VictorJuiz/thesis huggingface dataset:
Electronic excitations in semiconductors and insulators using the Sternheimer-GW method

In this thesis we describe the extension and implementation of the Sternheimer- GW method to a first-principles pseudopotential framework based on a planewaves basis. The Sternheimer-GW method consists of calculating the GW self-energy operator without resorting to the standard expansion over unoccupied Kohn- Sham electronic states. The Green's function is calculated by solving linear systems for frequencies along the real axis. The screened Coulomb interaction is calculated for frequencies along the imaginary axis using the Sternheimer equa- tion, and analytically continued to the real axis. We exploit novel techniques for generating the frequency dependence of these operators, and discuss the imple- mentation and efficiency of the methodology.
We benchmark our implementation by performing quasiparticle calculations on common insulators and semiconductors, including Si, diamond, LiCl, and SiC. Our calculated quasiparticle energies are in good agreement with the results of fully-converged calculations based on the standard sum-over-states approach and experimental data. We exploit the methodology to calculate the spectral func- tions for silicon and diamond and discuss quasiparticle lifetimes and plasmaronic features in these materials.
We also exploit the methodology to perform quasiparticle calculations on the 2-dimensional transition metal dichalcogenide system molybdenum disulfide (MoS2). We compare the quasiparticle properties for bulk and monolayer MoS2 , and identify significant corrections at the GW level to the LDA bandstructure of these materials. We also discuss changes in the frequency dependence of the electronic screening in the bulk and monolayer systems and relate these changes to the quasiparticle lifetimes and spectral functions in the two limits.

Keywords: Electronic structure
DFT
Many-body perturbation theory
GW
optical properties
Materials Science
Advisor: Giustino, F
'All the helth and life of the sacraments... I it am': Julian of Norwich and the sacrament of penance

This thesis explores a long-neglected area of Julian’s work, namely her devotional and pastoral understanding of the nature of sin and the sacrament of penance. Her two texts reveal a deep concern, set within the context of a rise in lay penitential piety, for those devout who continued to experience a sense of shame and dread of sin, even after confession to a priest. By means of a close comparative reading of Julian's short and long texts of A Revelation of Divine Love, and an examination of a wide range of Middle English devotional texts and manuals, as well as a breadth of Julian scholarship to date, I argue that Julian addresses the devotional and ecclesiastical concerns of late fourteenth-century England in the problem of sin and confession for the ordinary believer. By articulating her revelation in the penitential terms of the manuals of the Church, Julian reveals the extent to which the daily devotional life of 'holy moder church' is the means by which the saving love of Christ is realised and made accessible to the penitent.
Within her writing Julian seeks to reassure her reader that God has dealt with sin and triumphed over the devil but in order to do this she must alter their understanding of a contrition-centred sacrament. For this reason Julian sets up a crisis of understanding within her long text between the 'common teaching of holy church' and her revelation of love. This conflict is deliberately left unresolved in order that, in scholastic terms, two opposing arguments in opposition may jointly illuminate the necessity of sin and penance in bringing the soul to the proper state of humility and the mercy and grace of the loving Lord in forgiveness. In so doing it is argued that, within Julian’s writing, the pastoral process of penance is integral to those who desire a more intimate relationship with God.
The thesis consists of four chapters which first, locates Julian's short and long versions of A Revelation of Divine Love within the climate of the late-fourteenth century; secondly, it charts the rise of the significance of the role of the penitent within the history of penance which led to an increasing lack of confidence within the late fourteenth century in the ability of the confessional encounter to alleviate the sense of sin experienced by some devout souls; thirdly, I analyse the extent to which Julian's short and long version of a Revelation of Divine Love reflect and address this catechetical and penitential climate in her theology of sin and penance; and finally the thesis poses the question of the extent to which Julian's work can be considered as a penitential text which seeks to bring ease and comfort of the assurance of sins forgiven through the everyday practices of the Church. It is concluded that Julian's writing reveals a fascinating and significant contribution to late fourteenth-century thought on penance and brings a fresh reading of Julian's texts.

Keywords: Julian of Norwich
penance
Advisor: Gillespie, V
Chastity on the early modern English stage,  1611-1649  

