VictorJuiz/thesis huggingface dataset:
Creation and manipulation of quantum states in nanostructures

Nanostructures are promising building blocks for quantum technologies due to their reproducible nature and ability to self-assemble into complex structures. However, the need to control these nanostructures represents a key challenge. Hence, this thesis investigates the manipulation and creation of quantum states in certain nanostructures. The results of this thesis can be applied to quantum information processing and to extremely sensitive magnetic-field measurements.
In the first research chapter, we propose and examine methods for entangling two (remote) nuclear spins through their mutual coupling to a transient optically excited electron spin. From our calculations we identify the specific molecular properties that permit high entangling power gates for different protocols.
In the next research chapter, we investigate another method to create entanglement; this time between two remote electronic spins. This method uses a very sensitive magnetic-field sensor based on a crystal defect that allows the detection of single magnetic moments. The act of sensing the local field constitutes a two-qubit projective measurement. This entangling operation is remarkably robust to imperfections occurring in an experiment.
The third research chapter presents an augmented sensor consisting of a nitrogen-vacancy centre for readout and an `amplifier' spin system that directly senses tiny local magnetic fields. Our calculations show that this hybrid structure has the potential to detect magnetic moments with a sensitivity and spatial resolution far beyond that of a sensor based on only a nitrogen-vacancy centre, and indeed this may be the physical limit for sensors of this class.
Finally, the last research chapter investigates measurements of magnetic-field strength using an ensemble of spin-active molecules. Here, we describe a quantum strategy that can beat the common standard strategy. We identify the conditions for which this is possible and find that this crucially depends on the decoherence present in the system.

Keywords: entanglement
crystal defect
NMR
magnetic sensor
Advisor: Gauger, E
Benjamin, S
Lovett, B
Understanding the link between interleukin 17 and vaccine-induced protection in tuberculosis

Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis (M.tb), remains a global health problem and although BCG offers some protection against childhood disseminated disease and other mycobacterial infections, its efficacy against pulmonary TB varies between 0 and 80%. Modified Vaccinia virus Ankara expressing antigen 85A (MVA85A) is a novel TB vaccine designed to boost mycobacterium-specific CD4+ T cell response primed by BCG. MVA85A induces strong interferon (IFN)-γ responses, a cytokine known to be essential for protection following M.tb infection. A strong IFN-γ response is not a correlate of protection and in terms of the adaptive response, interleukin (IL)-17 is emerging as an important cytokine following vaccination as it is thought to help boost IFN-γ production by CD4+ T cells. This thesis shows that MVA85A induces IL-17 in PBMC and whole blood of human BCG – MVA85A vaccinees. This is replicated in mice receiving BCG – MVA85A intranasally. The administration of cholera toxin (CT) with BCG enhances IL-17 and confers improved protection following M.tb challenge, which is partially dependent on IL-17 and on the mucosal route of administration. Since CT is not a suitable adjuvant in humans, an alternative IL-17-inducing pathway was investigated. In human BCG – MVA85A-vaccinated volunteers, blocking the hydrolysing ability of the CD39, an apyrase responsible for hydrolysing pro-inflammatory ATP, enhances IL-17 production. Challenge of BCG – MVA85A-vaccinated CD39-/- mice with M.tb slightly improved the protective capacity of the vaccine, suggesting that a pathway dependent on ATP-driven inflammation may be a target for improving the immunogenicity of a vaccine against M.tb disease. Overall, this thesis has confirmed the important role of IL-17 in vaccine-induced protection against TB disease and identifies a possible target pathway for improvement of a novel vaccine.

