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.

An evaluation of orogenic kinematic evolution utilizing crystalline and magnetic anisotropy in granitoids

The Silurian-Devonian Galway Granite Complex (GGC ~425-380Ma) is defined here as a suite of granitoid plutons that comprise the Main Galway Granite Batholith and the Earlier Plutons. The Main Batholith is a composite of the Carna Pluton in the west and the Kilkieran Pluton in the east and extends from Galway City ~130km to the west. The Earlier Plutons are spatially, temporally and structurally distinct, situated northwest of the Main Batholith and include the Roundstone, Omey, Inis and Letterfrack Plutons. The majority of isotopic and structural data currently available pertain to the Kilkieran Pluton, several tectonic models have already been devised for this part of the complex. These relate emplacement of the Kilkieran Pluton to extension across a large east-west Caledonian lineament, i.e. the Skird Rocks Fault, during late Caledonian transtension. No chronological data have been published that directly and accurately date the emplacement of the Carna Pluton or any of the Earlier Plutons. There is also a lack of data pertaining to the internal structure of these intrusions. Accordingly, no previous study has established the mechanisms of emplacement for the Earlier Plutons and only limited work is available for the Carna Pluton. As a consequense of this, constituents of the GGC have not previously been placed in a context relative to each other or to regional scale Silurio-Devonian kinematics. The current work focuses on the Omey, Roundstone and Carna Plutons. Here, results of detailed field and Anisotropy of Magnetic Susceptibiliy (AMS) fabric studies are presented. This work is complemented by geological mapping that focuses on fault dynamics and contact relationships. Interpretation of AMS data is aided by rock magnetic experiment data and petrographic microstructural evaluations of representative samples. A new geological map of the the Omey Pluton demonstrates that this intrusion has a defined roof and base which are gently inclined parallel to the fold hinge of the Connemara Antiform. AMS and petrographic data show the intrusion is cross cut by NNW-SSE shear zones that extend into the country rock. These pre-date and were active during magma emplacement. It is proposed that the Omey pluton was emplaced as a discordant phacolith. Pre-existing subvertical D5 faults in the host rock were reactived during emplacement, due to regional sinistral transpression, and served as centralised ascent conduits. A central portion of the Roundstone Pluton was mapped in detail for the first time. Two facies are identified, G1 forms the majority of the pluton and coeval G2 sheets cross cut G1 at the core of the pluton. NNW-SSE D5 faults mapped in the country rock extend across the pluton. These share a geometrical relationship with the distribution of submagmatic strain in the pluton and parallel the majoity of mapped subvertical G2 dykes. These data indicate that magma ascent was controlled by NNW-SSE conduits that are inherently related to those identifed in the Omey Pluton. It is proposed that the Roundstone Pluton is a punched laccolith, the symmetry and structure of which was controlled by pre-exising host rock structures and regional sinistral transpressive stress which presided during emplacement. Field relationships show the long axis of the Carna Pluton lies parallel to mulitple NNW-SSE shear zones. These are represented on a regional scale by the Clifden-Mace Fault which cross cuts the core of this intrusion. AMS and petrographic data show concentric emplacement fabrics were tectonically overprinted as magma cooled from the magmatic state due to this faulting. It is proposed that the Clifden-Mace Fault system was active during ascent and emplacement of the magma and that pluton inflation only terminated as this controlling structure went into compression due to the onset of regional transtension. U-Pb zircon laser ablation inductively coupled mass spectrometry (LA-ICP-MS) data has been compiled from four sample sites. New geochronological data from the Roundstone Pluton (RD1 = ± 3.2Ma) represent the oldest age determination obtained from any member of the GGC and demonstrates that this pluton predates the Carna Pluton by ~10Ma and probably intruded synchronously with the Omey Pluton (~422.5 ± 1.7Ma). Chronological data from the Carna Pluton (CN2 = 412.9 ± 2.5Ma; CN3 = 409.8 ± 7.2Ma; CN4 = 409.6 ± 3.6Ma) represent the first precise magma crystallisation age for this intrusion. This work shows this pluton is 10Ma older than the Kilkieran Pluton and that the supply of magma into the Carna Pluton had terminated by ~409Ma. Chronological, magnetic and field data have been utilised to evaluate the kinematic evolution of the Caledonides of western Ireland throughout the construction of the GGC. It is proposed that the GGC was constructed during four distinct episodes. The style of emplacement and the conduits used for magma transport to the site of emplacement was dependent on the orientation of local structures relative to the regional ambiant stress field. This philosophy is used to critically evaluate and progress existing hypotheses on the transition from regional transpression to regional transtension at the end of the Caledonian Orogeny.