‘Chastity on the Early Modern English Stage’ seeks to explain the relationship between tragicomedy’s brief and short-lived English popularity and the royal cult of chastity which spanned exactly the same historical time-frame. This study attempts to define a cultural movement which influenced the political, religious, social, intellectual, aesthetic, and medical fields in the first half of the seventeenth-century and argues that the narrative tropes which structured, and assisted the spread of, the post-Elizabethan cult of chastity were the same tropes governing the tragicomedies so popular in the period.
The arguments made for tragicomedy are speculatively extended to all generic forms, with the intention of expanding an area of scholarship still dominated by formalist analysis. By focussing on narrative tropes and locating them within both fictional and non-fictional texts and in the presentation and discussion of significant events (from medical discoveries to liturgical arrangements and royal birthing rituals) this thesis aims to illustrate that the human and cosmic visions articulated by different dramatic genres were as relevant to early modern lives outside the theatre as they were to those within it. Genre is thus less a description of a text’s formal characteristics and more a set of truths governing certain human experiences both in texts and in life.
Focussing on Shakespeare’s The Winter’s Tale, two plays by John Ford, Caroline court masques and birthing rituals, Milton’s A Maske and a number of non-professional performances (from the Earl of Castlehaven’s trial to William Harvey’s demonstration of the circulation of the blood), ‘Chastity on the Early Modern English Stage’ describes the four tropes of chastity and their place in tragicomic experience from the death of Elizabeth I to the beheading of Charles I. While Charles’s death and the closure of the theatres are crucial reasons for the abrupt end of the cult of chastity and tragicomedy, this thesis argues that cause must also be attributed to the efforts of pro-Parliamentary and Puritan writers who, throughout the 1630s and 1640s, sought to claim the tropes of chastity for their own rhetoric and cause. Their success resulted in a redefinition of chastity as masculine, individuated, Parliamentarian, Protestant, intellectual, civic and prosaic instead of Catholic, royal, spectacular, feminised, Marian, pietised, and theatrical.

Keywords: Shakespeare
performance
Milton
John Ford
early modern
chastity
Advisor: Maguire, L
Achinstein, S
Clergy and community

The intention of this thesis is to make a contribution to the understanding of the eighteenth-century Church of England within the community in which it existed. Recognising the enormous variation that existed within the Church during the period, this study provides a close comparison of two archdeaconries, (something which is rarely undertaken in the historiography of the Church), both of which have never received attention from historians. In order to study the Church in these regions, the archdeaconries of Buckingham and Gloucester, detailed consideration is given to the role and activities of the parochial clergy in each archdeaconry. By concentrating upon the community, and the clergy's place within it, this thesis is able to provide a detailed picture of the social, political and economic integration of the clergy within these two specific regions, as well as their pastoral work and family life, the latter much neglected by historians. It devotes much attention to the property of the clergy, as a means of locating the clergy within local communities, and because of the great effect their property and income had upon other spheres of their everyday life. In doing this, this thesis demonstrates the diversity of experience of clergy within each archdeaconry, but it also shows some overall trends which marked the experience of parochial clergy in the period. It argues that the eighteenth-century clergyman was immersed in almost every aspect of community life, and although conscious of his distinctiveness as a parson, such integration represented a fusion of the ecclesiastical and secular, the incumbent's pragmatic response to the circumstances of the community of which he was a part.
Nietzsche and Proust

Affinities between Nietzsche and Proust have been suggested by a variety of influential critics (Georges Bataille and Maurice Blanchot, more recently Paul de Man, Alexander Nehamas and Richard Rorty), but this is the first full-length comparative study of the two writers. Proust was intimately familiar with nineteenth-century post-Kantian aesthetics, and indeed the narrator in A la recherche du temps perdu glosses his involuntary memories using an explicitly idealist philosophical vocabulary, but by developing Vincent Descombes's thesis that Proust's novel is more advanced than the philosophical interpretations it contains, I argue that Proust ultimately moves beyond the Schopenhauerian position which has often been imputed to him, and that he joins Nietzsche in an overcoming of dualistic metaphysics.
After first considering those critical works which have prepared the ground for a comparative study of the two writers - in particular Gilles Deleuze's Proust et les signes, whose Nietzschean contours I argue have been insufficiently appreciated - I then discuss the surprising amount Proust actually wrote about Nietzsche, in A la recherche and elsewhere, and focus on the theme of friendship, which is Proust's chosen terrain for his most extended engagement with the philosopher. In subsequent chapters I address 'Proust's perspectivism' in the light of Nietzsche's radical critique of traditional epistemology, and then turn to Proust's narrator's search for the self, which I argue culminates in an 'ubermenschlich' aesthetics of self-creation. I use Deleuze's emphasis on the difference and repetition in Proustian 'essences' so as to read involuntary memory as the intimation not of an essential self, but of the eternal return. In my final chapter I then attempt to break open the two writers' metamorphoses of the circle by stressing the asymmetries of temporal structure in their work, their exploitation of postmodern 'logics of the future perfect'.
Causal structure in categorical quantum mechanics

