VictorJuiz/thesis huggingface dataset:
Exploring the Fermi surfaces of novel quantum materials using high magnetic fields

This thesis presents the results of torque magnetometry and resistivity measurements of the electronic structure of novel quantum materials, specifically using the techniques of quantum oscillations and angle-dependent magnetoresistance oscillations. Measurements of the Fermi surfaces of these materials, alongside comparisons to the electronic structure predicted by density functional theory calculations, can elucidate much about the novel physical properties they exhibit and the competing interactions which govern their phase diagrams.
The first system studied is the Iron-based superconductor FeSe1-xSx, an isoelectronically doped version of a system of much current interest, FeSe. Doping up to x = 0.2 is found to suppress the structural transition in this system entirely, with superconductivity continually present at low temperatures. Shubnikov-de Haas measurements across this range find a small quasi-two dimensional Fermi surface that increases in size and warping continuously with doping, with orbital dependent effective masses that do not change significantly within the orthorhombic phase.
The second material studied is the antiferromagnetic intermetallic CeZn11 which, featuring an unpaired 4f electron, is considered a possible candidate for heavy fermion behaviour. De Haas-van Alphen oscillations are seen once the antiferromagnetic phase is suppressed, and comparable frequencies of oscillation are measured in the non-magnetic analogue LaZn11, although with relatively smaller effective masses. GGA+U calculations, once magnetic breakdown is considered, match well the measured frequencies, confirming CeZn11 to be a localised moment system with the 4f electron well below the Fermi level.
The final material studied is the transition metal dichalcogenide IrTe2, which undergoes dimerisation upon cooling into a number of possible charge modulated structures. Low temperature de Haas-van Alphen measurements find multiple domains of a quasi-two dimensional Fermi surface, no longer perpendicular to the lattice planes. Angular-dependent magnetoresistance oscillations observe a similarly tilted quasi-one dimensional Fermi surface, again with many domains present. Together these measurements confirm the unusual dimensionality of the dimerised Fermi surface of IrTe2.

Keywords: Quantum oscillations
Density functional theory
Advisor: Coldea, A
Expressions of grief on the early modern stage

This thesis investigates the ways mourning was performed on the early modern stage. "Expressions of Grief on the Early Modern Stage" re-evaluates widely accepted accounts of theatrical and literary mourning, intervening in two major debates. The first is the extent to which theatrical mourning is an expression of mourning for a Catholic past, a familiar account that is complicated by asking what happens when mourning is future-oriented, rehearsing for a death still to come. The second intervention disrupts the notion of a linear progression from stoical, anti-grief attitudes to increasing sympathy for mourners by revealing a variety of responses to staged mourning across this time period.
I identified seventy-eight plays from 1580-1642 that feature extended or notable scenes of mourning, and created a database to track accompanying gestures, associated playing companies, playhouses, and playwrights, and dates of composition and performance (when known). The thesis focuses on four aspects of the dramaturgy of mourning that emerged from this research: mourning as preemptive or strategic; mourning displaced by revenge; mourning performed as explicitly false; and, throughout, the way mourning deploys the vertical axis of the stage structure and the actor’s body. The following chapters examine mourning through the specific gestures of prostration and kneeling, through motion (the rising and falling in the history plays as revenge takes the place of mourning), and the metadramatic bracketing of mourning in fake funerals. Examining specific gestures and the use of the stage space, reveals the way mourning was performed both "out of joint" – that is, out of the expected time sequence – and "out of place", using verticality in unexpected ways, lowering the body to take control of the gaze and the dramatic moment; framing 'above' as strategically advantageous while the confined theatrical space forces the actors to descend.
Analysing prostration scenes in George Peele's David and Bethsabe and in Titus Andronicus reveals additional substantiation for Peele's role as a collaborator with Shakespeare. Looking at the three parts of Henry VI through the thematic lens of mourning contributes to the debate over the order of composition, offering tentative support for the 1-2-3 sequence. Tracking fake funerals over this time period revealed a sharp increase in this device after 1603, which the final chapter suggests is related to anxieties over public performances of mourning after Elizabeth I's death and one of the worst plague years on record.
Performances of theatrical mourning thus occur displaced in time, preemptive requests for a death not to happen rather than the belated wish to bring the dead back to life. Mourning in the theatre occurs out of place: testing classbased mourning scripts; moving up and down the vertical axis of the stage; performing a transitory state of emotion through transitory gestures; deploying submissive poses that turn out to hold surprising theatrical and strategic power.