Keywords: T cells
interleukin 17
cytokines
cholera toxin
tuberculosis
immunology
Advisor: McShane, H
Fletcher, H
Two-channel Kondo phases in coupled quantum dots

We investigate systems comprising chains and rings of quantum dots, coupled to two metallic leads. Such systems allow to study the competition between orbital and spin degrees of freedom in a nanodevice, and the effect this subtle interplay has on two-channel Kondo (2CK) physics. We demonstrate that a rich range of strongly correlated electron behaviour results, with non-Fermi liquid 2CK phases and non-trivial phase transitions accessible. We employ physical arguments and the numerical renormalization group (NRG) technique to analyse these systems in detail, examining in particular both thermodynamic and dynamical properties.
When leads are coupled to either end of a chain of dots, we show that the resulting behaviour on low temperature/energy scales can be understood in terms of simpler paradigmatic quantum impurity′⊨.Aneffectivelow-e≠rgysing≤-sπn2CKmodelisderivedforallodd-≤n>hcha∈s,whi≤thebehaviourofeven-≤n>hcha∈sisrelatedfundamentally→t
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In particular, for small interdot coupling, we show that an effective coupling mediated though incipient single-channel Kondo states drives all odd chains to the 2CK fixed point (FP) on the lowest temperature/energy scales. A theory is also developed to describe a phase transition in even chains. We derive an effective channel-anisotropic 2CK model, which indicates that the critical FP of such models must be the 2CK FP. This physical picture is confirmed using NRG for various chain systems.
We also examine the effect of local frustration on 2CK physics in mirror-symmetric ring systems. The importance of geometry and symmetry is demonstrated clearly in the markedly different physical behaviour that arises in systems where two leads are either connected to the same dot, or to neighbouring dots. In the latter case, we show for all odd-membered rings that two distinct 2CK phases, with different ground state parities, arise on tuning the interdot couplings. A frustration-induced phase transition thus occurs, the 2CK phases being separated by a novel critical point for which an effective low-energy model is derived. Precisely at the transition, parity mixing of the quasidegenerate local trimer states acts to destabilise the 2CK FPs, and the critical FP is shown to consist of a free pseudospin together with effective single-channel spin quenching. While connecting both leads to the same dot again results in two parity-distinct phases, a simple level-crossing transition now results due to the symmetry of the setup. The proposed geometry also allows access to a novel ferromagnetically-coupled two-channel local moment phase.
Driven by varying the interdot couplings and occurring at the point of inherent magnetic frustration, such transitions in ring structures provide a striking example of the subtle interplay between internal spin and orbital degrees of freedom in coupled quantum dot systems, and the resulting effect on Kondo physics.

Keywords: two-channel Kondo
quantum dots
numerical renormalization group
NFL
NRG
Kondo
non-Fermi liquid
Anderson model
Advisor: Logan, D
Kierkegaard and a Religionless Christianity

The central aim of this thesis is to analyse the influence of Kierkegaard on Bonhoeffer. This relationship has been almost universally recognized. And yet this area has received no comprehensive study, limited within the secondary literature to footnotes, digressions, and the occasional paper. Furthermore, what little literature there is has been plagued by several stereotypes. First, discussion is often limited to Discipleship. Second, Kierkegaard has been identified as an individualist and acosmist who rejected the church, leading many to consider Bonhoeffer the ecumenist and ecclesiologist as selectively agreeing with Kierkegaard, but ultimately rejecting his overall stance. This thesis will argue that neither stereotype is true, and suggest (a), that Kierkegaard’s influence can be found throughout Bonhoeffer’s work, and (b) that although a more stereotypical perspective may be present in SC, by the end of his life Bonhoeffer had gained a far deeper understanding across the breadth of Kierkegaard’s work. The importance of this thesis is not simply to ‘plug the gap’ of scholarship in this area, but also to suggest the importance of analysing Kierkegaard and Bonhoeffer together. This will focus on three specific areas. First, alongside the influence of Kierkegaard on Bonhoeffer, it will argue for the importance of using Bonhoeffer as an interpretive tool for understanding Kierkegaard. This thesis will show how Bonhoeffer adopted and adapted Kierkegaard’s work to his own situation, forcing Kierkegaard to answer questions that were not present during his own life. In this way, we are led to compare Kierkegaard and Bonhoeffer as individuals, and not simply their static declarations. Secondly, against the tendency to consider Kierkegaard and Bonhoeffer’s final attacks on Christendom as unfortunate endings to otherwise profound careers, it will be suggested that these attacks stand as the fulfilment of their earlier thought. It will be argued that despite their different contexts, both Kierkegaard and Bonhoeffer were led to the same conclusions concerning Christendom. Thirdly, given Kierkegaard’s submission to indirect communication and his somewhat 'prophetic' proclamations concerning one who will come after him and reform, this thesis will ask whether Bonhoeffer stands as something of a fulfilment to Kierkegaard’s thought in the guise of a Kierkegaardian ‘reformer’.

