VictorJuiz/thesis huggingface dataset:
On moduli stabilisation and cosmology in type IIB flux compactifications

This Thesis studies some aspects of string compactifications with particular em- phasis on moduli stabilisation and cosmology.
In Chapter 1 I motivate the study of string compactifications as a way to build on the successes of the Standard Model of Particle Physics and of the theory of General Relativity.
Chapter 2 constitutes an overview of the technical background necessary for the study of flux compactifications. I sketch how the desire to obtain a supersymmet- ric theory in four dimensions constrains us to consider compactifications of the ten dimensional theory in six dimensional Calabi-Yau orientifolds. I argue that it is strictly necessary to stabilise the geometry of this compact space in order to have a phenomenologically viable four dimensional theory. I introduce the large volume scenario of type IIB compactifications that successfully incorporates fluxes and sub- leading corrections to yield a four dimensional theory with broken supersymmetry and all geometrical moduli stabilised.
The next four Chapters are devoted to the study of some phenomenological aspects of moduli stabilisation and constitute the original work developed for this Thesis.
In Chapter 3 I investigate the consequences of field redefinitions in the stabilisation of moduli and supersymmetry breaking, finding that redefinitions of the small blow- up moduli do not significantly alter the standard picture of moduli stabilisation in the large volume scenario and that the soft supersymmetry breaking terms are generated at the scale of the gravitino mass.
Chapter 4 deals with the putative destabilisation of the volume modulus by very dense objects. The analysis of the moduli potential shows that even the densest astrophysical objects cannot destabilise the moduli, and that destabilisation is only achievable in the context of black hole formation and cosmological singularities.
In Chapter 5 I present a model of inflation within the large volume scenario. The inflaton is identified with a geometric modulus, the fibre modulus, and its potential generated by poly-instanton effects. The model is shown to be robust and consistent with current observational constraints.
In Chapter 6 I introduce a model of quintessence, where the quintessence field and its potential share the same origin with the inflationary model of the previous Chapter. This model constitutes a stringy realisation of supersymmetric large extra dimensions, where supersymmetry, the low gravity scale and the scale of dark energy are intrinsically connected.
I conclude in Chapter 7 outlining the direction of future research.

Keywords: moduli stabilisation
inflation
cosmology
quintessence
flux compactifications
Advisor: Conlon, J
An investigation of low-energy injection for electron storage rings

This thesis reports on low-energy injection studies, considering a multi-shot and multiturn injection method in radial phase space, using only one kicker magnet. A new model is presented in which the coupling between the radial and longitudinal phase space significantly increases the injection efficiency at low energies. Coupling with the longitudinal phase space takes place if the energy of the injected beam is different from the equilibrium ring energy and if there is dispersion at the septum position. Coupling with the vertical phase space, introduced by skew quadrupole fields, also increases the injection efficiency. A computer program, MCIS, has been written in order to make quantitative predictions from the new model. Calculations are presented for HELIOS, a superconducting synchrotron with a final electron energy of 700 MeV. The present injection energy is 200 MeV. The calculations show that if injection were to take place off-energy by δ m ≈ 1 %, then the injection energy could be lowered to a minimum of about 35 MeV. This prediction only takes into account single particle beam dynamics. The effect of most other parameters on the injection efficiency is also calculated.
Experimental studies of the injection process were performed during the commissioning period of Helios, which was carried out by a team under the author's direction. Data obtained at an injection energy of 100 MeV are compared with calculations. A precise measurement of the relative energy deviation of the injected beam δm has been made. The agreement with the model is good and it proves the presence of longitudinal coupling for the optimum injection conditions. The measurement of the optimum kicker strength also agrees with the model, as does the general behaviour of injection as a function of several parameters. The measurements lead to a high level of confidence in the model presented. The belief in the general validity of the model is reinforced by its agreement with the overall injection behaviour of accelerators other than HELIOS, which inject successfully at low energies.

