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- Publication3D fault zone architecture in Kardia Mine, Ptolemais Basin, GreeceResearch on normal faults derives mainly from outcrop- and seismic-based studies. Outcrops are characterized by their high resolution but often lack a 3D context, in contrast with seismic-based data that can be fully 3D but with limited resolution compared to outcrop data. The novelty of this study is the examination of a truly 3D dataset of seismic scale fault zones at outcrop resolution. The dataset has been acquired in the active, opencast Kardia lignite mine in the Ptolemais Basin, NW Greece. The basin is affected by two fault systems related to two extensional episodes. The first, Late Miocene episode resulted in the formation of the basin in response to NE-SW extension. The normal faults that occur in the Kardia mine formed during the second, Quaternary episode in response to NW-SE extension. Repeated visits at 3-monthly intervals over a 5-year period have allowed serial sections through the faults to be examined. These sections have been analysed in three dimensions, providing a unique insight into the structure of normal faults. The faults in the Ptolemais mines are unusual in that they are associated with little or no fault rock generation but instead detailed internal fault zone structure, which would normally be comminuted to fault rock, is preserved at very high strains. This feature of the faults allows detailed study of the geometric evolution of the faults and, in the case of the Kardia mine, interaction with synchronous bed-parallel slip surfaces. The total throw on a fault can be considered to be partitioned onto three components 1) throw on the main fault surface, 2) throw on subsidiary fault surfaces and 3) throw accommodated by continuous deformation. Measurement and analyses of these components for the fault zones in Kardia mine demonstrates that the first of these becomes more important with increasing throw consistent with progressive strain localisation during fault growth. Rapid lateral variations in the degree of throw partitioning over a fault zone reflect the range of scales of segmentation of the initial fault. Continuous deformation constitutes an integral element of fault structure at all stages of fault growth and its contribution to total throw decreases with increased throw suggesting that continuous deformation, such as normal drag, develops during the early stages of a fault zone development. Detailed three-dimensional mapping of a seismic scale normal fault shows various degrees of fault linkage with a gradual transition from hard- to soft-linkage with increasing scale of segmentation. Average shear strains measured across the normal fault zone at 81 locations vary by four orders of magnitude. Fault zone geometrical features indicative of linkage between fault segments occur over the full range of shear strains encountered supporting a model in which fault segment linkage is the primary control on the internal structure of the fault zone. By analogy this conclusion suggests that fault segment linkage may be the main control on the thickness and distribution of fault rock in areas where the details of fault zone structure are not preserved but are comminuted to fault rock. Bed-parallel slip within the multilayer sequence in Kardia mine occurred towards the beginning of the second phase of extension and overlapped in time with Quaternary normal faulting. Bed parallel slip, which is attributed to flexural-slip caused by reverse-drag folding in the hanging wall of a major fault, has a persistent top to the north slip direction. Bed-parallel slip surfaces occur throughout the excavated section and individual slip surfaces have slip up to 4.5 metres. 3D mapping of bed-parallel slip surfaces demonstrate that they display many of the features of dip-slip faults, for example, bed-parallel slip surfaces can be segmented both parallel and normal to the slip direction and on a wide range of scales. The displacement to length ratios derived for bed-parallel slip surfaces are typical of those for normal faults but are significantly lower than for the normal faults in Kardia mine. Backstripping of fault zone evolution at the locations of mutually offsetting bed-parallel slip surfaces and normal faults demonstrate how complex fault zone structure arises in the presence of synchronous bed-parallel slip. Bed-parallel slip surfaces formed during fault growth effectively introduce new displacement markers that can be used to examine the growth history of blind faults.
301 - PublicationAb-initio Simulations and Structure Fabrication at Atomic and Close-to-atomic Scale using Atomic Force Microscopy(University College Dublin. School of Mechanical and Materials Engineering, 2022)
; 0000-0002-8056-2198To increase the number of electronic components in a single integrated circuit chip, the functional feature size should be reduced to the atomic and close-to-atomic scale (ACS). For this, the application of molecules could be utilised as a channel for current conduction. This thesis focuses on the fundamental aspects of this theme to help us achieve atomic scale device fabrication in the future. A literature review on advances in moletronics and atomic and close-to-atomic scale manufacturing (ACSM) research with the application of atomic force microscopy (AFM) is given in chapter 1. ACS device manufacturing using molecules as the building block requires to overcome mainly three fundamental problems. Firstly the orientation of the molecule when placed between the electrodes plays a critical role in electronic transport. This is explained in chapter 2, which gives a detailed ab-initio simulation studies of current flow in inorganic molecule, such as polyoxometalates (POMs) and organic molecules such as phthalocyanines (Pc) and porphyrins (Pr), by incorporating them between gold electrodes. For the POM molecule, longitudinal orientation showed better conduction than lateral orientation, whereas for Pc and Pr molecules, the geometrically optimised orientation displayed better electronic transport properties than the tautomerized structure. Secondly, the bonding interaction between the electrode and the molecular terminal atoms helps us to determine the rate of electronic transport at the junction. Chapter 3 inspects this interaction through a periodic energy decomposition analysis on Pc and Pr derivatives. The attractive and repulsive energy terms of the bonding interactions proved that Pr molecules are better interactive over the gold substrate in comparison to Pc molecules. Electronic transport studies performed on their derivatives with and without thiol linkers further supported this result. Thus, a link between these two studies were established. This