Advisor: Maguire, L
Measurement of equation of state of compressed hydrogen and deuterium

Detailed understanding of the equation of state of light elements such as the hydrogen isotopes in the warm dense matter (WDM) regime is essential for the modeling of the inner structure of many astrophysical objects, in particular Jovian planets as well as inertial confinement fusion (ICF) research. In these systems quantum degeneracy and strong inter-particle forces play an important role making its theoretical description extremely challenging.
The Omega laser was used to drive a planar shock wave in cryogenically cooled deuterium creating WDM conditions. We used a set of independent diagnostics to measure the thermodynamic conditions of WDM including velocity interferometry (VISAR), streaked optical pyrometry (SOP) and x-ray Thomson scattering (XRTS). With a narrow-band x-ray backlighter probe at backscattering geometry the spectrally resolved XRTS accessed the boundary of collective and non-collective regimes making our measurement sensitive to both electron temperature and density.
This work presents a full set of measurements of the thermodynamic properties for different laser intensity drives creating warm dense deuterium at various degrees of degeneracy and coupling. The measured electron densities and temperatures ranged between 0.2 and 2.15×1023 cm−3 and 0.6 − 20 eV respectively. The scattering measurement confirmed the findings from the VISAR and SOP data and together densityfunctional molecular dynamics (DFT-MD) simulations provides a novel self-consistent approach for an accurate characterization of the microscopic structure of WDM.
Complementary to the laser compression work, findings from project employing static compression hydrogen with the use of diamond anvil cells is also be presented. The first direct measurement of the local field correction to the Coulomb interactions in degenerate plasma was obtained from inelastic scattering (20 keV probe) at the Diamond Light Source synchrotron facility.

Keywords: deuterium
fusion
hydrogen
plasma physics
x-ray scattering
planetary structure
equation of state
warm dense matter
Advisor: Jephcoat, A
Wark, J
Gregori, G
Integration of genetic data and genomic annotation in the analysis of genome wide association studies

This thesis explored the utility of genome wide association studies (GWAS) and meta-analysis to identify variants associated with serum pollutants levels and metabolic phenotypes. The secondary aims of these thesis were to annotate these variants with regulatory information from databases and to investigate the role of copy number variation in influencing gene expression and phenotype.
In the second and third chapters, we identified single nucleotide polymorphisms (SNPs) associated with pollutant and metabolic phenotypes. An example of a novel association was the relationship between SNPs in the ABCG2 gene and octachlorodibenzo-p-dioxin (OCDD). In the third chapter, we identified associations between metabolic phenotypes and SNPs. An example of an identified association was that between serum apolipoprotein B levels and rs7412, which is consistent with other GWAS. To fine map these loci and assign functional annotation, I created Bayesian credible sets and checked for overlap between SNPs in these credible sets and regulatory marks in the Encyclopaedia of DNA Elements (ENCODE) database. Annotating these credible set SNPs with functional information revealed various histone modifications and transcription factors that overlapped.
This study was also successful in identifying copy number variants (CNVs) from the PIVUS cohort. There were moderately strong associations between CNVs and some of the phenotypes studied. These associations did not appear to be mediated by the SNP within the CNVs, as the latter had higher P values of associations. In addition, I identified several clinically relevant CNV-expression quantitative trait loci (CNV-eQTL) associations a separate cohort of healthy individuals. Some of these associations were cell specific and/or context specific. Many of these CNVs contained SNPs which are lead SNPs in GWAS studies on a variety of different phenotypes.
In conclusion, this thesis was successful in identifying SNPs and CNVs associated with phenotypes, as well as annotating some of these variants with regulatory information. Further work is needed to clarify the mechanisms of regulation.

Advisor: Morris, A
Knight, J
Building the city of God: imperial patronage and local influence in Jerusalem from Theodosius I to Justinian (379-565 ad)

This thesis offers a fresh study of the sources on the history of the city of Jerusalem in the period between the reigns of the Roman emperors Theodosius the Great and Justinian I. In the Holy Land, this period roughly coincides with the arrival of St Jerome in 385 and the completion of Jerusalem’s last major church building before the Persian and Muslim conquests, the Nea church, dedicated in 543. One of the main aims of this thesis is to investigate the role of imperial patronage in the city and contrast it with the growing influence of local actors, i.e. bishops, monks, and rich pilgrims who settled there. My reading of the sources makes clear that Jerusalem and the imperial court were more closely connected than previously assumed. This manifested itself not only in imperial building projects, but also in the exchange of theological concepts and ideas. One of my key findings about this traffic is that the cult of saints was introduced to Jerusalem from Constantinople, while, in contrast, the veneration of the Virgin Mary originated in the holy city and reached the capital from there. The thesis offers a new interpretation of patriarchal politics in the times of the Christological controversies following the Council of Chalcedon (451) and of the political self-perception of Jerusalem from the beginning of the sixth century onwards, when the city with its loca sancta entered into a new form of relationship with the emperor Justinian, who bestowed his favour on Jerusalem in the form of imperial donations in return for the support of his ecclesiastical policies by the clergy and monks of Jerusalem.