Advisor: Mulvey, J
Doucas, G
Freedom of religion or belief - the quest for religious autonomy

In this thesis it is argued that while the concept of freedom of religion or belief itself is opaque and difficult to define, the right to religious freedom must contain certain basic factors – most importantly the right to individual (religious) autonomy. The individual autonomy approach is seen here as providing the necessary rationale for the protection of freedom of religion or belief. This rationale is not cemented in stone in the practice of the Convention and this has caused the Court to lose its focus on individual freedom. It is a dangerous tendency. It allows the focus to be placed on the role of the State and leaves freedom of religion or belief to be heavily affected by politics and fluctuating social attitudes. In this regard, this thesis looks for the meaning and scope of individual and collective religious autonomy and how it is and ought to be represented in the practice of the European Court of Human Rights. It is the aim of the author to contribute to a clearer and more principled understanding of Article 9 of the ECHR. The right to individual autonomy is thought to be able to provide the necessary focus for the European Court of Human Rights in creating a more robust framework for the protection of freedom of religion or belief different from current Court practice which shows inconsistency in its reasoning and theoretical chaos. This lack of clarity has also contributed to freedom of religion or belief being a relatively weak right. It is explored here as to how the principle of autonomy (as developed in this thesis) relates to other principles provided by the Court, namely the principle of State neutrality, pluralism and the effective protection of rights, but also the margin of appreciation and the autonomy of religious communities. The individual autonomy centred theoretical framework in the first part of the thesis will be engaged to analyse the conflict in the triangle of state-individual-community explored in the second part.

Keywords: international law
freedom of religion or belief
European and comparative law
human rights
autonomy
law and religion
Advisor: Sandra, F
A type of king: the figure of Arthur in mid-nineteenth to mid-twentieth century literature

This thesis analyses the figure of Arthur, in a period spanning the mid-nineteenth to mid-twentieth centuries, when that figure became increasingly protean and multifaceted, and the audience for the Arthurian legend grew in both size and variety. It argues that many authors wrote through Arthur, as well as about Arthur, using the figure to understand and test their own ideas about ideals (e.g. of manliness, kingship, or heroism) as well as problems (such as war, despotism, or ungodliness). This thesis analyses Arthur by considering him as a 'type', using a definition of the term that highlights a paradox: a type, in a scientific sense, is both perfect (an exemplary model) and normal (common enough to be representative). When applied to Arthur, it means that he is both a perfect, or near perfect, example, but is also to some extent a 'normal' human being. Different authors analysed in this thesis emphasise different aspects of the figure, according to whether they focus on Arthur's perfection or his normality. Other meanings of the word 'type' are also applied when relevant: the idea is not to force all versions of Arthur into a single or definitive category, but to retain the complexity of how Arthur is characterised and written about in texts. The ultimate aim of this thesis is to put the figure of Arthur into critical focus, and explain why he has been returned to so often in history.

Keywords: First World War
Alfred Lord Tennyson
Clemence Housman
King Arthur
Henry Irving
E.A. Robinson
Coningsby Dawson
chivalry
T.H. White
David Jones
Edwardian
Eglinton tournament
medievalism
Victorian
Second World War
Arthurian
Edward Bulwer Lytton
Edward Burne-Jones
J. Comyns Carr
Advisor: Robert, D
Carolyne, L
The ground and nature of religious belief in the work of John Macmurray, John Baillie and John Oman, with special reference to their understanding of the relation between ordinary experience and religious belief

The study expounds the views of Macmurray, Baillie and Oman on religious belief in the context of their other epistemological, anthropological and theological convictions. It is shown that each of the writers argues that religious belief is a response to a feature of everyday experience (human alienation, moral intuition and the sense of the holy respectively), that each of them takes the view that religious belief functions in order to achieve a valued end (community, willing obedience to divinely ordained duties and the on-going development of moral personality) which is regarded as both the will of God and essential to human flourishing, and that they also hold that religious beliefs may be confirmed in relation to the valued end which they aim to promote.
I argue that whilst each is not without their lacunas and inadequacies, the three writers provide insights which may be useful in understanding religious belief in a Christian context. I maintain, for instance, that Macmurray's argument that religion is a derivative response to a critical dimension of ordinary experience is an illuminating perspective. Again, it is argued that there are resources in Baillie's work to help in the articulation of the view that Christian belief is a response to an a priori encounter with the divine presence in experience. Again, Oman's emphasis on the role of feeling in the disclosure of the divine is plausible, and his analysis of the nature of religious belief is particularly rich in illuminating insights.
An important argument that runs through the thesis is that it is plausible to think that there are preconceptual experiences that are cognitively important. In this sense, the study aims to help underpin an experiential approach in the face of those critics who deny the conceptual possibility of such primal experiences.
Incorporating inter-sample variability into cardiac electrophysiology simulations