paves path for future work to select appropriate molecules and electrodes to demonstrate transistor actions for atomic scale device fabrication. Finally, the possibility of the fabrication of ACS electrodes with a single atomic protrusion for the attachment of molecules needs to be experimentally validated. As a first step towards this, fundamental studies using AFM to achieve atomic layer removal were carried out taking into account different machining parameters. This is given in chapter 4 and chapter 5. In chapter 4, mechanical AFM-based scratching techniques over gold and silicon using diamond tips were performed. In silicon substrate, material removal having a minimum depth of 3.2Å which is close to about 3 silicon atom thickness, has been achieved. On gold, a minimum depth of 9.7Å, close to 7 atom thickness has been achieved. In chapter 5, electrochemical AFM-based lithography over HOPG and silicon using platinum coated tips were carried out. Results showed that in bare silicon local anodic oxidation took place instead of material removal. Even in hydrofluoric (HF) treated silicon, oxidation occurred but in a controlled and well defined manner. From this, it can be deduced that HF treated silicon is better suited for structure fabrication than bare silicon. In the case of HOPG, different patterns such as nano-holes, nanolines and intrinsic patterns were machined and material removal close-to-a single atomic layer, ~3.35Å was achieved. Results from chapter 4 and 5 reveal that controlled AFM-based scratching techniques can ensure the fabrication of well-defined atomic structures for the application of molecular devices. Since ACSM represents the next phase of manufacturing, this thesis proposes some of the primary works required to realise ACSM using the currently available techniques and simulation methodologies to bring us one step closer in achieving considerable advancements in this field in the near future.89 - PublicationAbove and below ground responses to competition, and wood property variation in juvenile Sitka spruce clones(University College Dublin. School of Agriculture and Food Science, 2016)
; Stem growth, biomass partitioning and wood properties vary between genotypes, so information on how these traits interact with each other and are influenced by environment conditions is required. To this end, above and below ground growth, morphology and wood properties of a selection of elite juvenile Sitka spruce (Picea sitchensis (Bong.) Carr.) clones grown in Ireland were investigated in this study.The effects of intra- and inter-clonal competition were assessed for up to three years after planting in a field trial containing ramets (i.e. an independent individual of a clone produced by tissue cultures) planted in multi-clone (mixed) and mono-clonal (pure) plots. Stem height, diameter and biomass partitioning were found to be significant reduced for some clones when planted in mixed plots than in pure plots. Height and diameter results were more heterogeneous and competition was more asymmetrical in mixed than in pure plots. Plot type significantly increased fine root surface area in mixed plots and fine root length in pure plots for two fine root diameter classes for some clones. However, intra- or inter-clonal competition did not result in any significant changes in specific root length, specific root area, root:shoot ratio or root chemical composition.Increased height growth in the most vigorous clone was associated with significantly thinner cell walls and wider tracheids than the less vigorous clones, reducing mean wood density and other indicators of wood quality. The width of the early- and latewood band in each annual ring was a more important determinant of juvenile wood quality than the characteristics of the cells within each band. Radial tracheid width was significantly and positively correlated with ring width and stem height but was negatively correlated with wood density. Wood properties differed greatly between clones, suggesting that there is potential to improve juvenile wood properties through selective breeding while achieving modest gains in height.The results of this study demonstrated that competition-induced morphological changes did not occur either above or below ground for the majority of the studied Sitka spruce clones, but greater size heterogeneity was observed for clones planted in mixed plots than in pure stands. Additionally, the most vigorous clones had less-desirable wood properties than the less vigorous clones, which would reduce their wood quality.138 - PublicationThe acute responses to resisted sled sprinting (RSS)(University College Dublin. School of Public Health, Physiotherapy and Sports Science, 2022)
; 0000-0001-7480-8086Various sprint and resistance training methods are used to achieve improvements in sprint performance. Resisted sled sprinting (RSS) is a commonly used training method to improve sprint performance. Despite extensive investigation regarding the long-term training benefits of RSS, the acute external (mechanical load) and internal (psychophysiological load) stresses, elicited by RSS training stimuli in athletic populations remains unclear. Therefore, to elucidate the acute impact of RSS and inform RSS training prescription, this thesis examined, the acute responses to RSS in sprint trained field sport athletes. In introduction chapter 1 relays the background and rationale for this thesis, and the subsequent research questions developed, further to the aims, objective and methodological approaches set for each investigation. Chapter 2 discusses findings for a review of published literature pertaining to the acute effects of RSS. Assessment of physiological and perceived exertion, during both a relatively heavy and light RSS training bout in chapter 3 supplied a description of the acute psychophysiological effect and internal training load incurred from such training bouts. Findings described that relatively heavy loads inferred a greater physiological and perceived impact in lieu of comparable larger decline in subsequent URS or neuromuscular performance. The acute alterations in sprint kinetics to different RSS loads relative to unresisted sprint (URS) kinetics were assessed as in chapter 4. This generated detailed profiles of kinetic outputs during 20m RSS sprints at a spectrum of loads, describing the mechanical overload imposed, proposed efficacy and training stimulus targeted by each load-intensity. Finally, a priming protocol described in chapter 5, showed little evidence or efficacy for use of either heavy or very heavy RSS as a mechanism to acutely enhance URS performance. Together this body of evidence demonstrated that the acute responses elicited by RSS are sled load-intensity specific, that these responses are