Transport energy demand: techno-economic modelling and scenarios for Irish climate policy

The case for energy policy modelling is strong in Ireland, where stringent EU climate targets are projected to be overshot by 2015. Policy targets aiming to deliver greenhouse gas and renewable energy targets have been made, but it is unclear what savings are to be achieved and from which sectors. Concurrently, the growth of personal mobility has caused an astonishing increase in CO2 emissions from private cars in Ireland, a 37% rise between 2000 and 2008, and while there have been improvements in the efficiency of car technology, there was no decrease in the energy intensity of the car fleet in the same period. This thesis increases the capacity for evidenced-based policymaking in Ireland by developing techno-economic transport energy models and using them to analyse historical trends and to project possible future scenarios. A central focus of this thesis is to understand the effect of the car fleet‘s evolving technical characteristics on energy demand. A car stock model is developed to analyse this question from three angles: Firstly, analysis of car registration and activity data between 2000 and 2008 examines the trends which brought about the surge in energy demand. Secondly, the car stock is modelled into the future and is used to populate a baseline “no new policy” scenario, looking at the impact of recent (2008-2011) policy and purchasing developments on projected energy demand and emissions. Thirdly, a range of technology efficiency, fuel switching and behavioural scenarios are developed up to 2025 in order to indicate the emissions abatement and renewable energy penetration potential from alternative policy packages. In particular, an ambitious car fleet electrification target for Ireland is examined. The car stock model‘s functionality is extended by linking it with other models: LEAP-Ireland, a bottom-up energy demand model for all energy sectors in the country; Irish TIMES, a linear optimisation energy system model; and COPERT, a pollution model. The methodology is also adapted to analyse trends in freight energy demand in a similar way. Finally, this thesis addresses the gap in the representation of travel behaviour in linear energy systems models. A novel methodology is developed and case studies for Ireland and California are presented using the TIMES model. Transport Energy

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.

Application of mesoporous silica for the oral delivery of poorly water-soluble drugs