Advisor: McLynn, N
Organic/inorganic hybrid nanoparticulate resonant contrast agents

An intriguing frontier for magnetic resonance imaging (MRI) is the development of responsive Gd3+-based contrast agents (CAs) that can report physiological variations in the tissue microenvironment.[1] Heterogeneous biological milieu and quantification of the CA concentration at the site of interest are the major limitations of responsive concentration-dependent protic MRI probes. A ratiometric approach based on dualmode CAs containing a 19F MRI reporter, in addition to a paramagnetic moiety, is one of the feasible strategies to overcome this drawback.
Since high fluorine content is required for in vivo imaging, nanoparticles offer advantageous characteristics over molecular probes due to their large surface area and size, allowing the incorporation of high concentrations of uorinated probes and paramagnetic CAs. For emerging applications of Gd3+ complexes at ultra-high magnetic fields, it was found that not only octadentate (q = 1), but also highly kinetically stable nonadentate (q = 0) Gd3+-DOTA systems can be incorporated into the mesopores of silica nanoparticles, resulting in an 8-fold increase in proton longitudinal relaxivity from 0.7 mM-1 s-1 to 6.2 mM-1 s-1 at 4.7 T compared to their molecular counterparts. A further 7-fold increase in longitudinal relaxivity was achieved when the silica surface of such particles was functionalised with highly acidic propyl sulphonates, enabling faster proton transfer through a hydrogen-bonded hydronium network. pH responsiveness of Gd3+ complexes tethered to particles has, on the other hand, been achieved through either local mobility or water access regulated by pH-responsive polymers acting as gating valves on the mesopores.
Moreover, symmetric 19F MRI CAs were accommodated within micron- and nanosized matrices comprised of polyelectrolytes, quaternary ammonium first generation dendrimers and centrifugable oil-containing silica nanocapsules. For these, the biggest challenge has been posed by restricted local mobility, which notably shortens transverse relaxation time and attenuates the 19F NMR signal. Finally, polymers based on uorinated quaternary ammonium, pH-sensitive and Gd3+-DOTA methacrylates were prepared, exhibiting a dual 19F/1H MRI contrast with reverse pH response.

Advisor: Davis, J
Measurement of the neutrino oscillation parameters sin²θ23, Δm²32, sin²θ13, and δCP in neutrino and antineutrino oscillation at T2K

The T2K experiment is a long-baseline neutrino oscillation experiment, in which a muon neutrino beam is directed over a 295 km baseline from the J-PARC facility to the Super-Kamiokande detector. This allows neutrino oscillation to be studied in two channels: disappearance of νμ and appearance of νe. The T2K beam can be run either in neutrino or antineutrino configuration, for a neutrino beam which is predominantly composed of νμ or anti ¯νμ respectively.
This thesis presents the first oscillation analysis to combine neutrino-mode and antineutrino-mode data sets, giving the first ever sensitivity to the CP-violating phase δCP from T2K data alone, as well as the most precise T2K measurement of the other neutrino oscillation parameters. The analysis uses a Markov Chain Monte Carlo method to construct a sample from the Bayesian posterior distribution, from which the oscillation parameters of interest and their uncertainties are estimated. Data samples from the T2K near detector, ND280, are fit simultaneously with data from the far detector in order to reduce the uncertainty in the far-detector prediction.
When fitting the T2K data alone, the best-fit oscillation parameter values are sin2 θ23= 0.519+0.031-0.059, sin2 θ13= 0.0257+0.0106-0.0440, Δm232= 2.54+0.12-0.10 × 10-3eV2,and δCP=-1.91 rad. The 90% credible interval for δCP excludes values around π/2: δCP ∉ [0.38, 2.60] rad. When fitting the T2K data with a constraint on sin2 θ13 from measurements by reactor experiments, the best-fit oscillation parameter values are sin2 θ23= 0.519+0.061-0.029, sin2 θ13= +0.0014-0.0014, Dm232= 2.54+0.12-0.12 × 10-3eV2, and δCP=-1.72 rad. The 90% credible interval for δCP contains values δCP ∈ [-3.10,-0.17] rad, excluding the CP-conserving values 0 and ±π at 90% probability.