transient in nature, and that subsequent immediate and short-term URS performance is largely unaffected by execution of prior RSS efforts provided sufficient inter repetition recovery is supplied. However larger inter-individual variation in responses was evident as sled load-intensity exceeds 55 % velocity decrement. This load- intensity is proposed as a likely limit for accruing further training benefit. Furthermore, this thesis offered evidence that, when sled load-intensity is prescribed relative to measure of athletic ability, no sex-based differences in the acute effect of RSS occurs. In summary to attain a desired sprint training stimulus and ensure appropriate implementation of RSS in the context of athlete development, training load management and wider training regimes, RSS load prescription should be made on individual athlete basis and guided by load response relationship.49 - PublicationAdapting child-robot interaction to reflect age and gender(University College Dublin. School of Computer Science , 2016)
; ; Research and commercial robots have infiltrated homes, hospitals and schools, becoming attractive and proving impactful for children’s healthcare, therapy, edutainment, and other applications. The focus of this thesis is to investigate a little explored issue of how children’s perception of the robot changes with age, and thus to create such a robot to adapt to these differences. In particular, this research investigates the impact of gender segregation on children’s interactions with a humanoid NAO robot. To this end, a series of experiments was conducted with children aged between 5 and 12 years old. The results suggest that children aged between 9 and 12 years old do not support gender segregation hypothesis with a gendered robot.In order to dynamically adapt to children’s age and gender, a perception module was developed using depth data and a collected depth dataset of 3D body metrics of 428 children aged between 5 and 16 years old. This module is able to successfully determine children’s gender in real-world settings with 60.89% (76.64% offline) accuracy and estimate children’s age with a mean absolute error of only 1.83 (0.77 offline) years. Additionally, a pretend play testbed was designed in order to address the challenges of evaluating child-robot interaction by exploiting the advantages of multi-modal, multi-sensory perception. The pretend play testbed performed successfully at children’s play center, where a humanoid NAO robot was able to dynamically adapt its gender by changing its synthesized voice to match child’s perceived age and gender. By analyzing the free play of children, the results confirm the hypothesis of gender segregation for children aged younger than 8 years old. These findings are important to consider when designing robotic applications for children in order to improve engagement, which is essential for robot’s educational and therapeutic benefits.567 - PublicationAddressing gaps in cardiometabolic health and nutrition in women of reproductive ageMost women do not meet dietary guidelines before or during pregnancy, and overweight or obesity are becoming the predominant presentation in antenatal services. Novel strategies to improve health before pregnancy are of interest, but research with women outside of pregnancy is impacted by issues with recruitment and retention. Clinical risk categorisation schema such as the Edmonton Obesity Staging System (EOSS) and the Cardiometabolic Disease Staging System (CMDS), show promise in guiding treatment prioritisation in the general population, but their use in pregnancy has not been adequately considered. The World Health Organisation recommends that all women receive nutrition and weight counselling during pregnancy. Current antenatal practices, however, do not address nutrition as standard. There is also no consensus on which outcomes are most important for pregnancy nutrition interventions, with little consideration for the ‘patient voice’ in what is evaluated. The aims of this thesis are to investigate the potential of pre-existing clinical practice tools to address cardiometabolic health and nutrition in women of reproductive age and to explore the priorities for nutrition research from the perspective of key stakeholders, including women before and during pregnancy. Outside of pregnancy, we found the EOSS characterised more women with obesity (81.3%) as metabolically unhealthy. This high prevalence potentially limits the clinical utility of the tool in delineating risk. Conversely, we found the CMDS characterised 46.9% of these women as metabolically unhealthy. We also found a relationship between inflammatory marker C3 Complement protein and cardiometabolic phenotype. In our mixed-methods study, we women of reproductive age reported altruistic motivations for taking part in preconception research, were recruited mostly by digital means and prioritised wellbeing over traditional health measures. In pregnancy, the limitations of the EOSS system were also highlighted, given the high prevalence of “at risk” categorisation, especially in late pregnancy (98.9%). We found an antenatal lifestyle intervention that of healthy eating and low glycaemic index (GI) dietary advice was successful in reducing the dietary inflammatory potential of women with overweight or obesity. This suggests that a low GI and healthy eating intervention may be useful in improving inflammation and cardiometabolic health. Our data suggests that the International Federation of Gynaecology and Obstetrics Nutrition (FIGO) Checklist is an acceptable and likely feasible resource to facilitate conversations on nutrition and weight during routine antenatal care. Finally, we identified 13 core outcomes for pregnancy nutrition research. These are pregnancy complications, gestational weight change; maternal vitamin and mineral status including anaemia; mental health; diet quality; nutritional intakes; need for treatments, interventions, medications, and supplements; pregnancy loss or perinatal death; birth defects or congenital anomalies, neonatal complications, new-born anthropometry and body composition; maternal wellbeing and delivery complications. Measurement of this core outcome set as a standard support will assist in the advancement of antenatal nutrition, by generating evidence for outcomes most important to stakeholders, including pregnant women. In conclusion, our data suggests a greater focus on well-being is needed in women’s health. C3 complement protein may hold potential as a novel risk marker in obesity and the FIGO Nutrition Checklist may support clinicians in appropriately addressing healthy eating and weight women of reproductive age. This may have benefits for reducing inflammation in women with overweight or obesity.