The objective of this thesis was to improve the dissolution rate of the poorly waters-soluble drug, fenofibrate by processing it with a high surface area carrier, mesoporous silica. The subsequent properties of the drug – silica composite were studied in terms of drug distribution within the silica matrix, solid state and release properties. Prior to commencing any experimental work, the properties of unprocessed mesoporous silica and fenofibrate were characterised (chapter 3), this allowed for comparison with the processed samples studied in later chapters. Fenofibrate was a highly stable, crystalline drug that did not adsorb moisture, even under long term accelerated storage conditions. It maintained its crystallinity even after SC-CO2 processing. Its dissolution rate was limited and dependent on the characteristics of the particular in vitro media studied. Mesoporous silica had a large surface area and mesopore volume and readily picked up moisture when stored under long term accelerated storage conditions (75% RH, 40 oC). It maintained its mesopore character after SC-CO2 processing. A variety of methods were employed to process fenofibrate with mesoporous silica including physical mixing, melt method, solvent impregnation and novel methods such as liquid and supercritical carbon dioxide (SC-CO2) (chapter 4). It was found that it was important to break down the fenofibrate particulate structure to a molecular state to enable drug molecules enter into the silica mesopores. While all processing methods led to some increase in fenofibrate release properties; the impregnation, liquid and SC-CO2 methods produced the most rapid release rates. SC-CO2 processing was further studied with a view to optimising the processing parameters to achieve the highest drug-loading efficiency possible (chapter 5). In this thesis, it was that SC-CO2 processing pressure had a bearing on drug-loading efficiency. Neither pressure, duration or depressurisation rate affected drug solid state or release properties. The amount of drug that could be loaded onto to the mesoporous silica successfully was also investigated at different ratios of drug mass to silica surface area under constant SC-CO2 conditions; as the drug – silica ratio increased, the drug-loading efficiency decreased, while there was no effect on drug solid state or release properties. The influence of the number of drug-loading steps was investigated (chapter 6) with a view to increasing the drug-loading efficiency. This multiple step approach did not yield an increase in drug-loading efficiency compared to the single step approach. It was also an objective in this chapter to understand how much drug could be loaded into silica mesopores; a method based on the known volume of the mesopores and true density of drug was investigated. However, this approach led to serious repercussions in terms of the subsequent solid state nature of the drug and its release performance; there was significant drug crystallinity and reduced release extent. The impact of in vitro release media on fenofibrate release was also studied (chapter 6). Here it was seen that media containing HCl led to reduced drug release over time compared to equivalent media not containing HCl. The key findings of this thesis are discussed in chapter 7 and included: 1. Drug – silica processing method strongly influenced drug distribution within the silica matrix, drug solid state and release. 2. The silica surface area and mesopore volume also influenced how much drug could be loaded. It was shown that SC-CO2 processing variables such as processing pressure (13.79 – 41.37 MPa), duration time (4 – 24 h) and depressurisation rate (rapid or controlled) did not influence the drug distribution within the SBA- 15 matrix, drug solid state form or release. Possible avenues of research to be considered going forward include the development and application of high resolution imaging techniques to visualise drug molecules within the silica mesopores. Also, the issues surrounding SBA-15 usage in a pharmaceutical manufacturing environment should be addressed.

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.

Pyramidal quantum dots: single and entangled photon sources and correlation studies

Practical realisation of quantum information science is a challenge being addressed by researchers employing various technologies. One of them is based on quantum dots (QD), usually referred to as artificial atoms. Being capable to emit single and polarization entangled photons, they are attractive as sources of quantum bits (qubits) which can be relatively easily integrated into photonic circuits using conventional semiconductor technologies. However, the dominant self-assembled QD systems suffer from asymmetry related problems which modify the energetic structure. The main issue is the degeneracy lifting (the fine-structure splitting, FSS) of an optically allowed neutral exciton state which participates in a polarization-entanglement realisation scheme. The FSS complicates polarization-entanglement detection unless a particular FSS manipulation technique is utilized to reduce it to vanishing values, or a careful selection of intrinsically good candidates from the vast number of QDs is carried out, preventing the possibility of constructing vast arrays of emitters on the same sample. In this work, site-controlled InGaAs QDs grown on (111)B oriented GaAs substrates prepatterned with 7.5 μm pitch tetrahedrons were studied in order to overcome QD asymmetry related problems. By exploiting an intrinsically high rotational symmetry, pyramidal QDs were shown as polarization-entangled photon sources emitting photons with the fidelity of the expected maximally entangled state as high as 0.721. It is the first site-controlled QD system of entangled photon emitters. Moreover, the density of such emitters was found to be as high as 15% in some areas: the density much higher than in any other QD system. The associated physical phenomena (e.g., carrier dynamic, QD energetic structure) were studied, as well, by different techniques: photon correlation spectroscopy, polarization-resolved microphotoluminescence and magneto-photoluminescence.

Novel ingredients from brewers' spent grain - bioactivity in cell culture model systems and bioactivity retention in fortified food products

