VictorJuiz/thesis huggingface dataset:
Characterisation of photonic crystals fabricated by holographic lithography

Holographic lithography is a new technique developed for the fabrication of threedimensional photonic crystals in polymer. Four coherent laser beams are interfered to generate a three-dimensionally periodic interference pattern in a film of photoresist. Subsequent processing steps render a three-dimensional photonic crystal, whose structure is commensurate with the original interference pattern.
Two interference patterns are discussed in detail: a face-centred cubic pattern with a conventional lattice constant of 922nm in air and a face-centred cubic pattern with a conventional cube side of 397nm in air (interference wavelength 355nm). Three types of basis are presented for the interference pattern with a 922nm lattice constant: a righthanded, a left-handed and a non-chiral basis. Photonic crystals have been fabricated with both a chiral and a non-chiral basis and evaluated by scanning electron microscopy. Optical transmission measurements are presented for the non-chiral photonic crystals and are interpreted in both a Bragg scattering model and a photonic bandstructure model. A 'GaAs' and a 'diamond' basis are presented for the interference pattern with a 397nm lattice constant. Photonic crystals have been fabricated with the 'GaAs' basis and evaluated by scanning electron microscopy.
Small model theorems for data independent systems in Alloy

A system is data independent in a type T if the only operations allowed on variables of type T are input, output, assignment and equality testing. This property can be exploited to give procedures for the automatic verification of such systems independently of the instance of the type T. Alloy is an extension of first-order logic for modelling software systems. Alloy has a fully automatic analyzer which attempts to refute Alloy formulas by searching for counterexamples within a finite scope. However, failure to find a counterexample does not prove the formula correct. A small model theorem is a theorem which shows that if a formula has a model then it has a model within some finite scope. The contribution of this thesis is to give a small model theorem which applies when modelling data-independent systems in Alloy. The theorem allows one to detect automatically whether an Alloy formula is data independent in some type T and then calculate a threshold scope for T, thereby completing the analysis of the automatic analyzer with respect to the type T. We derive the small model theorem using a model-theoretic approach. We build on the standard semantics of the Alloy language and introduce a more abstract interpretation of formulas, by way of a Galois insertion. This more abstract interpretation gives the same truth value as the original interpretation for many formulas. Indeed we show that this property holds for any formula built with a limited set of language constructors which we call data-independent constructors. The more abstract interpretation is designed so that it often lies within a finite scope and we can calculate whether this is the case and exactly how big the finite scope need be from the types of the free variables in the formula. In this way we can show that if a formula has any instance or counterexample at all then it has one within a threshold scope, the size of which we can calculate.

Keywords: Automated verification
data independence
Alloy
Advisor: Roscoe, B
Social evolution and sex allocation theory

The study of sex allocation is one of the most successful areas in evolutionary biology: its theoretical predictions have been supported by experimental, observational and comparative approaches. Here, I develop sex allocation theory as follows: (1) I use fertility insurance theory to predict the sex ratio strategy of the malaria parasite, in response to human medical interventions that increase mortality and decrease fertility of the parasite’s various sexual stages; (2) Haplodiploidy has been suggested as a driver of the evolution of eusociality, as under this genetic system a female may be more related to her sister than to her own offspring. I examine a model considering queen versus worker control over the sex ratio of the colony and show that haplodiploidy alone does not explain the evolution of helping; (3) I follow up this study of the haplodiploidy hypothesis by examining the idea that split-sex ratios may favour the evolution of eusociality in haplodiploid species.
I study the two mechanisms of split sex ratios, that are found in natural populations and may have been important in the transition to eusociality: queen virginity and queen replacement. I focus on the impact of worker reproduction by considering the effect of woker producing a fraction of the colony offspring and by considering variation in the workers’ offspring sex ratio. My analysis shows that worker reproduction does not promote the evolution of helping in haplodiploid species; (4) I examine the evolution and function of a sterile soldier caste in parasitoid wasps from the genus Encyrtidae. Two main functions have been hypothesized for the emergence of soldiers: spiteful mediation of a sex ratio conflict in mixed-sex broods, and altruistic protection and 7 facilitation of the development of relatives.
I develop a model considering variation in the oviposition behaviour of females, that may produce single-sex or mixed-sex broods. I show that, in accordance with previous theory, females are expected to produce more soldiers than males, under the sex ratio conflict hypothesis. I also show that one of the consequences of this costly conflict is that females are favoured to produce single-sex broods over mixed-sex broods.