Categorical quantum mechanics is a way of formalising the structural features of quantum theory using category theory. It uses compound systems as the primitive notion, which is formalised by using symmetric monoidal categories. This leads to an elegant formalism for describing quantum protocols such as quantum teleportation. In particular, categorical quantum mechanics provides a graphical calculus that exposes the information flow of such protocols in an intuitive way. However, the graphical calculus also reveals surprising features of these protocols; for example, in the quantum teleportation protocol, information appears to flow `backwards-in-time'. This leads to question of how causal structure can be described within categorical quantum mechanics, and how this might lead to insight regarding the structural compatibility between quantum theory and relativity.
This thesis is concerned with the project of formalising causal structure in categorical quantum mechanics. We begin by studying an abstract view of Bell-type experiments, as described by `no-signalling boxes', and we show that under time-reversal no-signalling boxes generically become signalling. This conflicts with the underlying symmetry of relativistic causal structure. This leads us to consider the framework of categorical quantum mechanics from the perspective of relativistic causal structure. We derive the properties that a symmetric monoidal category must satisfy in order to describe systems in such a background causal structure. We use these properties to define a new type of category, and this provides a formal framework for describing protocols in spacetime. We explore this new structure, showing how it leads to an understanding of the counter-intuitive information flow of protocols in categorical quantum mechanics. We then find that the formal properties of our new structure are naturally related to axioms for reconstructing quantum theory, and we show how a reconstruction scheme based on purification can be formalised using the structures of categorical quantum mechanics. Finally, we discuss the philosophical aspects of using category theory to describe fundamental physics. We consider a recent argument that category-theoretic formulations of physics, such as categorical quantum mechanics, can be used to support a variant of structural realism. We argue against this claim. The work of this thesis suggests instead that the philosophy of categorical quantum mechanics is subtler than either operationalism or realism.

Keywords: quantum information
relativity
causal structure
Advisor: Coecke, B
Abramsky, S
The structure and specificity of immunoglobulins

An investigation into the structures of the antigen-binding fragments (Fab) of mouse monoclonal immunoglobulins by X-ray crystallography, is presented. The family of immunoglobulins studied, Gloops 1-5, possess the ability to bind to both the peptide antigen and the parent protein: Hen Egg-white Lysozyme.
The Gloop1 and Gloop4 Fabs were generated by proteolytic cleavage of the antibody, and crystallisation trials yielded crystals of uncomplexed Fabs of both species. Attempts to grow Fab:antigen complex crystals proved unsuccessful. Partial purification of the heterogeneous Gloop4 Fab was found to be essential for the success of the crystallisations.
Data were collected on crystal forms of Gloop1, Gloop2 and Gloop4 on an area detector. The structures of three Gloop2 crystal forms were solved by the molecular replacement technique, using models consisting of Fab domain pairs. Two of the crystal forms were refined by molecular dynamics methods at maximum resolutions of 3.3Å and 2.8Å, and the third by rigid body methods alone at 3.5Å resolution.
Analysis of the Gloop2 structures between the crystal forms and with other Fabs indicated no atypical features in the domains. The elbow bend of the Gloop2 Fabs differed by up to 7°. The relative association of variable and constant domain pairs was also seen to vary between the Fabs. The changes in domain pairing caused significant differences in the relative disposition of the complementarity determining regions (CDRs), although there was no evidence for conformational change within individual CDRs. The Gloop2 combining site is dominated by a groove of approximate dimensions 12Åx9Åx7Å, containing many aromatic side-chains and a pair of glutamic acid residues in analogous positions to a those found in a FabrHen egg-white Lysozyme complex.

Advisor: Taylor, G
Precedent, commentary, and legal rules in the Madhhab-Law tradition: Ibn Quṭlūbughā's (d. 879/1474) al-Taṣḥīḥ wa-al-tarjīḥ

This thesis examines the role that scholarly digests and commentaries played in the formation of legal rules in the Muslim legal institution known as the madhhab. I posit that a shared approach to legal rule-determination, and the respect of juristic precedent that it entails, underlies the jurisprudential processes of all of the four post-classical Sunni madhhabs (the Ḥanafī, Mālikī, Shāfi'ī, and Ḥanbalī), and unites them in a wider ‘madhhab-law tradition’.
Taking the Ḥanafī madhhab as a case study, the thesis analyses a commentary written by the late Mamluk jurist Ibn Quṭlūbughā (d. 879/1474) upon the digest of the celebrated Abbasid-era Abū al-Ḥusayn al-Qudūrī (d. 428/1037). In discussing the madhhab's heritage of precedent, Ibn Quṭlūbughā's commentary weaves an intricate tapestry of quotations and references from previous jurists and works, providing us with insight into how author-scholars reacted to, and interacted with, other jurists over space and time. Chapter 1 provides a short introduction to the lives of Qudūrī and Ibn Quṭlūbughā, and the contexts within which they produced their works. Chapter 2 employs both quantitative and qualitative analysis of the commentary, in order to deduce historical and geographical patterns out of which a periodisation of rule-determination in the Ḥanafī madhhab is proposed. In Chapter 3, Ibn Quṭlūbughā's jurisprudential theory of rule-determination is studied, examining both the justifications and the processes employed by jurists in arriving at a legal rule in the Ḥanafī madhhab. Chapter 4 then turns to the craft of commentary itself, analysing over eighty case examples for the logical relationships, rhetorical devices, and legal arguments that inform the actual practice of rule-determination through commentary. A final chapter then summarises the conclusions, and situates them within a broader discussion as to the nature of the madhhab-law tradition.