Functional food ingredients, with scientifically proven and validated bioactive effects, present an effective means of inferring physiological health benefits to consumers to reduce the risk of certain diseases. The search for novel bioactive compounds for incorporation into functional foods is particularly active, with brewers’ spent grain (BSG, a brewing industry co-product) representing a unique source of potentially bioactive compounds. The DNA protective, antioxidant and immunomodulatory effects of phenolic extracts from both pale (P1 - P4) and black (B1 – B4) BSG were examined. Black BSG extracts significantly (P < 0.05) protected against DNA damage induced by hydrogen peroxide (H2O2) and extracts with the highest total phenolic content (TPC) protected against 3-morpholinosydnonimine hydrochloride (SIN-1)-induced oxidative DNA damage, measured by the comet assay. Cellular antioxidant activity assays were used to measured antioxidant potential in the U937 cell line. Extracts P1 – P3 and B2 - B4 demonstrated significant (P < 0.05) antioxidant activity, measured by the superoxide dismutase (SOD) activity, catalase (CAT) activity and gluatathione (GSH) content assays. Phenolic extracts P2 and P3 from pale BSG possess anti-inflammatory activity measured in concanavalin-A (conA) stimulated Jurkat T cells by an enzyme-linked immunosorbent assay (ELISA); significantly (P < 0.05) reducing production of interleukin-2 (IL-2), interleukin-4 (IL-4, P2 only), interleukin-10 (IL-10) and interferon-γ (IFN-γ). Black BSG phenolic extracts did not exhibit anti-inflammatory effects in vitro. Hydroxycinnamic acids (HA) have previously been shown to be the phenolic acids present at highest concentration in BSG; therefore the HA profile of the phenolic extracts used in this research, the original barley (before brewing) and whole BSG was characterised and quantified using high performance liquid chromatography (HPLC). The concentration of HA present in the samples was in the order of ferulic acid (FA) > p-coumaric acid (p-CA) derivatives > FA derivatives > p-CA > caffeic acid (CA) > CA derivatives. Results suggested that brewing and roasting decreased the HA content. Protein hydrolysates from BSG were also screened for their antioxidant and anti-inflammatory potential. A total of 34 BSG protein samples were tested. Initial analyses of samples A – J found the protein samples did not exert DNA protective effects (except hydrolysate H) or antioxidant effects by the comet and SOD assays, respectively. Samples D, E, F and J selectively reduced IFN-γ production (P < 0.05) in Jurkat T cells, measured using enzyme linked immunosorbent assay (ELISA). Further testing of hydrolysates K – W, including fractionated hydrolysates with molecular weight < 3, < 5 and > 5 kDa, found that higher molecular weight (> 5 kDa) and unfractionated hydrolysates demonstrate greatest anti-inflammatory effects, while fractionated hydrolysates were also shown to have antioxidant activity, by the SOD activity assay. A commercially available yogurt drink (Actimel) and snack-bar and chocolate-drink formulations were fortified with the most bioactive phenolic and protein samples – P2, B2, W, W < 3 kDa, W < 5 kDa, W > 5 kDa. All fortified foods were subjected to a simulated gastrointestinal in vitro digestion procedure and bioactivity retention in the digestates was determined using the comet and ELISA assays. Yogurt fortified with B2 digestate significantly (P < 0.05) protected against H2O2-induced DNA damage in Caco-2 cells. Greatest immunomodulatory activity was demonstrated by the snack-bar formulation, significantly (P < 0.05) reducing IFN-γ production in con-A stimulated Jurkat T cells. Hydrolysate W significantly (P < 0.05) increased the IFN-γ reducing capacity of the snack-bar. Addition of fractionated hydrolysate W < 3 kDa and W < 5 kDa to yogurt also reduced IL-2 production to a greater extent than the unfortified yogurt (P < 0.05).