Keywords: Natural Selection
Behavioural Ecology
Sociobiology
Sex ratios
Advisor: West, S
Gardner, A
Topics in portfolio choice: qualitative properties, time consistency and investment under model uncertainty

The study of expected utility maximization in continuous-time stochastic market models dates back to the seminal work of Merton 1969 and has since been central to the area of Mathematical Finance. The associated stochastic optimization problems have been extensively studied. The problem formulation relies on two strong underlying assumptions: the ability to specify the underpinning market model and the knowledge of the investor's risk preferences. However, neither of these inputs is easily available, if at all. Resulting issues have attracted continuous attention and prompted very active and diverse lines of research. This thesis seeks to contribute towards this literature and questions related to both of the above issues are studied. Specifically, we study the implications of certain qualitative properties of the utility function; we introduce, and study various aspects of, the notion of robust forward investment criteria; and we study the investment problem associated with risk- and ambiguity-averse preference criteria defined in terms of quasiconcave utility functionals.

Keywords: Time Consistency
Model Uncertainty
Portfolio Optimization
Mathematical Finance
Advisor: Obloj, J
Zariphopoulou, T
Split intransitivity in old Japanese

According to the Unaccusative Hypothesis (Perlmutter 1978), intransitive verbs fall in two distinct classes: the unaccusatives (whose subjects originate as direct objects) and the unergatives (whose subjects originate as subjects). Although there are studies of split intransitivity in Modern Japanese and European languages, very few exist for earlier stages of Japanese. To fill in part of this gap, this thesis presents a comprehensive investigation of split intransitivity in Old Japanese (largely, 8th century Japanese).
The descriptive and analytic work of this research is based on the newly developed ‘Oxford Corpus of Old Japanese’ (OCOJ). It consists of original and romanized Old Japanese texts, with a wide range of information including the original orthography, part-of-speech, morphology and syntactic constituency in the form of XML tags following TEI conventions. It is part of a larger collaborative research project: ‘Verb semantics and argument realization in pre-modern Japanese: A comprehensive study of the basic syntax of pre-modern Japanese’, in which my DPhil project is situated. As part of my DPhil project, I took part in the analysis and tagging of the OCOJ, in addition to contributing to translation.
My original contribution to knowledge is a comprehensive investigation and in-depth analysis of the lexical-semantic aspects of split intransitivity in relation to its morpho-syntactic expressions in Old Japanese. This includes: exploring to what extent intransitive verbs could be classified as unaccusative and unergative, what factors are involved in the classification, how they interact, what are the possible ways of representation, and the theoretical implications it brings to linguistic theory in general. Syntactically, I looked into manifestations specific to Old Japanese (e.g. perfective auxiliary selection), and also examined to what extent diagnostics – which show split intransitivity in English, Italian and Modern Japanese (e.g. N+V compounding and resultative construction) – could be applied to Old Japanese. Semantically, I investigated various semantic factors and proposed basic and complex models of the interaction between intentionality and affectedness in Old Japanese. I also proposed a ‘complex format for representing simple event structures’ which enhances the understanding of semantic aspects of split intransitivity. As such, the results of my research not only contribute to a detailed understanding of Old Japanese verbs, but also have implications for linguistic theory in general.

Keywords: unergatives
Japanese
unaccusatives
split intransitivity
Advisor: Frellesvig, B
Analysing layered security protocols

Many security protocols are built as the composition of an application-layer protocol and a secure transport protocol, such as TLS. There are many approaches to proving the correctness of such protocols. One popular approach is verification by abstraction, in which the correctness of the application-layer protocol is proven under the assumption that the transport layer satisfies certain properties, such as confidentiality. Following this approach, we adapt the strand spaces model in order to analyse application-layer protocols that depend on an underlying secure transport layer, including unilaterally authenticating secure transport protocols, such as unilateral TLS. Further, we develop proof rules that enable us to prove the correctness of application-layer protocols that use either unilateral or bilateral secure transport protocols. We then illustrate these rules by proving the correctness of WebAuth, a single-sign-on protocol that makes extensive use of unilateral TLS.
In this thesis we also present a full proof of the model's soundness. In particular, we prove that, subject to a suitable independence assumption, if there is an attack against the application-layer protocol when layered on top of a particular secure transport protocol, then there is an attack against the abstracted model of the application-layer protocol. In contrast to existing work in this area, the independence assumption consists of eight statically-checkable conditions, meaning that it can be checked statically, rather than having to consider all possible runs of the protocol.
Lastly, we extend the model to allow protocols that consist of an arbitrary number of layers to be proven correct. In this case, we prove the correctness of the intermediate layers using the high-level strand spaces model, by abstracting away from the underlying transport-layers. Further, we extend the above soundness results in order to prove that the multi-layer approach is sound. We illustrate the effectiveness of our technique by proving the correctness of a couple of simple multi-layer protocols.

