity of bacteriophages in wastewater samples was also examined by PCR amplification of the major capsid protein sequences, conserved within T4-type bacteriophages from Myoviridae family. Phylogenetic analysis of capsid sequences revealed that dairy wastewater contained mainly diverse and uncharacterized phages, while some showed a high level of similarity with phages from geographically distant environments.

Techniques for engineering quantum states

In this thesis I theoretically study quantum states of ultracold atoms. The majority of the Chapters focus on engineering specific quantum states of single atoms with high fidelity in experimentally realistic systems. In the sixth Chapter, I investigate the stability and dynamics of new multidimensional solitonic states that can be created in inhomogeneous atomic Bose-Einstein condensates. In Chapter three I present two papers in which I demonstrate how the coherent tunnelling by adiabatic passage (CTAP) process can be implemented in an experimentally realistic atom chip system, to coherently transfer the centre-of-mass of a single atom between two spatially distinct magnetic waveguides. In these works I also utilise GPU (Graphics Processing Unit) computing which offers a significant performance increase in the numerical simulation of the Schrödinger equation. In Chapter four I investigate the CTAP process for a linear arrangement of radio frequency traps where the centre-of-mass of both, single atoms and clouds of interacting atoms, can be coherently controlled. In Chapter five I present a theoretical study of adiabatic radio frequency potentials where I use Floquet theory to more accurately model situations where frequencies are close and/or field amplitudes are large. I also show how one can create highly versatile 2D adiabatic radio frequency potentials using multiple radio frequency fields with arbitrary field orientation and demonstrate their utility by simulating the creation of ring vortex solitons. In the sixth Chapter I discuss the stability and dynamics of a family of multidimensional solitonic states created in harmonically confined Bose-Einstein condensates. I demonstrate that these solitonic states have interesting dynamical instabilities, where a continuous collapse and revival of the initial state occurs. Through Bogoliubov analysis, I determine the modes responsible for the observed instabilities of each solitonic state and also extract information related to the time at which instability can be observed.

Comparative genomics of Bifidobacteria

Chapter 2 of this thesis describes the sequence analysis of 14 bifidobacterial genomes from various species of the genus Bifidobacterium, and the determination of their open pan-genome trend. This analysis first determined the total number of genes to be considered as the reservoir of functions available to representatives of this genus. Many identified genes are still uncharacterized, but may be involved in the adaptation to the gut environment. This comparative genomic analysis also determined a pool of ortholog functions used to infer their phylogenetic relationship, thereby providing a more robust approach compared to that based solely on the16S rRNA-encoding gene. The genome sequence of an isolate from the insect hindgut Bifidobacterium asteroides PRL2011 was fully characterized in Chapter 3, surprisingly revealing a putative respiratory metabolism, which was also found to be present in other insect isolates, suggesting that respiration was an ancient feature of this genus, but also an adaptative trait to different atmosferic oxygen levels. Chapter 4 of this thesis outlines a comparative study which focused on the analysis of representatives of the Bifidobacterium breve species, revealing that the genetic variability among members of this species principally consists of genes with a role in adaptation to host environment and gut colonization. Finally, Chapter 5 describes the analysis of the genome sequence of Bifidobacterium animalis subsp. lactis BLC1, a probiotic bacterium widely used in food industries as an ingredient of functional foods, providing information that will allow future investigations of this species.

Learning to drive: from hazard detection to hazard handling

Hazard perception has been found to correlate with crash involvement, and has thus been suggested as the most likely source of any skill gap between novice and experienced drivers. The most commonly used method for measuring hazard perception is to evaluate the perception-reaction time to filmed traffic events. It can be argued that this method lacks ecological validity and may be of limited value in predicting the actions drivers’ will take to hazards encountered. The first two studies of this thesis compare novice and experienced drivers’ performance on a hazard detection test, requiring discrete button press responses, with their behaviour in a more dynamic driving environment, requiring hazard handling ability. Results indicate that the hazard handling test is more successful at identifying experience-related differences in response time to hazards. Hazard detection test scores were strongly related to performance on a driver theory test, implying that traditional hazard perception tests may be focusing more on declarative knowledge of driving than on the procedural knowledge required to successfully avoid hazards while driving. One in five Irish drivers crash within a year of passing their driving test. This suggests that the current driver training system does not fully prepare drivers for the dangers they will encounter. Thus, the third and fourth studies in this thesis focus on the development of two simulator-based training regimes. In the third study participants receive intensive training on the molar elements of driving i.e. speed and distance evaluation. The fourth study focuses on training higher order situation awareness skills, including perception, comprehension and projection. Results indicate significant improvement in aspects of speed, distance and situation awareness across training days. However, neither training programme leads to significant improvements in hazard handling performance, highlighting the difficulties of applying learning to situations not previously encountered.