Artefact detection and removal algorithms for EEG diagnostic systems

The electroencephalogram (EEG) is a medical technology that is used in the monitoring of the brain and in the diagnosis of many neurological illnesses. Although coarse in its precision, the EEG is a non-invasive tool that requires minimal set-up times, and is suitably unobtrusive and mobile to allow continuous monitoring of the patient, either in clinical or domestic environments. Consequently, the EEG is the current tool-of-choice with which to continuously monitor the brain where temporal resolution, ease-of- use and mobility are important. Traditionally, EEG data are examined by a trained clinician who identifies neurological events of interest. However, recent advances in signal processing and machine learning techniques have allowed the automated detection of neurological events for many medical applications. In doing so, the burden of work on the clinician has been significantly reduced, improving the response time to illness, and allowing the relevant medical treatment to be administered within minutes rather than hours. However, as typical EEG signals are of the order of microvolts (μV ), contamination by signals arising from sources other than the brain is frequent. These extra-cerebral sources, known as artefacts, can significantly distort the EEG signal, making its interpretation difficult, and can dramatically disimprove automatic neurological event detection classification performance. This thesis therefore, contributes to the further improvement of auto- mated neurological event detection systems, by identifying some of the major obstacles in deploying these EEG systems in ambulatory and clinical environments so that the EEG technologies can emerge from the laboratory towards real-world settings, where they can have a real-impact on the lives of patients. In this context, the thesis tackles three major problems in EEG monitoring, namely: (i) the problem of head-movement artefacts in ambulatory EEG, (ii) the high numbers of false detections in state-of-the-art, automated, epileptiform activity detection systems and (iii) false detections in state-of-the-art, automated neonatal seizure detection systems. To accomplish this, the thesis employs a wide range of statistical, signal processing and machine learning techniques drawn from mathematics, engineering and computer science. The first body of work outlined in this thesis proposes a system to automatically detect head-movement artefacts in ambulatory EEG and utilises supervised machine learning classifiers to do so. The resulting head-movement artefact detection system is the first of its kind and offers accurate detection of head-movement artefacts in ambulatory EEG. Subsequently, addtional physiological signals, in the form of gyroscopes, are used to detect head-movements and in doing so, bring additional information to the head- movement artefact detection task. A framework for combining EEG and gyroscope signals is then developed, offering improved head-movement arte- fact detection. The artefact detection methods developed for ambulatory EEG are subsequently adapted for use in an automated epileptiform activity detection system. Information from support vector machines classifiers used to detect epileptiform activity is fused with information from artefact-specific detection classifiers in order to significantly reduce the number of false detections in the epileptiform activity detection system. By this means, epileptiform activity detection which compares favourably with other state-of-the-art systems is achieved. Finally, the problem of false detections in automated neonatal seizure detection is approached in an alternative manner; blind source separation techniques, complimented with information from additional physiological signals are used to remove respiration artefact from the EEG. In utilising these methods, some encouraging advances have been made in detecting and removing respiration artefacts from the neonatal EEG, and in doing so, the performance of the underlying diagnostic technology is improved, bringing its deployment in the real-world, clinical domain one step closer.

Shining light on food microbiology; applications of luciferase-tagged microorganisms in the food industry

Bioluminescence is the production of light by living organisms as a result of a number of enzyme catalysed reactions caused by enzymes termed luciferases. The lux genes responsible for the emission of light can be cloned from one bioluminescent microorganism into one that is not bioluminescent. The light emitted can be monitored and quantified and will provide information on the metabolic activity, quantity and location of cells in a particular environment, in real-time. The primary aim of this thesis was to investigate and identify several food industry related applications of lux-tagged microorganisms. The first aim was to monitor a lux-tagged Cronobacter sakazakii in reconstituted infant milk formula, in realtime. The second aim was to investigate a bioluminescent-based early warning system for starter culture disruption by bacteriophages and antibiotic residues. The third of this thesis was to examine the use of a bioluminescent-based assay to test the activity of bioengineered Nisin derivatives M21V and S29A against foodborne pathogens in laboratory media and selected foods.

Representations of Catholicism in selected works by Colm Tóibín

The aim of this thesis is to provide an original and extensive study of Colm Tóibín as the “secular revisionist who acknowledges Catholicism as an enduring element of Irish society” (Ryan, Ireland and Scotland 251). Tóibín is uniquely placed to interpret many aspects of Ireland in the latter half of the twentieth century and I will argue that intertwined with his revisionism of Irish history is a reimagining of Ireland and Catholicism in fictive terms. An extensive amount of material from Tóibín’s time as a journalist and travel writer will feature in my research because it validates my argument concerning his prolonged engagement with Catholicism. Similarly, a broad range of Tóibín’s prose will be studied because it affords opportunities for an exploration of a literary Catholic oeuvre in his fiction. Therefore, I am emphasizing that a crucial linkage of Catholicism is identifiable throughout Tóibín’s diverse canon of work. However, I will argue that divergences of attitude and mode can be found in how Tóibín depicts Catholicism in his journalism and fiction. My argument identifies Tóibín’s recurrent journalistic questioning of the Church’s teaching and leadership but I classify a benignity towards Catholicism in his travel writing and fiction. Overall, Tóibín’s fiction merits significant status in this thesis because of the representations of Catholicism in the work of a writer who has been short-listed three times for The Booker Prize.

