VictorJuiz/thesis huggingface dataset:
Work, heat, and power of quantum processes

The central purpose of this thesis is to study the familiar processes of quantum information theory from a thermodynamic point of view.
Chapter 1 introduces equilibrium thermodynamics and its laws. The laws are then motivated in a statistical mechanics approach which explicitly employs the language of quantum information theory.
Chapter 2 is dedicated to the concept of work extraction, in particular in non- equilibrium scenarios. In this context a generalised notion of equilibrium called passivity is introduced. The chapter’s final section gives an introduction and an overview of various approaches to work extraction ranging from classical to explicitly quantum scenarios.
Chapter 3 considers the question of powerful unitary operations. Focussing on the case of qubits (or rather wits, short for ‘work bits’) the chapter’s first result is an explicit protocol for maximally powerful driving for any given initial state. Building onto this, the chapter’s second main result is a proof that the evolution time (and hence the power of the corresponding work deposition process) can be decreased by a factor of 1/N for an array of N wits if global driving is permitted (rather than individual driving in parallel).
Lastly, the thermodynamics of completely-positive and trace-preserving (CPTP) maps is considered in Chapter 4. It is shown that the energy change during such a process can be split into three parts: a work-like equilibrium contribution, a heat-like equilibrium contribution, and a third genuinely non-equilibrium energy difference. All three terms obtain their meaning when considering how much work can be extracted from the input and output state of the CPTP process, respectively. Furthermore, the identification of work and heat in this manner complies with a recently published version of the second law, which applies to the same class of processes. This is demonstrated by considering unital and thermal maps.

Keywords: quantum batteries
non-equilibrium thermodynamics
quantum information theory
theoretical physics
quantum thermodynamics
Advisor: Vedral, V
Neutron reflection study on surfactant systems at different interfaces

The interfacial behaviour of several surfactant mixtures containing zwitterionic surfactants has been studied employing surface tension measurements and neutron reflection experiments. The mixing of surfactants at air–liquid interface could not be well understood using the pesudophase approximation and the regular solution model. By introducing the expansion of excess free energy to analysis the surface tension and neutron reflection data simultaneously, it is found that the mixing deviates strongly from ideal and the excess free energy is asymmetric.
It is observed that the presence of ionic surfactant at solid–liquid interface enhanced the adsorption of zwitterionic surfactants. The configuration of the surfactant molecule in the inner layer adjacent to the surface is invoked to explain the underlying mechanism. Maxima in the adsorption just above the CMC occurred at all three compositions studied for the mixed system SDS with dodecyl dimethylammonium propanesulfonate (DSB). The neutron reflection experiments suggest that the phenomenon may result in part from the mixture and in part from ion segregation in the micelles.
Structural studies on a series of dodecyl dimethylammonium acetate with different inter–charge spacer revealed that the configuration of the surfactants changes dramatically as the headgroup gets larger. Combined with the higher pKa value, it is highly possible that the carboxybetaine with longer spacer is adsorbed in its undissociated form, and the headgroup is oriented towards the air. This configuration might explain why the saturated monolayer structure is favoured over the micellization.

Keywords: Surfactant mixtures
Neutron Reflection
Advisor: Penfold, J
Thomas, R
The utilisation of biomarkers of a reduced immune response to predict squamous cell carcinoma in long-term renal transplant recipients

Cutaneous squamous cell carcinoma (SCC) is the most common malignancy in renal transplant recipients (RTR) with an incidence up to 250 times that of the general population. SCC is frequently recurrent and more aggressive than in non-transplant cohorts. Immunological and clinical measures have been developed to stratify RTR by future SCC risk but their comparative performance in long-term RTR has not been assessed.
We hypothesised that biomarkers of two potential mechanisms underlying a reduced immune response may predict SCC development. These biomarkers comprised ‘signatures’ of immune regulation developed in RTR who have successfully ceased immunosuppression without development of graft dysfunction ('operational tolerance') and immunophenotypic changes associated with immunosenescence. Immunosenescence leads to a reduction of immune responses with increasing age.
A prospective cohort study was undertaken of 117 long-term RTR, half with a history of previous SCC. RTR were stratified by phenotype based on a majority ('CD57hi') or minority ('CD57lo') of peripheral blood CD8+ T cells expressing CD57. CD57hi RTR were 2.4 times more likely to develop SCC during follow-up, independent of age or history of previous SCC. This was more predictive than previously developed clinical and immunological measures. CD57hi RTR exhibited other functional and phenotypic changes associated with immunosenescence.
Signatures of operational tolerance did not predict SCC risk but were heavily influenced by the effect upon circulating B cells due to immunosuppressive regime, particularly azathioprine and calcineurin inhibition. Further evaluation indicated that azathioprine use was associated with the presence of donor-specific antibodies.
This study indicates that biomarkers of 'operational tolerance' are confounded by immunosuppression use and may not be suitable for clinical application in their current format. Biomarkers of immunosenescence, such as the CD57hi phenotype proposed in this study, may identify RTR at increased risk of subsequent SCC who may benefit from pre-emptive immunosuppression reduction.