Copper mining in Ireland during the later Bronze Age

Accepted Version

Lucy

Lucy ! contemporary jazz waltz. The structure of this piece is fairly expansive (A,A,B.A,C,D,A,A,B,A). and after an opening theme in F major which is melodically pretty, the piece segues into a fairly straight ahead Jazz waltz which then leads to the solo section before a return of the initial theme

Summer morning

Contemporary Latin

Characterisation of the role of canonical BMP-Smad 1/5/8 signalling in the development of ventral midbrain dopaminergic neurons

Ventral midbrain (VM) dopaminergic (DA) neurons, which project to the dorsal striatum via the nigrostriatal pathway, are progressively degenerated in Parkinson’s disease (PD). The identification of the instructive factors that regulate midbrain DA neuron development, and the subsequent elucidation of the molecular bases of their effects, is vital. Such an understanding would facilitate the generation of transplantable DA neurons from stem cells and the identification of developmentally-relevant neurotrophic factors, the two most promising therapeutic approaches for PD. Two related members of the bone morphogenetic protein (BMP) family, BMP2 and growth/differentiation factor (GDF) 5, which signal via a canonical Smad 1/5/8 signalling pathway, have been shown to have neurotrophic effects on midbrain DA neurons both in vitro and in vivo, and may function to regulate VM DA neuronal development. However, the molecular (signalling pathway(s)) and cellular (direct neuronal or indirect via glial cells) mechanisms of their effects remain to be elucidated. The present thesis hypothesised that canonical Smad signalling mediates the direct effects of BMP2 and GDF5 on the development of VM DA neurons. By activating, modulating and/or inhibiting various components of the BMP-Smad signalling pathway, this research demonstrated that GDF5- and BMP2-induced neurite outgrowth from midbrain DA neurons is dependent on BMP type I receptor activation of the Smad signalling pathway. The role of glial cell-line derived neurotrophic factor (GDNF)-signalling, dynamin-dependent endocytosis and Smad interacting protein-1 (Sip1) regulation, in the neurotrophic effects of BMP2 and GDF5 were determined. Finally, the in vitro development of VM neural stem cells (NSCs) was characterised, and the ability of GDF5 and BMP2 to induce these VM NSCs towards DA neuronal differentiation was investigated. Taken together, these experiments identify GDF5 and BMP2 as novel regulators of midbrain DA neuronal induction and differentiation, and demonstrate that their effects on DA neurons are mediated by canonical BMPR-Smad signalling.

Composition portfolio and commentaries

In an attempt to provide an analytical entry point into my compositional practice, I have identified eight themes which are significantly recurrent: reduction – the selection of a small number of elements; imperfection – a damaged or warped characteristic of sound; hierarchy – a concern with the roles of instruments with regard to their relative prominence; motion – apparently static sound masses consist of fine internal movement; listener perception – expectations for change influence the experience of affect; translation – the transitioning of electronic sounds to the acoustic realm, and vice versa; immersion – the creation of an accommodating soundscape; blurring – smearing and overlapping sounds or genres. Each of these eight factors is associated with relevant precedents in the history and theory of music that have been influential on my work. These include the minimalist compositions of Steve Reich and Arvo Pärt; the lo-fi aesthetic of Boards of Canada and My Bloody Valentine; concerns with political hierarchy in the work of Louis Andriessen; the variations of dynamics and microtonal shifts of Giacinto Scelsi; Leonard B. Meyer's account of expectation in music; cross-fertilisation of the acoustic and electronic in pieces by Gérard Grisey and Gyorgy Ligeti; the immersive technique of Brian Eno's ambient music; and the overlapping sounds of Aphex Twin. These eight factors are variously applicable to the eleven submitted pieces, which are individually analysed with reference to the most significant of the categories. Together they form a musical language that sustains the interaction of a variety of techniques, concepts and genres.

Chillaxin'

A jazz piece for solo piano and/or jazz ensemble. This piece combines traditional and contemporary approaches. It is primarily old style swing but incorporates many modern harmonic techniques/devices, as evidenced in the score, such as: the use of upper structure triads, drop two voicing techniques, and voicing in fourths.

Full moon dance

A Jazz Celtic World Music Fusion Jig. A jig time melody placed in a setting where the rhythm section plays in 4/4 and 6/4 time simultaneously over contemporary modal jazz voicings