Keywords: Epistemology
Kierkegaard
Bonhoeffer
Attack on Christendom
Christology
Idealism
Ethics
Ecclesiology
Attack on Idealism
Advisor: Pattison, G
Study of DNA double strand break repair in Dictyostelium discoideum

The homologous recombination (HR) pathway contributes to genome integrity by mediating double strand break (DSB) repair using a homologous DNA sequence as a template. In mammals Rad51 and Brca2 are molecules central to this process. Little is known about HR repair in Dictyostelium. However, research previously conducted on DSB repair using this organism has shown that DSB repair pathways are highly conserved when compared to humans. This encouraged study of HR in this organism. In this study, through a bioinformatics search I have identified putative orthologues of most human HR proteins and most interestingly of BRCA2, which cannot be found in other lower eukaryotes used as models for DSB repair, such as the budding yeast S.cerevisiae. Brcp, the Dictyostelium BRCA2 ortholog, shows similar domain structure when compared to BRCA2-related proteins identified in other organisms. To verify the implication of HR proteins in DSB repair, I developed a method to monitor recruitment of DNA repair proteins on chromatin upon DSB induction. Findings of this study suggest that both Brcp and Rad51 get recruited to chromatin upon DSB induction and are therefore implicated in DSB repair in Dictyostelium. To further study Brcp function and based on findings suggesting that disruption of brcp might be lethal, I developed a novel system for specific and conditional depletion of endogenous Dictyostelium proteins. Utilizing this system, I conducted phenotypic studies in a strain depleted of Brcp to examine its role in DNA repair. Overall this study shows that the HR pathway in Dictyostelium shows great similarity to vertebrates, making Dictyostelium an appealing model for the study of DSB repair and specifically HR.

Keywords: DNA repair
DNA damage response
DNA damage
Dictyostelium
Advisor: Lakin, N
Aerosol-cloud-precipitation interactions

Aerosols are thought to have a large effect on the climate, especially through their interactions with clouds. The magnitude and in some cases the sign of aerosol effects on cloud and precipitation are highly uncertain. Part of the uncertainty comes from the multiple competing effects that aerosols have been proposed to have on cloud properties. In addition, covariation of clouds and aerosol properties with changing meteorological conditions has the ability to generate spurious correlations between cloud and aerosol properties.
This work presents a new way to investigate aerosol-cloud-precipitation interactions while accounting for the influence of meteorology on cloud and aerosol. The clouds are separated into cloud regimes, which have similar retrieved cloud properties, to investigate the regime dependence of aerosol-cloud-precipitation interactions. The strong aerosol optical depth (AOD)- cloud fraction (CF) correlation is shown to have the ability to generate spurious correlations. The AOD-CF correlation is accounted for by investigating the frequency of transitions between cloud regimes in different aerosol environments. This time-dependent analysis is also extended to investigate the development of precipitation from each of the regimes as a function of their aerosol environment.
A modification of the regime transition frequencies consistent with an increase in stratocumulus persistence over ocean is found with increasing AI (aerosol index). Increases in transitions into the deep convective regime and in the precipitation rate consistent with an aerosol invigoration effect are also found over land. Comparisons to model output suggest that a large fraction of the observed effect on the stratocumulus persistence may be due to aerosol indirect effects. The model is not able to reproduce the observed effects on convective cloud, most likely due to the lack of parametrised effects of aerosol on convection. The magnitude of these effects is considerably smaller than correlations found by previous studies, emphasising the importance of meteorological covariation on observed aerosol-cloud-precipitation interactions.