Keywords: Neutrino physics
Neutrino
Antineutrino
Neutrino oscillation
CP violation
Advisor: Weber, A
Towards the synthesis of the ABC fragment of pectenotoxin-4

This thesis details the optimisation and development to the synthesis of the ABC fragment of pectenotoxin-4, a 26-membered macrolide marine natural product bearing 19 stereogenic centres, three tetrahydrofuran rings, one spiroketal and one bicyclic ketal.
Introduction
This section briefly discusses the isolation, structure elucidation, and biological activity of penctenotoxins, along with a review of previous synthetic efforts on the pectenotoxin family, especially the ABC fragment. It also summarises our group’s work in pursuing the total synthesis of this compound.
Results and Discussion
This section details synthetic efforts to improve the overall yield of the ABC fragment. In particular, it contains the optimisation of a low yield Carreira alkynylation reaction and a revised protecting group strategy to allow orthogonal deprotection on the ABC fragment for further elaborations. The revised route for the ABC fragment of pectenotoxin-4 contains 21 longest linear steps (27 steps in total) from D-mannitol with an overall yield of 2.1% (on average 83% per step).

Advisor: Donohoe, T
A computational model to understand the relationship between cardiac microstructure and diffusion MRI

The normal microstructure of the heart is fundamental to its healthy mechanical and electrical function. In diseases such as hypertrophic cardiomyopathy or myocardial infarction there is remodelling of the microstructure which can lead to heart dysfunction and even death. Diffusion MRI measures the magnitude and direction of the diffusion of water molecules within tissue, and can therefore be used to infer structural information about biological tissue. There remains some uncertainty about the relationship between cardiac microstructure and the diffusion MRI signal that it produces. Monte Carlo models can be used to increase the understanding of this relationship as well as to design optimal MRI sequences and propose image biomarkers related to specific microstructural changes. This Thesis presents a computational framework for the simulation of diffusion MRI in cardiac tissue, including an anatomically realistic model of cellular geometry, a Monte Carlo method to simulate the diffusion of water molecules and the calculation of diffusion MRI signals. The model is shown to simulate diffusion MRI results which correspond well with experimental data from five ex vivo rat hearts over a range of gradient strengths and diffusion times. Neither introducing membrane permeability nor increasing the diffusivity in the extracellular space compared with that within the cells showed a marked effect. The introduction of type IB disarray into the model, as commonly found in hypertrophic cardiomyopathy, caused the diffusion to become less anisotropic while the amount of diffusion remained constant. This model will allow the investigation of the relationship between different types and degrees of remodelling and the diffusion MRI signal, which will further the use of diffusion MRI as a clinical tool in the detection and quantification of cardiac remodelling in disease.

Advisor: Grau, V
Experiments on multi-level superconducting qubits and coaxial circuit QED

Superconducting qubits are a promising technology for building a scalable quantum computer. An important architecture employed in the field is called Circuit Quantum Electrodynamics (circuit QED), where such qubits are combined with high quality microwave cavities to study the interaction between artificial atoms and single microwave photons. The ultra-strong coupling achieved in these systems allows for control and readout of the quantum state of qubits to perform quantum information processing. The work on circuit QED performed in this thesis consisted of realizing an experimental setup for qubit experiments in a new laboratory, investigating the coherence and decay of higher energy levels of superconducting transmon qubits and finally demonstrating a novel coaxial form of circuit QED.
Designing and building a 3D circuit QED setup involved the following main accomplishments: producing high quality 3D cavities; designing and installing the cryogenic microwave setup as well as the room temperature amplification and data acquisition circuitry; successfully developing a recipe for the fabrication of Josephson junctions; controlling and measuring superconducting 3D transmon qubits at 10mK. Several qubits were fully characterised and have shown coherence times of several microseconds and relaxation times up to 25μs.
Superconducting qubits in fact possess higher energy levels that can provide significant computational advantages in quantum information applications. In experiments performed at MIT, preparation and control of the five lowest states of a transmon qubit was demonstrated, followed by an investigation of the phase coherence and decay dynamics of these higher energy levels. The decay was found to proceed mainly sequentially with relaxation times in excess of 20μs for all transitions. A direct measurement of the charge dispersion of these levels was performed to explore their characteristics of dephasing. This experiment was also reproduced on a 3D transmon fabricated and measured in Oxford, where due to a higher effective qubit temperature a multi-level decay model including thermal excitations was developed to explain the observed relaxation dynamics.
Finally, a coaxial transmon, which we name the coaxmon, is presented and measured with a coaxial LC readout resonator and input/output coupling ports placed inline along the third dimension. This novel coaxial circuit QED architecture holds great promise for developing a scalable planar grid of qubits to build a quantum computer.

Keywords: transmon
coaxmon
quantum computing
circuit quantum electrodynamics
coherence
higher levels
decoherence
superconducting qubits
artificial atom
3D cavity
Advisor: Leek, P