The musical enculturation of Irish traditional musicians: An ethnographic study of learning processes

The enculturation of Irish traditional musicians involves informal, non-formal, and sometimes formal learning processes in a number of different settings, including traditional music sessions, workshops, festivals, and classes. Irish traditional musicians also learn directly from family, peers, and mentors and by using various forms of technology. Each experience contributes to the enculturation process in meaningful and complementary ways. The ethnographic research discussed in this dissertation suggests that within Irish traditional music culture, enculturation occurs most effectively when learners experience a multitude of learning practices. A variety of experiences insures that novices receive multiple opportunities for engagement and learning. If a learner finds one learning practice ineffective, there are other avenues of enculturation. This thesis explores the musical enculturation of Irish traditional musicians. It focuses on the process of becoming a musician by drawing on methodologies and theories from ethnomusicology, education, and Irish traditional music studies. Data was gathered through multiple ethnographic methodologies. Fieldwork based on participant-observation was carried out in a variety of learning contexts, including traditional music sessions, festivals, workshops, and weekly classes. Additionally, interviews with twenty accomplished Irish traditional musicians provide diverse narratives and firsthand insight into musical development and enculturation. These and other methodologies are discussed in Chapter 1. The three main chapters of the thesis explore various common learning experiences. Chapter 2 explores how Irish traditional musicians learn during social and musical interactions between peers, mentors, and family members, and focuses on live music-making which occurs in private homes, sessions, and concerts. These informal and non-formal learning experiences primarily take place outside of organizations and institutions. The interview data suggests these learning experiences are perhaps the most pervasive and influential in terms of musical enculturation. Chapter 3 discusses learning experience in more organized settings, such as traditional music classes, workshops, summer schools, and festivals. The role of organizations such as Comhaltas Ceoltóirí Éireann and pipers’ clubs are discussed from the point of view of the learner. Many of the learning experiences explored in this chapter are informal, non-formal, and sometimes formal in nature, depending on the philosophy of the organization, institution, and individual teacher. The interview data and field observations indicate that learning in these contexts is common and plays a significant role in enculturation, particularly for traditional musicians who were born during and after the 1970s. Chapter 4 explores the ways Irish traditional musicians use technology, including written sources, phonography, videography, websites, and emerging technologies, during the enculturation process. Each type of technology presents different educational implications, and traditional musicians use these technologies in diverse ways and some more than others. For this, and other reasons, technology plays a complex role during the process of musical enculturation. Drawing on themes which emerge during Chapter 2, 3, and 4, the final chapter of this dissertation explores overarching patterns of enculturation within Irish traditional music culture. This ethnographic work suggests that longevity of participation and engagement in multiple learning and performance opportunities foster the enculturation of Irish traditional musicians. Through numerous and prolonged participation in music-making, novices become accustomed to and learn musical, social, and cultural behaviours. The final chapter also explores interconnections between learning experiences and also proposes directions for future research.