Keywords: Syria
Egypt
fiqh
madhhab
Islamic jurisprudence
Hanafism
Mamluk
tradition
Islamic law
Hanafi
legal writing
Advisor: Melchert, C
Functional analysis of mutations in isocitrate dehydrogenase involved in gliomagenesis

The main subject of my thesis is the investigation of mechanisms of glioma tumorigenesis associated with the recently identified mutations in isocitrate dehydrogenase. Gliomas account for 80% of primary brain cancers. They represent a diverse group of tumours, and are graded from I-IV based on histopathological features. Whilst grade I tumours may be curable with surgery alone, grade II and III gliomas inevitably progress to glioblastoma multiforme (GBM), which is highly resistant to current therapies and carries a very poor prognosis. Despite an improved understanding of the pathways and mechanisms involved in the development of glioma and its progression to grade IV disease, current and novel treatments have so far failed to significantly improve outcome.
Isocitrate dehydrogenase (IDH) enzymes catalyse the oxidative decarboxylation of isocitrate to α-ketoglutarate (α-KG). Somatic mutations in genes encoding IDH1 and IDH2 were first identified in glioma and subsequently in acute myeloid leukemia and other solid tumours. These heterozygous point mutations occur at the arginine residue of the enzymes active site and cause both loss of normal enzyme function and gain-of-function, causing the reduction of α-KG to D-2-hydroxyglutarate (D-2HG), which accumulates. D-2HG may act as an oncometabolite through the inhibition of various α-KG dependent enzymes, stimulating angiogenesis, histone modifications and aberrant DNA methylation. Possibly, IDH1/2 mutations may also cause oncogenic effects through dysregulation of the tricarboxylic acid (TCA) cycle, or by increasing susceptibility to oxidative stress. The exact role of mutant IDH1/2 in tumorigenesis however remains unclear.
In the work outlined in this thesis, I have demonstrated that the expression of mutant IDH1/2 in glioma cell lines leads to 2-HG accumultation and a reduction in α-KG production and results in HIF1α accumulation and a reduction in 5hmC production. Furthermore, the brain-specific expression of mutant Idh1 in mice also results in 2-HG accumulation and reduced α-KG production, whilst a reduction in 5hmC levels are also seen. This data appears to support the theory that IDH1/2 mutant activity results in the inhibition of α-KG dependent enzymes, either through the accumulation of 2-HG or due to a reduction in α-KG levels. The brain-specific expression of mutant Idh1 in mice also results in increased cellular proliferation and an increase in the expression of the neural stem cell marker, nestin. However gliomas do not develop, perhaps suggesting that additional mutations are required in conjunction with those occuring in IDH1/2 in order to initiate tumourigenesis.
Clinically, IDH1/2 mutations may represent a novel therapeutic target in glioma and may also serve as useful diagnostic, prognostic and predictive biomarkers. However, a better understanding of the pathogenesis of mutant IDH is required, to enable effective IDH1/2 directed therapies to be developed in the future.

Keywords: Isocitrate Dehydrogenase
glioma
Oncology
glioblastoma
Tumour metabolism.
Cancer
Advisor: Tomlinson, I
A commentary on Stesichorus

An abstract of a commentary - which must follow the winds and turns of the text it explains - cannot reasonably be expected. The present opportunity may, however, be used to summarise the principles behind my own specimen. Any commentary tries (at least in theory) to examine its subject's work from as many viewpoints - historical, philological, etc. - as are appropriate and possible. When the works, like Stesichorus', only exist in a highly fragmentary state, this impossible ideal seems slightly more capable of fulfilment than usual: there is less text and so more time (and space) to explain it. This approach from a large number of different viewpoints is not only more attainable in Stesichorus' case, it is more necessary: isolated scraps of poetry, whose context is often totally uncertain, require full examination before their secrets can be yielded up. Hence, for instance, the amount of effort devoted by other scholars - and now by me - to the subject of Stesichorus and art. And hence the exceedingly detailed scope of the commentary. For evern one word fragments have a philological and, sometimes, a stylistic value. And the speculation of earlier critics must be evaluated and preserved if plausible, or candidly denounced if unlikely, in an attempt to prevent repetition of the error.