Keywords: precipitation
climate
satellite
cloud
aerosol
aerosol-cloud interactions
Advisor: Stier, P
Selective traditions: feminism and the poetry of Colette Bryce, Leontia Flynn and Sinead Morrissey

This thesis seeks to argue for the problematising role of tradition and generational influence in the work of three Northern Irish poets publishing since the late 1990s. The subjects, Colette Bryce (b. 1970), Leontia Flynn (b. 1974) and Sinéad Morrissey (b. 1972), emerged coterminously, each publishing with major UK publishers. Together they represent a generation of assured female poetic voices. This study presents one of the first critical considerations of the work of these poets, and it remains conscious of the dominance of conceptions of tradition and lineage which are notable in poetry from Northern Ireland from the twentieth-century onwards. In suggesting that this tradition is problematised for emerging women poets by precursor-peer dominance and the primacy of male perspectives in the tradition, this thesis combines a study of poetics, themes relating to gender, detachment and paratexts. From consideration of these elements, it proposes that contemporary poets are not necessarily subject to the powers of tradition and influence, but rather, are capable of a selective approach that in turn demonstrates the malleability of contemporary traditions.
The approaches are laid out in four chapters which move from a consideration of “threshold” paratexts (following from the work of Gérard Genette), including book reviews and dedications, through studies of thematic divergence and detachment, the changing status of women’s poetry traditions within Northern Ireland and beyond, the significance of gendered subjects in poetry, and influence found not in thematic or paratextual aspects, but in the individual aspects of poetic form. These aspects combine to form poems and the tradition(s) in which they continue. The thesis provides extensive coverage of the work of Bryce, Flynn, and Morrissey, combining close readings with the application of theoretical frameworks interrogating the implications of literary traditions on later writers (especially when the writers are temporally and culturally close), giving particular consideration to gender and feminist politics. It explores a variety of different critical truisms applied to the poetic generations that precede the younger poets and identifies both compliance and divergences from the contemporary Northern Irish canon. In doing so, this study simultaneously illuminates the frailties of the popular, overwhelmingly male, tradition, particularly as regards to representations of women, and provides direction for studies of post-millennial Northern Irish poetry.

Keywords: tradition and influence studies
Irish studies
Sinead Morrissey
Northern Irish literature
Irish poetry
Leontia Flynn
women's writing
Colette Bryce
Ulster poetry
Poetry
Contemporary poetry
Advisor: O'Donoghue, B
The development of organolead reagents in organic synthesis

This thesis describes the synthesis of novel lead(IV) tetracarboxylates and the development of their use in carbon-carbon bond formation processes, with a particular emphasis on the construction of chiral, quaternary centres. Organolead(IV) tricarboxylates have been widely used in the functionalisation of a range of β-dicarbonyl compounds, and the available evidence suggests that these reactions occur by a ligand coupling mechanism. For this reason, by using chiral lead(IV) compounds, it may be possible to achieve a transfer of asymmetry in the bond formation reaction.
A variety of achiral and chiral dicarboxylic acid ligands were synthesised, either by reaction of phthalic or camphoric anhydride with a range of diols, or by elaboration of the camphoric acid skeleton directly. A range of novel lead(IV) compounds were constructed using these ligands, both as bis-complexes and as mixed ligand complexes. The complexes were characterised by a combination of IR and NMR techniques, including 207Pb NMR spectroscopy, and elemental analysis. The reactivity of some of the complexes was demonstrated via reaction with allyltributyltm.
The lead(IV) complexes were used in the α-phenylation of a range of β-dicarbonyl substrates. Yields ranged from poor to excellent, but in all cases the enantiomeric excesses of the reactions were found to be no greater than 12%. Studies of these complexes by 207Pb NMR spectroscopy revealed that each complex was present as more than one species in solution, which is thought to be the reason for the poor overall transfer of chirality in the phenylation reactions.
The arylation procedure uses catalytic mercury(II) acetate, which can in turn introduce further potential ligands to the exchanging system. It was found that alternative catalysts, such as mercury(II) chloride, could be used successfully in the α-phenylation reaction.