85 - PublicationAdvanced analytical strategies for the characterisation of biotherapeutics(University College Dublin. School of Chemical and Bioprocess Engineering, 2022)
; 0000-0002-6770-0621Monoclonal antibodies (mAbs) are the most dominant selling class of biotherapeutics in the global market. These complex biomolecules are produced through mammalian cell culture and are prone to structural heterogeniety. This heterogeniety can have an adverse effect on the overall stability and efficacy of the drug product and must be closely monitored through product characterisation. Characterisation of mAbs can be carried out on the intact, subunit and peptide level. The drawback with traditional characterisation techniques include high sample requirement, high level of expertise needed to produce reporducible data and the methods involved are usually time consuming. The objective of this work was develop characterisation strategies at all three levels using novel instrumentation to overcome these drawbacks and improve our understanding of product characteristics at all stages of the mAb production cycle.211 - PublicationAdvanced distribution network modelling with distributed energy resources(University College Dublin. School of Electrical and Electronic Engineering , 2015)The addition of new distributed energy resources, such as electric vehicles, photovoltaics, and storage, to low voltage distribution networks means that these networks will undergo major changes in the future. Traditionally, distribution systems would have been a passive part of the wider power system, delivering electricity to the customer and not needing much control or management. However, the introduction of these new technologies may cause unforeseen issues for distribution networks, due to the fact that they were not considered when the networks were originally designed.This thesis examines different types of technologies that may begin to emerge on distribution systems, as well as the resulting challenges that they may impose. Three-phase models of distribution networks are developed and subsequently utilised as test cases. Various management strategies are devised for the purposes of controlling distributed resources from a distribution network perspective. The aim of the management strategies is to mitigate those issues that distributed resources may cause, while also keeping customers' preferences in mind.A rolling optimisation formulation is proposed as an operational tool which can manage distributed resources, while also accounting for the uncertainties that these resources may present. Network sensitivities for a particular feeder are extracted from a three-phase load flow methodology and incorporated into an optimisation. Electric vehicles are the focus of the work, although the method could be applied to other types of resources. The aim is to minimise the cost of electric vehicle charging over a 24-hour time horizon by controlling the charge rates and timings of the vehicles. The results demonstrate the advantage that controlled EV charging can have over an uncontrolled case, as well as the benefits provided by the rolling formulation and updated inputs in terms of cost and energy delivered to customers.Building upon the rolling optimisation, a three-phase optimal power flow method is developed. The formulation has the capability to provide optimal solutions for distribution system control variables, for a chosen objective function, subject to required constraints. It can, therefore, be utilised for numerous technologies and applications. The three-phase optimal power flow is employed to manage various distributed resources, such as photovoltaics and storage, as well as distribution equipment, including tap changers and switches. The flexibility of the methodology allows it to be applied in both an operational and a planning capacity.The three-phase optimal power flow is employed in an operational planning capacity to determine volt-var curves for distributed photovoltaic inverters. The formulation finds optimal reactive power settings for a number of load and solar scenarios and uses these reactive power points to create volt-var curves. Volt-var curves are determined for 10 PV systems on a test feeder. A universal curve is also determined which is applicable to all inverters. The curves are validated by testing them in a power flow setting over a 24-hour test period. The curves are shown to provide advantages to the feeder in terms of reduction of voltage deviations and unbalance, with the individual curves proving to be more effective. It is also shown that adding a new PV system to the feeder only requires analysis for that system.In order to represent the uncertainties that inherently occur on distribution systems, an information gap decision theory method is also proposed and integrated into the three-phase optimal power flow formulation. This allows for robust network decisions to be made using only an initial prediction for what the uncertain parameter will be. The work determines tap and switch settings for a test network with demand being treated as uncertain. The aim is to keep losses below a predefined acceptable value. The results provide the decision maker with the maximum possible variation in demand for a given acceptable variation in the losses. A validation is performed with the resulting tap and switch settings being implemented, and shows that the control decisions provided by the formulation keep losses below the acceptable value while adhering to the limits imposed by the network.
483 - PublicationAdversarial AI models for Cyber SecurityTechnology is influencing our lives in numerous ways. With the explosive growth of ubiquitous systems and data availability, many security threats arise, and an appetite to manage and mitigate such risks. As a result, cyber security has become an indispensable necessity and takes center stage to protect against known and unknown adversaries. Furthermore, with the proliferation of algorithms and computing systems, Machine Learning (ML)/Artificial Intelligence (AI) have become significant in tackling cyber security problems. The performance benefits provided by the applications built using ML/AI will be impactful when the security and reliability properties of the system are robust. Designing robust and secure real-world Machine Learning Systems in Cyber Security (MLSCS) is a multi-disciplinary endeavor and requires an in-depth understanding of the machine learning life cycle. ML has to be resilient to malicious attacks at all stages of the ML life cycle and protect themselves from the compromise of the system’s integrity, availability, and confidentiality security objectives. A large body of work studying failure modes of ML systems operating in adversarial environments is explored in the literature. But unfortunately, they miss the adversary view of all stages of ML life cycle, exposing them to larger attack surfaces. Furthermore, the adversary threat models and mitigation techniques discussed in the literature can be incoherent with the stakeholder’s goals, slowing down the defense process and making systems vulnerable. This thesis proposes an adversary modeling framework Cloud Atlas for AI models based on the properties of adversarial science with four principal components. It evaluates the security robustness of MLSCS under realistic threat models, covering all stages of ML life cycle, and respects cyber security domain-specific constraints. More specifically, a detailed threat taxonomy is proposed encompassing all stages of the ML life cycle, which forms the basis for the threat modeling component. Novel offensive and defensive methods are designed, including a new Explainable Artificial Intelligence (XAI) based attack surface to continuously evaluate the security and robustness of MLSCS in the assessment component. Recently proposed standards are extended to communicate relevant threats and weaknesses to stakeholders and end-users, thereby improving trust in the underlying system in reporting component. Finally, the adversary risk mitigation component supports new methodologies to quantify and transfer risks.