Keywords: TLS
protocol layering
strand spaces
WebAuth
computer security
security protocols
Advisor: Lowe, G
The conformation of lysozyme in solution

This thesis describes an investigation of the conformation of a small protein, lysozyme from hen egg-white, in aqueous solution which was carried out by means of nuclear magnetic resonance (nmr) spectroscopy. The conformation in the crystalline state had previously been investigated by X-ray diffraction, and a model of this conformation (the X-ray structure) was available. The solution and crystalline states could therefore be compared.
Before conformational studies could be undertaken, several problems associated with the nmr spectroscopy of a protein had to be overcome. The spectrum of lysozyme (in this work 1H resonances were studied) consists of a large number of broad overlapping lines. The individual resonances needed to be resolved and then assigned to specific protons in the molecule. Two different methods were devised to increase the resolution of the spectrum. First, the linewidths of resonances were reduced by a factor of about two by a mathematical manipulation of the spectrum (convolution difference). Secondly, the number of resonances observed in any given spectrum was reduced. This was achieved either by difference spectroscopy (the subtraction of two slightly different spectra) or by use of specific sequences of rf pulses in the Fourier transform nmr experiment. Using these methods, about sixty resonances were completely and separately resolved.
The object of literary criticism

The intentionally ambiguous title of my thesis suggests both the notion of the object at which literary criticism is directed and also the notion of the objective toward which it is directed. The first involves the problems of the identity and ontological status of the literary work, while the second involves the two primary aims of literary criticism: interpretation and evaluation. These four issues are individually analyzed in separate chapters, and my positions on them are presented and defended, while rival positions are critically examined. Moreover, I demonstrate that all four issues are conceptually very closely related and that positions on one inevitably influence positions on the others.
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'And from his side came blood and milk': the martyrdom of St Philotheus of Antioch in Coptic Egypt

My thesis examines the function and development of the cult of saints in Coptic Egypt. For this purpose I focus primarily on the material provided by the texts forming the Coptic hagiographical tradition of the early Christian martyr Philotheus of Antioch, and more specifically - the Martyrdom of St Philotheus of Antioch (Pierpont Morgan M583). This Martyrdom is a reflection of a once flourishing cult which is attested in Egypt by rich textual and material evidence. This text enjoyed great popularity not only in Egypt, but also in other countries of the Christian East, since his dossier includes texts in Coptic, Georgian, Ethiopic, and Arabic.
This thesis examines the literary and historical background of the Martyrdom of Philotheus and similar hagiographical texts. It also explores the goals and concerns of the authors and editors of Coptic martyr passions and their intended audience. I am arguing that these texts were produced in order to perform multiple functions: to justify and promote the cult of a particular saint, as an educational tool, and as an important structural element of liturgical celebrations in honour of the saint.
Another aim of this work is to stress the entertainment value of such texts. I explore the sources used by Coptic hagiographers for creating such entertaining stories, as well as the methods they used to re-work certain theological concepts and make them more accessible to the audience.
The thesis begins with description of the manuscript tradition of Philotheus and a brief outline and comparison of its main versions. The second chapter discusses the place of the Martyrdom of Philotheus in Coptic hagiography and its connection to the so-called cycles. The next two chapters explore the motifs and topoi characteristic of Coptic martyr passions, especially the legend of Diocletian the Persecutor and the image of Antioch as the Holy City in Coptic hagiography, as these two motifs appear in one way or another in the majority of the martyr passions. Chapter 5 is dedicated to one of the focal points in the Martyrdom - the miracle of resurrection and the tour of hell – and its literary and theological background. Chapter 6 discusses representations of magic and paganism in Coptic hagiography and some of the concerns of Coptic hagiographers. In the last chapter I explore the geography of the cult, its iconographic and hymnographic dimensions and the transformation of the perception of the saint; the second part of this chapter discusses the questions of performance, authorship and audience.

Keywords: hagiography
Coptic
cult of saints
martyr
Advisor: Taylor, D
Surface modified polymers to introduce antibacterial activities

This thesis is concerned with the chemical surface modification of several commercial industrial polymers in order to introduce antibacterial activity. Surface modification of polymers including LDPE, PE-fibre, MDPE, UHMPE and PS-XAD4 by carbene insertion reaction and diazo coupling was carried out using two diazo systems, urea diaryl diazo system and bis (dimethylamino) diaryl system. Successful surface modification on polymers was achieved while bulk properties of polymers were maintained.
ATR IR and combustion analysis were used to characterize modified polymer. Clear ATR IR absorption peaks and colour change during diazo coupling indicated successful surface modification. Surface coverage of modified polymers was calculated using nitrogen content detected by combustion analysis. Modified polymers binding with several biocidal agents including hydrogen peroxide, bleach and penicillin V were prepared and antibacterial activity was tested against S. aureus and E. coli. Modified polymers using the urea diazo system showed negative bioassay results, while modified polymer using the bis (dimethylamino) diaryl system showed excellent antibacterial activity.