Advisor: Moloney, M
Fully relaxed heavy ion reactions in the mass 80 region

This thesis describes a set of experiments to investigate the properties of fully relaxed reactions in the mass 80 region. Symmetric and asymmetric entrance channels, leading to similar compound nuclei, have been compared in order to determine the characteristics of the reaction mechanism.
The symmetric system 40Ca + 40Ca has been studied at laboratory energies of 197.3 and 230.5 MeV. The fissionlike products were detected by a series of six time of flight telescopes, placed at angles between 10° and 52.4° to the beam, and a Bragg curve spectrometer-multiwire proportional chamber telescope, situated at 30°. Data were collected in both singles and coincidence modes. To complement this measurement, fully damped yields from 28Si + 50,52,54 Cr at 130 MeV and from 28Si + 50Cr at 150 MeV were measured using an array of four avalanche counter-silicon surface barrier detector telescopes spanning the angular range between 20° and 50°. The avalanche counters used in this experiment are of a new design which was developed in Oxford. We present the features of this design and discuss the detectors' operational characteristics.
Several possible interpretations of the data are considered. It is shown that diffusion models of deep-inelastic scattering tend to underpredict the measured fully relaxed cross sections. Rotating finite range model calculations of fission barriers point to the possibility of fast-fission in this mass region; a process hitherto associated with much heavier systems. Furthermore, such models also predict that these systems may fission asymmetrically. The more commonly employed rotating liquid drop model of the nucleus is unable to predict either of these effects. The data are compared with those reported in the literature for other systems in this mass region. It is argued that all these results are consistent with fast-fission and asymmetric fission, thus obviating the need for the previously proposed interpretation in terms of intermediate mechanisms.

Advisor: Smith, A
The behavioural ecology of the Mara, Dolichotis patagonus

This thesis presents the results of a 3 year field study on the behavioural ecology of the mara on the Valdés Peninsula in Argentina. The main goal was to investigate why the mara's social system incorporates both monogamy and communal denning, a combination unknown in other mammals. The research techniques used were behavioural observations and radio-tracking.
Radio-tracking of 9 maras revealed that pairs were continually moving into new areas, suggesting that their ranging behaviour is adapted to an irregular pattern of resource distribution. Two maras had prevailing ranges of 35 ha and moved yearly over about 200 ha. Ranges floated around a geographic centre. One constraint on the animals' movements may be the need to stay near a den site for pupping. Maras were diurnal, and spent on average 46% of the day grazing. Ranges may overlap up to 33%, but range use between neighbouring pairs were negatively correlated suggesting that animals were avoiding each other--pairs may be occupying floating territories.
Evidence that maras are monogamous in the wild is presented. The factors leading to monogamy are argued to be: (i) females are irregularly dispersed because of the distribution of food; and (ii) the brevity of the female's oestrus (1-2 hrs). A male attempting to mate polygynously would have difficulties in finding and securing a female; thus males may do best by staying with one female to ensure a successful mating. Males may enhance their reproductive success by watching for predators so that their females can spend more time feeding to meet the energetic demands of lactation and gestation.
During the pupping season, August to January, groups of 1 to 22 pairs gather at single dens. Several dens may be located near each other to form denning communities. Most pairs produce only one litter a year and there is a peak of births in September and October. Pairs visit the den once a day for a period of 5-6 weeks to nurse their young. Den sites are not limited; and the reason maras den communally appears to be the increased protection from predators accruing to pups and adults in larger groups.
Two possible routes are suggested in the evolution of the mara's social system: (i) from a monogamous starting point it has become advantageous to creche pups; or (ii) ancestral maras were more colonial and probably polygynous, but have been forced to space out because of changes in the distribution of food, which has led to monogamy.
Finally, maras were compared with other caviomorph rodents, lagomorphs, and monogamous ruminants and were shown to be most similar to the latter in their adaptations to the environment a remarkable example of convergent evolution.

Advisor: Macdonald, D