103 - PublicationAmerican literatures of dislocation in the age of Cold War transnationalism(University College Dublin. Clinton Institute For American Studies, 2016)
; The thesis of this study is that American imperial power during the Cold War era irrevocably altered traditional modes of dislocation by reshaping the twentieth-century global terrain through the expansion of socio-political, economic, and cultural networks, thus changing how international travel and national identity are understood over time. The redefining of international experience has prompted categorical shifts of the conceptual and vernacular parameters of dislocation dependent upon the arrangements of international networks in accordance with Cold War coordinates. The ambivalence of subjectivity and autonomy characteristic of the dislocated perspectives of expatriatism, exile, and diaspora, and their production of narratives that explore the masking and unmasking of liberation and oppression embedded in nationalist discourse throughout socio-political, economic, and cultural domains, are symptomatic of these shifts. My examination focuses on selected literatures of dislocation that operate at formative geopolitical sites and historical moments in the Cold War era to determine how they critically confront and dialogically deconstruct the performative and pedagogical narrative strategies of the nation-state paradigm. Thus, in an age of globalisation that necessitates new and evolving strategies of consolidating and safeguarding hegemony in the face of transnational expansions, these literatures illuminate multiple traces of power bound within the local, national, and global manifestations of the American (neo)imperial project.Chapter One will examine the ambivalent expatriate identity of William S. Burroughs’s dislocation within the geopolitical infrastructure of Moroccan experimental internationalism as represented by Tangier’s International Zone status. Burroughs constructs a counter-narrative against post-WWII colonialism and nationalism, which serves to undercut the consolidation of US foreign power in evidence during the Cold War. Chapter Two will compare how James Baldwin and Eldridge Cleaver confronted exile in Europe and North Africa, negotiated formal racist American policy during the Civil Rights Movement, and employed New Leftist socialist and postcolonial ideologies that informed the Black Power and Anti-war Movements. Comparing the two demonstrates the extent to which “American power follows one everywhere” (Baldwin) as US military and economic power proliferated at the height of the Cold War. Chapter Three will interrogate the plurality of identity in the diaspora narrative of Junot Díaz, thus shifting the focus of the dissertation to the Americas. Here I focus on the lasting effects of state-defined determinism on the Dominican diaspora, its origins based on Caribbean histories prescribed by the Cold War US policy toward Latin America that endorsed dictators in the region, and the difficulties of reconciling hybridity and normative identity politics.111 - PublicationAn Algorithmic Theory of the Policy Process(2022)With a few exceptions, current theories of the policy process do not model or measure the policy process using the graphical process notations that are common within information science, business administration and many natural sciences. The reason is that in the post-war period the needs of business process analysis came to dominate social science applications of process science whilst the needs of public policy process analysis remained largely unaddressed. As a result, modern graphical process notations can encode and quantify the instrumental properties of cost and efficiency of a business process, but not the normative properties of transparency, accountability or legitimacy of the much more complex policy making process. There have been many other unfortunate consequences. Business process modelling evolved into business process reengineering and became a critical enabler of a period of unprecedented hyper-globalization commencing in the 1990’s. However, it did so by encoding and quantifying the instrumental dimensions of cost and efficiency of globalized production processes and not their normative dimensions of domestic employment and social welfare transfers. We live with the consequences to this day of the emergence of destabilizing populist national movements and rising security and defense tensions between former trading partners. However, in recent years, there have been several important new developments. Firstly, a new class of process modelling tools has emerged at the juncture of the disciplines of information science and business administration that can model much more complex governance and policy-making processes as rules based declarative process graphs instead of sequence based imperative process graphs. Secondly, information science is now introducing a capacity for normative reasoning and moral dilemma resolution into a range of technologies from multi-agent systems and artificial societies to self-driving vehicles and autonomous battle drones. This creates new opportunities for a collaboration between policy process analysis and information science to reengineer legacy policy making processes and organizations in terms of normatively driven declarative processes. Not only must these reengineered policy making processes score better against instrumental criteria of cost and efficiency but also against the normative criteria of transparency, accountability, and legitimacy. Consequently, the metrics presented in this dissertation re-connect public policy process analysis with the tools and results of decades of process research in the fields of information science, business administration and many natural sciences, and supports a new theory of the public policy process as an algorithm whose purpose is the generation of solutions to public goods allocation problems. To illustrate the principles of the techniques involved and the utility of the approach, a case study analysis and prediction of Chinese public health policy response to the COVID-19 pandemic of 2020/21 is presented.
88 - Publication'An analysis of the ongoing erosion of the presumption of innocence in Irish law’This thesis provides a comprehensive overview of the presumption of innocence in Irish law. It argues that the scope of the presumption of innocence is not confined to narrow evidential rules at criminal trials but is a broader right extending beyond the trial setting to Garda investigations. It also argues that the presumption of innocence continues to be eroded both by legislation and judicial findings. It demonstrates this by analysing case law from Ireland, the European Court of Human Rights and England and Wales. This study complements the work of Hamilton (Hamilton, C, The Presumption of Innocence and Irish Criminal Law (Irish Academic Press 2007)) in two ways – by conducting historical research on the treatment of the presumption of innocence in Ireland prior to Woolmington v DPP and by analysing the ongoing erosion of the presumption of innocence in Irish law in the period from 2007 to 2021, which is not covered by Hamilton’s book. Chapters 1 and 2 are foundational. Chapter 1 engages with the great debates about the presumption of innocence. Chapter 2 conducts a historical survey of the presumption of innocence in England and Ireland and the degree to which the courts have interacted with the presumption. Chapter 3 examines the extent to which the presumption of innocence is under significant threat of erosion by reverse onus provisions. Chapter 4 argues that the presumption of innocence is eroded by legislation that criminalises silence. In Chapter 5 the problem of drawing adverse inferences at trial from an accused person’s failure to account during Garda questioning is discussed. The ‘failure to account’ provisions are analysed. Chapter 6 analyses the more general abridgment of the right to silence and the presumption of innocence by the introduction of ‘failure to mention’ provisions for ordinary criminal offences. The absence prescribed caution is also analysed in depth. The European Union Directive on the presumption of innocence is examined. The broader trend of weighing up competing interests in the administration of justice is analysed in Chapter 7 to explain the broader context in which the erosion of the presumption of innocence has occurred.