Keywords: Immune senescence
Operational Tolerance
Squamous cell carcinoma
Renal Transplantation
Advisor: Wood, K
Harden, P
Topics in the theory of Selmer varieties

The Selmer varieties of a hyperbolic curve X over &Qopf; are refinements of the Selmer group arising from replacing the Tate module of the Jacobian with higher quotients of the unipotent étale fundamental group. It is hoped that these refinements carry extra arithmetic information. In particular the nonabelian Chabauty method developed by Kim uses the Selmer variety to give a new method to find the set X(&Qopf;). This thesis studies certain local and global properties of the Selmer varieties associated to finite dimensional quotients of the unipotent fundamental group of a curve over &Qopf;. We develop new methods to prove finiteness of the intersection of the Selmer varieties with the set of local points (and hence of the set of rational points) and new methods to implement this explicitly, giving the first examples of explicit nonabelian Chabauty theory for rational points on projective curves.

Keywords: Diophantine Geometry
Arithmetic Fundamental Groups
Number Theory
Advisor: Kim, M
The role of Galectin-3 in the subventricular zone response to demyelination

Multiple sclerosis (MS) is a debilitating neurological condition that causes demyelination and axon degeneration. While relapsing forms of the disease have been treatable for many years, progressive forms lack definitive treatment. An hypothesised therapy involves neural stem cells repairing and replacing damaged oligodendrocytes and neurons. The subventricular zone (SVZ) is a known site of adult neurogenesis and is adjacent to the corpus callosum (CC) white matter region. Previous studies have suggested that SVZ stem cells give rise to oligodendrocytes in the demyelinated CC in both MS and its animal models. This thesis examines the hypothesis that the pro-inflammatory molecule Galectin-3 (Gal-3) impacts on the SVZ regenerative response. The thesis firstly shows a juxtaposition of inflammation between the SVZ and CC, with the SVZ becoming less inflamed during cuprizone treatment while the CC becomes more inflamed. This observation occurs with Gal-3+ astrocytes and microglia, CD45+ haematopoietic cells, and PHi3+ proliferating cells. The absence of Gal-3 in knockout transgenic mice does not, however, alter this inflammation. The thesis then shows an increase in knockout mice compared to wild-type mice of myelin basic protein levels in layer six of the motor cortex, as well as suggesting knockout mice have more SVZ cells migrating into the CC. These findings lead to the hypothesis of Gal-3 absence allowing SVZ cells to migrate into the CC and possibly lower cortical layers, and contributing to better remyelination. This mechanism is evaluated further with in vitro studies, which show that Gal-3 enhances neuronal differentiation in SVZ neurosphere cultures. Gal-3 absence does not, however, cause a significant change in the proportion of oligodendrocytes in SVZ neurosphere cultures, or in the number of oligodendrocytes after cuprizone treatment. Overall this thesis provides results that could impact on the best utilisation of SVZ stem cells to treat MS.

Advisor: Szele, F
Development and application of enantioselective H-bond donor organocatalysts

This thesis presents the application and development of H-bond donor organocatalysts. Chapter 2 presents an intramolecular Michael addition of β-dicarbonyls onto α,β-unsaturated esters catalyzed by tertiary amine/H-bond donor bifunctional catalysts, achieving up to 88% ee.
Chapter 3 outlines the design and synthesis of a new family of cinchona-derived H-bond donor/ammonium salt phase-transfer catalysts. The ability of these asymmetric phase-transfer catalysts to activate less reactive substrates than their tertiary amine analogues and to induce higher levels of enantiocontrol than commercially available phase-transfer catalysts was demonstrated in an intramolecular Michael addition.
Chapter 4 details the highly successful application of these new H-bond donor/ammonium salt phase-transfer catalysts to the enantio- and diastereoselective nitro-Mannich reaction of α-amido sulfones with nitroalkanes.
Preliminary investigations into a novel phase-transfer catalyzed asymmetric ketimine reduction demonstrate the ability of these catalysts to provide access to new methods.