Control circuits for avalanche photodiodes

Avalanche Photodiodes (APDs) have been used in a wide range of low light sensing applications such as DNA sequencing, quantum key distribution, LIDAR and medical imaging. To operate the APDs, control circuits are required to achieve the desired performance characteristics. This thesis presents the work on development of three control circuits including a bias circuit, an active quench and reset circuit and a gain control circuit all of which are used for control and performance enhancement of the APDs. The bias circuit designed is used to bias planar APDs for operation in both linear and Geiger modes. The circuit is based on a dual charge pumps configuration and operates from a 5 V supply. It is capable of providing milliamp load currents for shallow-junction planar APDs that operate up to 40 V. With novel voltage regulators, the bias voltage provided by the circuit can be accurately controlled and easily adjusted by the end user. The circuit is highly integrable and provides an attractive solution for applications requiring a compact integrated APD device. The active quench and reset circuit is designed for APDs that operate in Geiger-mode and are required for photon counting. The circuit enables linear changes in the hold-off time of the Geiger-mode APD (GM-APD) from several nanoseconds to microseconds with a stable setting step of 6.5 ns. This facilitates setting the optimal `afterpulse-free' hold-off time for any GM-APD via user-controlled digital inputs. In addition this circuit doesn’t require an additional monostable or pulse generator to reset the detector, thus simplifying the circuit. Compared to existing solutions, this circuit provides more accurate and simpler control of the hold-off time while maintaining a comparable maximum count-rate of 35.2 Mcounts/s. The third circuit designed is a gain control circuit. This circuit is based on the idea of using two matched APDs to set and stabilize the gain. The circuit can provide high bias voltage for operating the planar APD, precisely set the APD’s gain (with the errors of less than 3%) and compensate for the changes in the temperature to maintain a more stable gain. The circuit operates without the need for external temperature sensing and control electronics thus lowering the system cost and complexity. It also provides a simpler and more compact solution compared to previous designs. The three circuits designed in this project were developed independently of each other and are used for improving different performance characteristics of the APD. Further research on the combination of the three circuits will produce a more compact APD-based solution for a wide range of applications.

Invertebrate diversity in Irish and British forests

Ireland and Britain were once covered in natural forest, but extensive anthropogenic deforestation reduced forest cover to less than 1% and 5 %, respectively, by the beginning of the 20th century. Large-scale afforestation has since increased the level of forest cover to 11% in Ireland and 12% in Britain, with the majority of planted forests comprising small monoculture plantations, many of which are of non - native conifer tree species. At present the forest cover of Ireland and Britain generally consists of small areas of remnant semi-natural woodland and pockets of these plantation forests within a predominantly agricultural landscape. Invertebrates comprise a large proportion of the biodiversity found within forested habitats. In particular, spiders and carabid beetles play an important role in food webs as both predators and prey and respond to small-scale changes in habitat structure, meaning they are particularly sensitive to forest management. Hoverflies play an important role in control and pollination and have been successfully used as indicators of habitat disturbance and quality. This research addressed a number of topics pertinent to the forest types present in the contemporary Irish and British landscapes and aimed to investigate the invertebrate diversity of these forests. Spiders and carabid beetles were sampled using pitfall trapping and hoverflies were sampled using Malaise net trapping. Topics included the impacts of afforestation, the importance of open space, the choice of tree species, and the use of indicators for biodiversity assessment, as well as rare native woodlands and the effect of grazing on invertebrate diversity. The results are discussed and evidence-based recommendations are made for forest policy and management to protect and enhance invertebrate biodiversity in order to promote sustainable forest management in Ireland and Britain.

The double bind for non-traditional families in post-primary settings; to tell or not to tell their family identity

This thesis involved researching normative family discourses which are mediated through educational settings. The traditional family, consisting of father, mother and children all living together in one house is no longer reflective of the home situation of many Irish students (Lunn and Fahey, 2011). My study problematizes the dominant discourses which reflect how family differences are managed and recognised in schools. A framework using Foucauldian post structural critical analysis traces family stratification through the organisation of institutional and interpersonal relations at micro level in four post-primary schools. Standardising procedures such as the suppression of intimate relations between and among teacher and student, as well as the linear ordering of intergenerational relations, such as teacher/student and adult/child are critiqued. Normalising discourses operate in practices such as notes home which presume two parents together. Teacher assumptions about heterosexual two-parent families make it difficult for students to be open about a family setup that is constructed as different to the rest of the schools'. The management of family difference and deficit through pastoral care structures suggests a school-based politics of family adjustment. These practices beg the question whether families are better off not telling the school about their family identity. My thesis will be of interest to educational research and educational policy because it highlights how changing demographics such as family compositions are mis-conceptualised in schools, as well as revealing the changing forms of family governance through regimes such as pastoral care. This analysis allows for the existence of, and a valuing for, alternative modes of family existence, so that future curricular and legal discourses can be challenged in the interest of equity and social justice.