323 - PublicationAndy Devane and the Architecture of the Modern Irish Office Block, 1963-1979. The Demanding Art of Orderly Development(University College Dublin. School of Architecture, Planning and Environmental Policy, 2022)
; 0000-0001-8302-3360In 2017, a small cohort of the architectural profession quietly marked the centenary of Andrew (Andy) Devane’s birth, an event that was eclipsed by the news that permission had been granted to demolish his seminal building, AIB Bankcentre in Ballsbridge. The coincidence of the two events polarized the realisation that his work was not duly recognised and that his legacy was under threat. This project began as a shared initiative between Robinson Keefe & Devane (RKD) and the author. It has been funded by the Irish Research Council Enterprise Partnership Scheme with close collaboration between the author in the role of academic researcher, RKD as the enterprise partner and the School of Architecture, Planning and Environmental Policy (APEP) at University College Dublin as the academic partner. The raw and vast RKD archive is the foundation for the research undertaken. Other strands of investigation include the Devane family archive, oral history, extensive analysis of secondary sources and visits to Devane’s buildings. The thesis focuses on Devane’s three Dublin office buildings which were designed and built within the years 1963-1979. It closely examines the conditions for architectural practice in the period and presents a thorough architectural biography of an Irish twentieth century architect. This thesis enriches our understanding of Devane and his work, Dublin and its twentieth-century development, and the architectural culture of the time.48 - PublicationAnisotropic heisenberg quantum spin chains: excitations and neutron-scattering cross sectionsThe research presented here focuses on the theoretical investigation of spinons in quasi one-dimensional quantum spin chains from the perspective of neutron scattering, with emphasis placed on the calculation of dynamic spin structure factors for both unpolarised and polarised incident neutrons. Two anisotropic versions of the Heisenberg spin chain are considered for such an examination: the spin-$1/2$ antiferromagnetic $XXZ$ model and the spin-$1/2$ ferromagnetic $XYZ$ model.The $XYZ$ model supports spinon scattering (modelled at finite temperature) and is related to the so-called Villain mode. The introduction of a perturbation in the form of an external transverse magnetic field or Dzyaloshinskii-Moriya interaction (DMI) leads to the emergence of incommensurability in the system; such a result is a signature of fractional excitations. The presence of these interactions also give rise to a chiral response associated with the spinons in the polarised term of the scattering cross section. The inelastic scattering cross section is computed for both unpolarised and polarised neutrons.In relation to the antiferromagnetic $XXZ$ model, emphasis is on spinon pair creation (modelled at $T = 0\ {\rm K}$). Motivated by the presence of a chiral response in the case of the $XYZ$ model mentioned above, a new technique is developed in order to incorporate DMI and the transverse magnetic field so that one can determine if there is a chiral property associated with the two-spinon system. This technique is numerical in nature and is based on Green function methods. Using the results produced by the Green function approach, the inelastic cross section in the presence of an external transverse magnetic field is computed for the first time. The result is compared with experimental neutron scattering data; good agreement is demonstrated between theory and experiments on ${\rm CsCoBr}_3$.Finally, the Green function approach is generalised to account for the interactions between spin chains in magnetic compounds described by a staggered field. Various dynamic structure factors are computed for this scenario with results compared to experiment; good agreement between the theory and experiments on ${\rm RbCoCl}_3$ is shown.
303 - PublicationAporia In Architectural Design(University College Dublin. School of Architecture, Planning and Environmental Policy, 2022)
; 0000-0002-7596-7748This project is concerned with the nature of knowledge in architectural design. Despite the increasing variety of approaches to design practice and design studies, the nature of design inquiry remains controversial. The primary aim of this project is to cast a new light on the nature of design inquiry by combining the concept of aporia with design inquiry. Traditionally, the term aporia denotes a perplexing state of mind and a problem at hand caused by equally plausible but mutually exclusive propositions. Thus understood, aporia is either a searching or a stopping device in an inquiry, or both. We situate aporia within the previous accounts to detect if aporia is compatible with them and if it can supplement these accounts. We analyse concrete examples of situations in architectural design when, due to an emerging contradiction, a shift in inquiry becomes necessary. In these aporetic situations, designers lose traction in their inquiry because they discover equally good reasons to think two or more things, such that these reasons stand in an apparent contradiction to each other. The project explains that, on the one hand, encountering aporia in architectural design enables and generates the inquiry by establishing the necessity for a shift in design approach. On the other hand, aporia specifies the elements in the design situation that must be changed, supplies the direction, and propels the inquiry. We demonstrate that to understand the nature of design inquiry fully, at its best, and to claim that design inquiry can lead to knowledge, it is necessary to suppose that aporia (as traditionally understood) occupies an important place in such an inquiry. The project examines the reasons for design inquiries to be aporetic and considers the consequences of this on epistemological claims in architecture.96 - PublicationThe application of spectroscopic techniques for the prediction of phosphorus dynamics in agricultural soils(University College Dublin. School of Biosystems and Food Engineering, 2021)
; 0000-0002-8019-2991Sustainable management of soil phosphorus (P) is important, because fertiliser supply is limited to the mining of finite phosphate rock and over-application of P causes harm to the environment. Currently in Ireland, only one parameter (Morgan's P (mg l-1)) is used to describe the supply of available P for crop uptake. Knowledge about P dynamics would allow an advance on current agronomic advice that relies on a quantification of current state to define what action a farmer should take. Dynamic P parameters (e.g. Langmuir sorption maximum, binding energy and maximum buffer capacity) are usually derived from sorption isotherms that are too time-consuming for routine analysis. Infrared (IR) spectroscopy offers a rapid analysis technique that can potentially replace some extractive and digestive techniques. The aim of this study was to develop a framework for incorporating soil P dynamics, quantified using rapid, low cost methods, into Irish agronomic advice to optimise productivity while supporting water quality policy. This was addressed by considering the accuracy of IR spectroscopic predictions of parameters that describe P sorption in soil, the accuracy of pedotransfer functions to predict P isotherm parameters, by identifying different mechanisms driving P isotherm properties and by defining a conceptual framework of categorisation for soils based on their P sorption parameters coupled with STP data. First horizon subsamples (n = 225) were taken from the archive of the Soil Information System (SIS) Ireland (Creamer et al., 2016) at Johnstown Castle, Wexford. Phosphorus sorption Index (PSI, R2c = 0.63, R2v = 0.65), phosphorus sorption capacity remaining (PSCr, R2c = 0.77, R2v = 0.67), phosphorus sorption capacity total (PSCt, R2c = 0.75, R2v = 0.60), Langmuir isotherm parameters in the 0 – 25 mg P l-1 range of added