Keywords: Surface Modification
Introducing Antibacterial Activities
Advisor: Moloney, M
Nutritional assessment and intervention in children with severe neurological disabilities

Providing adequate nutrition to children with severe neurological disabilities is extremely difficult due to the high prevalence of oral-motor dysfunction in this group. Short stature and light weight for height are common in disabled children and undernutrition is believed to play a role in this poor growth.
This programme of study investigated the effect of gastrostomy-tube feeding in disabled children with oral-motor dysfunction and evaluated the energy balance and body composition of disabled children fed both orally and via gastrostomy-tube over twelve months. The Quality of Life of the children and their carers was also evaluated.
Energy intake was measured using three-day dietary diaries and energy expenditure with indirect calorimetry and doubly labelled water. Total body water using oxygen-18 dilution was used to evaluate body composition along with standard anthropometry.
Improved growth, nutritional status and general health were seen at six and twelve months after gastrostomy-tube placement. The Quality of Life of the children and their carers also significantly increased. Both energy intake and energy expenditure were found to be lower than reference standards, but energy balance was positive indicating that inadequate nutrition was not the sole cause of poor growth. Body composition was also found to be significantly different from reference. Fat-free mass was significantly low for age and for height. Fat mass was higher in gastrostomy-tube fed children, but lower or normal in disabled children fed orally. Physical activity levels were low for the entire group of disabled children yet the gastrostomy-tube fed children displayed much higher levels of disability.
Gastrostomy-tube feeding has a positive impact upon the growth, health and Quality of Life of disabled children and their carers. Careful follow-up is critical in order to optimize health and body composition.
Coarse-grained rocks of Ascension Island

The lavas and pyroclastics of Ascension Island contain a suite of coarse grained igneous blocks which range in composition from olivine-gabbro to peralkaline-granite paralleling, but extending beyond the compositional range of the volcanics. The lavas range from alkali-basalt through hawaiite, trachybasalt, trachyandesite and trachyte to comendite. True basalt is relatively rare and there is a scarcity of analyses with 57 < Si02 < 63 wt %.
No high pressure mineral assemblages and hence no possible mantle fragments have been found. Petrographic and isotopic data suggest that a suite of gabbros from Dark Slope Crater crystallised from a magma derived from a MORB-like source. The remaining blocks and all the lavas evolved from magmas derived from a less depleted source.
The chemical variation seen in the lavas and blocks is best explained by crystal fractionation mechanisms in a relatively shallow magma chamber. The gabbroic blocks exhibit cumulus textures suggesting that they formed by accumulation of settling crystals. The intermediate to acid blocks compare much more closely in composition with the evolved lavas and are probably their slowly cooled equivalents. There is petrographic evidence that partial melting of intermediate coarse grained material gave rise to melts of granitic composition but these are not chemically equivalent to the acid lavas and blocks. A pegmatoid body crystallised in situ and closed system crystal fractionation alone resulted in a very similar sequence of mineral assemblages to the blocks and lavas and a peralkaline final liquid.
High 87 S4/ 86 Sr ratios in the evolved lavas and blocks are attributable to contamination by a small quantity of highly radiogenic oceanic sediment.
Comparison with other oceanic volcanoes suggests that these differentiation processes are much less important in determining the evolutionary path of the magma than its apparent starting composition.

Advisor: Atkins, F
Bell, J
Atkins, D
France's response to the Ivorian crisis under Gbagbo through the lens of IR regime theory

There exists a certain consensus among scholars and French diplomats that the golden era of the exceptionally close and amicable relations between France and its former sub-Saharan colonies is over. Nevertheless, the conclusions that these researchers arrive at regarding the current state of France’s African policy are rather different. The aim of the thesis is to determine which of the three paradigms concerning France’s African policy – the incremental adaptation, normalisation or confusion – best describes the French response to the crisis in Côte d’Ivoire under the Gbagbo regime. The contribution of the thesis is the analysis of continuities and changes of this specific Franco-African relationship, also known as Françafrique, within the framework of international relations regime theory. The thesis argues that France’s diplomacy towards the Ivorian crisis and her role in the multilateral conflict resolution strategy, reveal her growing inability to defend the constitutive principle of the Françafrique regime: grandeur. Her pursuit of middle power status through maintaining hegemonic relations to her favourite former colony was considerably challenged by various domestic and systemic factors, among which the Ivorian power struggles and Gbagbo’s duplicitous politics played a considerable part. Moreover, the thesis also points to the persistence of some old rules and decision-making procedures of the Françafrique regime, especially the resilience of informal networks. These old practices collide with France’s growing desire to make her African policy more transparent, coherent and efficient. It is therefore concluded that the coexistence of these opposite tendencies in France’s response to the Ivorian crisis under Gbagbo, as well as the inconsistent resort to the Françafrique principle, rules and decision-making procedures are best explained by the confusion paradigm of France’s African policy.

Advisor: Mustapha, A
Soares de Oliveira, R