Keywords: H-bond donor
Phase transfer
Organocatalysis
Enantioselective
Advisor: Dixon, D
Ab initio modelling of magnetoelectric materials

The search for magnetoelectric materials, i.e. materials that respond with a polarisation (magnetisation) when an external magnetic (electric) field is applied, has become more important in recent years---both for the standalone magnetoelectricity and as part of the cross-coupling in modern multiferroics. To date, applications of magnetoelectrics (MEs) in technology are hampered by either small coupling strengths or low operating temperatures.
In the present work, the linear magnetoelectric coupling is examined by means of density functional theory with the aim to understand the physics of the coupling, and in turn open up pathways in the search for improved coupling properties.
The spin part of the ME coupling tensor was shown to be the sum of the electronic and the lattice contribution. Recently developed first-principles frameworks allow us to gain insights into the microscopic mechanisms of the coupling and are applied to compute the response in modifications of the prototypical ME Cr2O3 and isostructural compounds. We find that strains at ambient pressures influence the lattice contribution significantly. At higher pressures, a magnetic phase transition is shown to destabilise magneto-active phonon modes and lead to a divergence of the longitudinal lattice response due to magnetic softness, with a coupling strength 650 times larger than its zero-pressure value. Equivalently, a divergence of the electronic response is measured at the transition from insulator to metal---previously suggested in literature, but to date not measured. The largest value of the electronic response is shown to be 31.4ps/m, which is larger than the ambient value by a factor of 70, and also large in terms of the absolute value. We exemplify both the magnetic softness and band-gap alterations by doping the Cr2O3 parent structure with Fe and Ti. We show that doping provides a powerful way to include magnetic frustration resulting in a ten-fold increase of magnetic contributions to the lattice response. When the dopants lower the Cr2O3 band gap, the electronic response is measured to be ten times larger than reported for pure Cr2O3. Finally, the high-symmetry configurations of the spin flop phase of Cr2O3 are modelled. A combined phenomenological and group-theoretical analysis reveals a novel ME coupling mechanism only present in the spin flop phases. Akin to the ferroaxial mechanism in multiferroics, a chiral in-plane transverse coupling term is observed, whose Landau invariant is of 5th order.

Keywords: magnetoelectrics
materials science
magnetism
chromia
DFT
cr2o3
ab initio
physics
density functional theory
first principles
multiferroics
doping
Advisor: Yates, J
Optogenetic gene therapy for vision restoration

Inherited retinal dystrophies are a heterogeneous group of retinal diseases that often lead to blindness. The diverse range of causative gene mutations poses great challenges to developing therapies to improve the vision of affected people. One technique being investigated is optogenetics for vision restoration, a technique that aims to deliver light-sensitising molecules to the affected retina. This research project provides data on a range of variables that need to be optimised in order to successfully restore vision using an optogenetic gene therapy approach.
Fifteen wild type, chimeric and fusion constructs based on human opsins were compared by in vitro and in vivo tests to select the optimal light-sensitising construct. Of these, wild type rhodopsin, melanopsin and melanopsin–Gα subunit fusion constructs show the most promise for future studies.
For delivery of the light-sensitising construct, the adeno-associated virus (AAV) serotype AAV2/2(7m8) was shown to perform best compared to two other AAV serotypes when tested in degenerate mouse eyes and macaque and human retinal explants. The importance of the delivery route to the eye, the use of a targeted versus non-targeted approach and the AAV vector concentration were all tested in in vivo experiments.
In addition to testing such variables, the gene expression changes in target retinal bipolar cells in late-stage retinal degeneration were examined by microarray analysis of bipolar cell enriched samples isolated by fluorescence-activated cell sorting. Genes important for G protein signalling were generally expressed at a similar level in the degenerate state, while genes associated with oxidative stress and metabolism were differentially expressed.
Collectively, these data will inform the choice of construct, delivery method and target cell in future research into optogenetic strategies for vision restoration.

Keywords: Opsin
Microarray
Gene therapy
Retina
Retinal degeneration
Bipolar cell
Optogenetics
Advisor: MacLaren, R
Hankins, M
Reduced dimensionality transition state theory with multi-dimensional tunnelling