P (Smax25, R2c = 0.70, R2v = 0.60; k25, R2c = 0.66, R2v = 0.62; MBC25, R2c = 0.66, R2v = 0.60) and Langmuir isotherm parameters in the 0 – 50 mg P l-1 range of added P (Smax50, R2c = 0.75, R2v = 0.67; k50, R2c = 0.79, R2v = 0.47; MBC50, R2c = 0.74, R2v = 0.53) were predicted using MIR to a standard suitable for rough screening of agricultural soils. Langmuir sorption maximum, Smax50, was reliably predicted using multiple linear regression (MLR) with S50, OM and Mehlich-3 Fe (R2c = 0.91 and R2v = 0.95). The chemical data were also used to better understand the different isotherm shapes identified in the Irish soil population, where 64 % had Gile's non-strict L shape isotherm mechanism and 27 % were classified as having C shape isotherms. A conceptual framework based on P sorption parameters that incorporated STP was defined for agricultural soils. It was recommended that current Index classes be re- evaluated to consider having a target value (as Index 3) and to split those requiring reduction, or drawn-down, into a class near the target and a class that is far from the target. This split would contribute to a tool for critical source area (CSA) identification for P management. It was found that soils could be reliably classified into the new framework using values predicted from both MIR spectroscopy and pedotransfer functions. Optimisation of the framework for P sorption specific management of agricultural soils will require two additional steps: (1) further development of the MIR methodology for field use and (2) field validation of the thresholds and interpretation proposed.18 - PublicationThe application of whole genome sequencing approaches to elucidate the genetic structure, phylogeny and infection dynamics of Mycobacterium avium subspecies paratuberculosis in Ireland(University College Dublin. School of Veterinary Medicine, 2022)
; 0000-0002-7175-9626Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne’s disease (JD) in ruminants, a chronic enteric disease that is a burden on the cattle industry. Having a clear picture of the genetic diversity of a pathogen provides an understanding of its biology and epidemiology, both of which are crucial for improving and refining control of the disease. The main aim of this thesis was therefore to apply whole genome sequencing (WGS) methodology as a means of studying MAP genetic diversity and infection dynamics across the island of Ireland. To initiate the WGS analyses, several techniques for method optimisation were first pursued, including DNA extraction, library preparation and computational analysis of sequence data. I then used these optimised methods to explore whether there was an obvious genetic basis for the suspected attenuation of a clinical Irish MAP isolate, CIT003, that had been used in an experimental infection study of cattle that failed to progress to infection. These analyses found mutations in several genes that may have led to attenuation of the CIT003 strain used, including prpB, which encodes methylcitrate lyase (MCL), a key enzyme in the methylcitrate metabolic cycle responsible for metabolising fatty acids. These in silico leads these were then followed up by in vitro culture experiments, revealing the potential impact of these mutations on growth in vivo. The next stage was to apply WGS to a collection of 197 MAP isolates from the years 2013- 2019, spanning 27 Irish counties. When compared with previously used MIRU-VNTR methods, WGS demonstrated considerably better resolution, revealing that Irish isolates fell into eight distinct clades separated by as much as ~200 SNPs. Isolate data also revealed cases of mixed infection within herds, as well as identical isolates being present in different areas of the country, suggesting MAP infection is spread across the island via cattle trade networks. An attempt to expand upon the temporal depth in the Irish MAP dataset by sequencing isolates from 2004 and 2005 was attempted, but this effort was met with contamination issues present in the samples. By integrating published datasets from across Europe, Australia, Canada, and the US it was found that most European isolates clustered together with Irish isolates, while most Canadian, US and Australian isolates formed their own clades. A simple preliminary coalescent model in BEAST indicated that most Irish and European isolates share a common ancestry somewhere within the last 50-100 years. The BEAST model also estimated a substitution rate of 0.25-0.27 SNPs/genome/year for MAP, which is consistent with previously published rates. The final approach was to use WGS at a finer scale on specific problem herds identified during the work, seeking to establish the levels of genetic diversity within these herds, and resolve potential transmission chains. Isolates within the problem herd ‘Cork 10’ were found to be highly similar, with the combination of WGS and computational approaches able to resolve a transmission chain linking the similar isolates together. However, herd ‘Tyrone CaA’ showed high intra-herd variation, confounding the resolution transmission chains. The opportunistic nature of sampling carried out in these herds limited the temporal depth captured, and in both cases affected the ability to resolve transmission chains. Overall, the data presented in this thesis highlights the utility and resolution offered by WGS and sheds new light on the MAP global genetic diversity, as well as infection transmission and persistent infection in herds in Ireland.209 - PublicationThe applications of mobile athlete self-report measures in elite Gaelic Games(University College Dublin. School of Public Health, Physiotherapy and Sports Science, 2020)Advances in athlete monitoring practices are permeating from elite, professional sports to sub-elite and amateur programmes through continuous developments in both the technology itself and the underpinning research. Sports practitioners utilise data in new ways to find a competitive edge, encouraged by an expectation of excellence from athletes who are now more knowledgeable than ever. However, the introduction of technology to a process is not without its challenges, and whilst new methods in sports performance analysis have been game-changing, the use of athlete self-report measures seems yet to realise its potential. As a relatively new progression, there is a dearth of evidence on mobile athlete self-report measures (M-ASRM), particularly in team sports. It remains unclear what the appropriate and inappropriate uses of M-ASRM data are, and how measure design and implementation affect this utility. This programme of research utilised mixed methods to investigate the applications of M-ASRM in elite Gaelic games. Through reviews of the market and the literature, objective analyses of M-ASRM data and exploration of stakeholder experiences, the findings of this thesis have illuminated the concept of M-ASRM in athlete monitoring, by identifying what they are and what they are not, informing their appropriate use cases and the requirements for successful implementation in team sport. Findings from the quantitative methods suggest that rigorous instrument development and implementation in large, controlled studies are required to understand pertinent interpretation of M-ASRM data and use in objective or predictive analysis models. Findings from the qualitative methods suggest established subjective value in communication and information disclosure, remote athlete management, informing decision making and facilitating advanced planning. However, significant barriers to use were identified through an underestimation of the requirements for successful implementation. The challenges related to the measure itself and its limitations, but largely concerned the human factors in recording, reviewing, disseminating and acting on data, in addition to forging stakeholder understanding and engagement. The results of the research are triangulated and underpinned in technology acceptance theory, concluding with the development of considerations for successful M-ASRM implementation in team sport.