Sudden cardiac death kills 5-10 people per 10,000 population in Europe and the US each year. Individual propensity to arrhythmia and sudden cardiac death is typically assessed through clinical biomarkers. Variability in these biomarkers is a major challenge for risk stratification. Variability is observed at a wide range of spatio-temporal scales within the heart, from temporal fluctuations in ion channel behaviour, to inter-cell and inter-regional differences in ion channel expression, to structural differences between hearts. The extent to which variability manifests between spatial and temporal scales remains unclear but has a potentially crucial role in determining susceptibility to arrhythmia.
In this dissertation we present a multi-scale study of the causes and consequences of variability in electrophysiology. At a sub-cellular level we demonstrate that, taking into account inter-individual variability in ion channel conductance, mRNA expression levels in failing human hearts predict the electrophysiological remodelling observed experimentally.
On a tissue scale, we advocate the use of phenomenological models where information on subcellular processes is unavailable. We introduce a modification to a phenomenological model to capture beat-to-beat variability in action potential repolarisation recorded from four individual guinea pig myocytes. We demonstrate that, whilst temporal variability is dramatically reduced by inter-cell coupling, differences in their mean action potential duration may become apparent at a tissue level.
The ventricular myocardium has a heterogeneous structure not captured by the simplified representation of conduction used above. In our final case study, we challenge a model of conduction by directly comparing simulations to optical mapping recordings of ventricular activation from failing and non-failing human hearts. We observe that good fits to experimental data are obtained only when endocardially bound structures are not in view, suggesting a role in conduction for these structures that are often ignored in cardiac simulations.
Finally, we present future directions for the work presented. We make the case for reporting of inter-sample variability in experimental results and conclude that whilst variability may not always manifest across scales, its impact should be considered in both theoretical and experimental studies.

Keywords: variability
simulation
computational biology
cardiac electrophysiology
Advisor: Burrage, K
Rodriguez, B
Mirams, G
Multi-periodic variability in low mass x-ray binaries

An introduction is given to the fields of low mass X-ray binaries (LMXBs), soft X-ray transients (SXTs) and related classes of objects. Aspects such as evolution, variability and populations are reviewed.
The methods of time series analysis are listed and the new method of Bayesian spectrum analysis and parameter estimation is outlined. In particular the methods required to analyze multi-periodic variability in LMXB light curves are described, as used in subsequent chapters. Artificial datasets are used to examine the robustness of the Bayesian frequency analysis methods. An ad hoc method of deconvolving the effects of data sampling is then detailed.
The optical variability of V404 Cyg is analyzed using the methods of the preceding chapter. Orbital and short period variations are examined in several wavebands and the implications for this black-hole candidate discussed. Models for the short period variation are compared to the observed behaviour, to locate the origin of this effect. Modelling of ellipsoidal variability in V404 Cyg, J0422+32 and several faint X-ray transients allows the determination of the inclination for these systems. Other important physical parameters are also considered and compared to previous values cited in the literature.
The globular cluster LMXB AC211 is then examined to try to shed some light on the complex orbital variability observed. Several photometric and spectroscopic datasets are combined to provide an overall, relative probability for the two possible periods.
The distributions of neutron star and black-hole masses are analyzed to provide constraints on models of the neutron star equation of state. Inclinations obtained from ellipsoidal analysis and the excess noise seen in SXT light curves, are discussed.
Exploiting whole-PDB analysis in novel bioinformatics applications

The Protein Data Bank (PDB) is the definitive electronic repository for experimentally-derived protein structures, composed mainly of those determined by X-ray crystallography. Approximately 200 new structures are added weekly to the PDB, and at the time of writing, it contains approximately 97,000 structures. This represents an expanding wealth of high-quality information but there seem to be few bioinformatics tools that consider and analyse these data as an ensemble. This thesis explores the development of three efficient, fast algorithms and software implementations to study protein structure using the entire PDB.
The first project is a crystal-form matching tool that takes a unit cell and quickly (< 1 second) retrieves the most related matches from the PDB. The unit cell matches are combined with sequence alignments using a novel Family Clustering Algorithm to display the results in a user-friendly way. The software tool, Nearest-cell, has been incorporated into the X-ray data collection pipeline at the Diamond Light Source, and is also available as a public web service.
The bulk of the thesis is devoted to the study and prediction of protein disorder. Initially, trying to update and extend an existing predictor, RONN, the limitations of the method were exposed and a novel predictor (called MoreRONN) was developed that incorporates a novel sequence-based clustering approach to disorder data inferred from the PDB and DisProt. MoreRONN is now clearly the best-in-class disorder predictor and will soon be offered as a public web service.
The third project explores the development of a clustering algorithm for protein structural fragments that can work on the scale of the whole PDB. While protein structures have long been clustered into loose families, there has to date been no comprehensive analytical clustering of short (~6 residue) fragments. A novel fragment clustering tool was built that is now leading to a public database of fragment families and representative structural fragments that should prove extremely helpful for both basic understanding and experimentation.
Together, these three projects exemplify how cutting-edge computational approaches applied to extensive protein structure libraries can provide user-friendly tools that address critical everyday issues for structural biologists.