Full-dimensional quantum reactive scattering (QRS) calculations provide the most accurate dynamical results which include the rate constants for a chemical reaction. However, the computational costs involved in the calculations scale significantly with the size of the reacting system. Transition State Theory with Multi-Dimensional Tunnelling (TST/MT) and Reduced Dimensionality (RD) methods are two methods that are more efficient in computing reaction rate constants for general polyatomic reacting systems. In RD methods, only a subset of degrees of freedom are treated explicitly in calculations. In TST/MT, reaction rate constants are obtained by multiplying the TST reaction rate constants with a transmission coefficient, calculated based on the adiabatic ground state potential energy and other relevant properties obtained along the minimum energy path.
In this thesis, TST with zero-, small-, and large-curvature tunnelling approximations (abbreviated as TST/ZCT, TST/SCT and TST/LCT respectively) were applied to previously constructed RD potential energy surfaces (RD PES) with and without a mapped interpolation (MI) procedure. They were applied to the reactions CH4 +H, C2H6 +H, cyc-C3H6 +H, CH4 +CH3, CH3D+CH3 and CD4 +CD3 to test the TST/MT methods against accurate QRS calculations on the same PESs on these reactions. The use of MI improved the results by correcting the shape of the adiabatic ground state potential energy curves and the threshold energies of the reactions. TST/ZCT (MI) shows poor agreement with QRS results due to the lack of accounting for reaction path curvature, and TST/LCT (MI) shows moderate agreement for CH4 +CH3 with large reaction path curvature. For all reactions, TST/SCT (MI) shows the best agreement to QRS results and experimental data. Such agreement suggests the potential applicability of the TST/MT methods to larger polyatomic systems under the RD framework.
Primary kinetic isotope effects (KIE) for CH4+CH3 are shown to be significant due to the substitution of the exchanged hydrogen atom with a much heavier deuterium isotope. Secondary KIE for CH3D+CH3 are shown to be less significant and do not contribute much to the reaction rate constants in the case of CD4+CD3.

Advisor: Shan, X
Clary, D
Ritual in development: Improving children’s ability to delay gratification

To be accepted into social groups, individuals must internalise and reproduce appropriate group conventions, such as rituals. The high fidelity copying of such rigid and socially stipulated behavioural sequences places heavy demands on executive function abilities. Given previous research showing that challenging executive functioning also improves it, it was hypothesised that prolonged engagement in ritualistic behaviours would improve executive functioning in children, in turn improving their ability to delay gratification. A three month circle-time-games intervention with primary school children in two contrasting cultural environments (Slovakia and Vanuatu) was conducted. In both environments we found the intervention improved children's executive function and in turn their ability to delay gratification. Moreover, these effects were amplified when the intervention task was imbued with ritual, rather than instrumental, cues. The findings presented in this thesis have potentially far-reaching implications for child-rearing and educational practices, suggesting ritual participation may be necessary for the cultivation of future mindedness.

Keywords: cross-cultural psychology
ritual
future discounting
delay of gratification
experimental anthropology
executive function
Advisor: Whitehouse, H
Mckay, R
Desire and the ethics of advertising

The aim of this thesis is to examine advertising from the point of view of Christian ethics: how it works, what is wrong with it and how it might go right as a practice. It argues that much existing criticism of advertising is justified, but that its power to create desire might be turned towards serving the good of the education of desire, leading us towards, or strengthening, a love of God, and helping us relate to products and services based on this love. This is significant because learning to desire well is central to living a Christian life, and because advertising influences how many people desire today. In contrast to authors who simply criticise advertising, often as part of a general critique of consumer culture, this thesis offers a constructive and detailed examination of the practice itself, looking at how its techniques work and how they might be reformed into an ‘art of advertising’. In making this argument the thesis draws primarily on Augustine, in addition to Plato, and modern critics of advertising. First, it describes desire, before examining how advertisements create desire, followed by an assessment of existing criticisms of this process. It then develops an account of the education of desire, identifying what an art of advertising should aim to achieve, before examining the techniques by which an advertisement might achieve this. The argument is intended to contribute to a project within Christian ethics of critiquing advertising, and presenting a workable ethical vision for the future of the industry.

Keywords: Platonism
Capitalism
Advertising
Art
Ethics
Plato
Christianity
Virtue
Education of desire
Desire
Religion
Advertisements
God
Augustine
Advisor: Biggar, N
On the design of productive ecosystems

Humans critically depend on the adequate design of productive ecosystems. With every design comes trade-offs. Agriculture is a clear case in point. We currently produce more than enough food for everyone on the planet but at a severe environmental cost. The degradation of our environment in turn threatens the long-term security of crop production. This negative feedback cycle suggests there is something wrong with the way our current human engineered ecosystems are designed. One striking feature of current industrial designs is that they are incredibly simple: monocultures, founded on reductionist ideas of how ecosystems operate. This thesis explores the challenges and opportunities we face with adding complexity back into the design of ecosystems. The world’s first database on interspecific plant-soil feedback experiments is created and used to test theory on temporally lagged plant competition and facilitation. New concepts on the selection of competitive strength across trophic levels and its contrasting effects on population versus community level productivity are elucidated. The need to consider local management of diversified ecosystems in the context of global drivers of ecosystem change is validated.

Advisor: Willis, K