393 - PublicationApplied Diffraction Imaging: Conventional vs. Machine Learning ApproachDiffractions are oft overlooked in favour of specular reflections for seismic imaging. Diffractions, however, are formed by objects and discontinuities which are comparable or smaller than the wavelength. Therefore, if the diffractions can be imaged, these objects and discontinuities can be directly imaged. Said features are geologically noteworthy as structural and stratigraphic features of interest which may directly affect hydrocarbon migration, flow, and trapping. While straightforward in theory, in application separating the diffractions from the wavefield is a complex and intricate task. This thesis aims to discuss what makes separation so problematic and attempts to address various methods for allaying some of these issues. Additionally, this thesis intends to tackle the real benefits diffraction imaging can add to a conventional seismic image. To achieve these goals, existing separation techniques are analysed in pre-migration and post-migration domains. These analytical methods leave a volume which contains both diffractions and noise and require additional inputs such as a dip field. Ergo, any errors present in the dip field are incorporated into the diffraction image, diminishing its quality. In this thesis, adaptations to existing methods have been proposed as well as a novel method in the pre-migration domain. These new methods incorporate common geophysical techniques to obtain a cleaner separation. The novel method, histogram-based separation, is an analytical curve-fitting technique to identify diffractions without the presence of noise. Deep learning has also been integrated with the methods. Firstly, with pre-migration separation deep learning has been used to automatically identify and separate diffractions, obtaining a cleaner separation in a faster time. Another neural network is also trained which can apply a post-migration-based diffraction imaging scheme directly on stacked, migrated, seismic data, something hitherto impossible. These methods have been applied to seismic and GPR data highlighting the benefits of diffraction imaging.
66 - PublicationApplying Computational Fluid Dynamics Simulations for Aerodynamic Studies of Long-span BridgesIn the design of long-span bridges, estimating the wind effects is a critical requirement to evaluate and eliminate the risks of wind-induced problems on structural safety and serviceability. This thesis aims to validate the use of Computational Fluid Dynamics (CFD) simulations in bridge aerodynamic studies. A comprehensive review of the literature on the use of wind tunnel testing and CFD modelling for wind issues on long-span bridges was prepared. The lack of confidence of the bridge industry in applying CFD simulations within the design process due to insufficient validation and standardized guidance for use was noticed. Also, the need for a robust workflow for CFD modelling of wind effects for long-span bridge design and bridge operation was identified. Hence, a workflow using open-source software was proposed, which can be conveniently adopted to investigate bridge aerodynamics in bridge engineering practice. A general guidance was also formed where examples were provided to demonstrate specific features. A group of three-dimensional (3D) Reynolds-Averaged Navier-Stokes (RANS) simulations and Detached Eddy simulations (DESs) were performed on sectional bridge deck models at a scale of 1/50. These simulations replicated wind tunnel tests conducted during the design of the Rose Fitzgerald Kennedy bridge in Ireland. Sensitivity studies of the mesh, domain sizes, and turbulence models were conducted during the development of the CFD model, and showed that these factors have appreciable effects on the results of the CFD simulations. When comparing aerodynamic coefficients calculated by simulations and wind tunnel tests, a general agreement was achieved though some discrepancies were found. Similar levels of discrepancies were witnessed in the literature and was most likely due to the sensor interference during wind tunnel tests. In addition, the effects of secondary structures on the aerodynamic coefficients of bridge decks were investigated and shown to be significant. This emphasized the necessity to include these secondary structures when investigating bridge aerodynamics, while existing studies in this area often neglect them. A group of full-bridge simulations were performed at full scale, which was the first to include boundary conditions mapped from Weather Research and Forecasting (WRF) simulations, a high-precision terrain model, and a full-bridge geometry with all the secondary structures. The pseudo-transient time history of wind velocities determined by CFD simulations achieved an extraordinary agreement field measurement data from sensors at multiple locations on the bridge, which was also unprecedented in this area. Results of these full-bridge simulations are also used to initialise simulations at local regions of bridge deck segments. Validations of these local simulations were completed through comparisons of wind velocities predicted by local simulations, full-bridge simulations, and field measurement data. Aerodynamic forces are calculated from these local simulations and compared with results determined by wind tunnel coefficients with field measurement data, Eurocode equations with field measurement data, and Eurocode equations with estimated wind velocities. Aerodynamic forces predicted by CFD simulations were shown to align with the philosophy of sustainable design. Overall, this thesis provided unprecedented validations for the use of CFD simulations at multiple geometric scales. It demonstrated the great performance of CFD simulations in investigating wind effects under realistic wind conditions, which are often challenging for wind tunnel tests to incorporate. The outcome of this thesis is being presented to the NSAI National Committee on revision of the National Annex of the Eurocode on Wind (EN 1991-1-4). But most importantly, great confidence can be drawn from the outcome of this thesis, in using CFD simulations as a robust approach to estimate wind effects on long-span bridges.
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