Keywords: peptides
disorder prediction
parallelization
PDB
nearest-cell
proteins
space group
neural network
crystallography
protein data bank
clustering
nearest cell
unit cell
bioinformatics
fragments
RONN
training
structural biology
MoreRONN
OpenMP
Advisor: Esnouf, R
Antigenic and immunomodulatory properties of HIV-1 gp120 N-linked glycosylation

The HIV-1 surface glycoprotein, gp120, is made of a rapidly mutating protein core and an extensive carbohydrate shield which are, respectively, encoded by the viral genome and synthesised by the host cell. In contrast to host cell glycoproteins however, gp120 contains a population of unprocessed oligomannose-type glycans that interact with host lectins, promote HIV infection, and alter cell signalling. They also form the basis of the epitopes of several broadly neutralising antibodies isolated against HIV, making them a key feature for immunogen design. The mechanistic basis of how HIV glycans are differentially processed by the host cell was demonstrated on a recombinant gp120 model, suggesting that steric occlusion within the patch of densely packed glycans lead to lack of processing by ER and Golgi α-mannosidases. Furthermore, an elevated level of oligomannose-type glycans was evidenced on gp120 isolated from HIV-1JRCSF virions produced in PBMCs, compared to recombinant material (respectively ~79% and ~29% of total N-linked glycans), along with a subset of highly processed and sialylated, bi-, tri- and tetra-antennary complex-type glycans, which could be involved in direct interaction with key host cell immune receptors and strongly suppress both antibody and T-cell immune responses. The effect of variation in viral production systems was analysed, with envelope glycoprotein derived from pseudoviral particles produced in HEK 293T cells exhibiting predominantly an oligomannose population (98%), compared to gp120 isolated from a single-plasmid infectious molecular clone (56%). Finally, mutation of one or several glycosylation site(s), known to be required for oligomannose-restricted neutralizing antibodies, was shown to induce a subtle redistribution within the oligomannose series whilst maintaining overall oligomannose levels. The gp120 glycan profile is therefore robust to mutations and also remarkably similar across primary viral isolates from Africa, Asia and Europe and consequently represents an attractive target for vaccine development.

Keywords: gp120
glycosylation
HIV
Advisor: Scanlan, C
Wormald, M
Inexpensive uncertainty analysis for CFD applications

The work presented in this thesis aims to provide various tools to be used during design process to make maximum use of the increasing availability of accurate engine blade measurement data for high fidelity fluid mechanic simulations at a reasonable computational expense.
A new method for uncertainty propagation for geometric error has been proposed for fluid mechanics codes using adjoint error correction. Inexpensive Monte Carlo (IMC) method targets small uncertainties and provides complete probability distribution for the objective function at a significantly reduced computational cost. A brief literature survey of the existing methods is followed by the formulation of IMC. An example algebraic model is used to demonstrate the IMC method. The IMC method is extended to fluid mechanic applications using Principal Component Analysis (PCA) for reduced order modelling. Implementation details for the IMC method are discussed using an example airfoil code. Finally, the IMC method has been implemented and validated for an industrial fluid mechanic code HYDRA.
A consistent methodology has been developed for the automatic generation of the linear and adjoint codes by selective use of automatic differentiation (AD) technique. The method has the advantage of keeping the linear and the adjoint codes in-sync with the changes in the underlying nonlinear fluid mechanic solver. The use of various consistency checks have been demonstrated to ease the development and maintenance process of the linear and the adjoint codes. The use of AD has been extended for the calculation of the complete Hessian using forward-on-forward approach. The complete mathematical formulation for Hessian calculation using the linear and the adjoint solutions has been outlined for fluid mechanic solvers. An efficient implementation for the Hessian calculation is demonstrated using the airfoil code.
A new application of the Independent Component Analysis (ICA) is proposed for manufacturing uncertainty source identification. The mathematical formulation is outlined followed by an example application of ICA for artificially generated uncertainty for the NACA0012 airfoil.

Keywords: Monte Carlo
Adjoint error correction
manufacturing uncertainty
Automatic Differentiation
Uncertainty analysis
Independent Component Analysis
Advisor: Giles, M