VictorJuiz/thesis huggingface dataset:
Implementing segmented ion trap designs for quantum computing

With all the key elements of quantum computing in ion traps demonstrated by the research community, the focus is now placed on building more sophisticated traps with larger numbers of ions to allow practical scale information processing. One promising avenue is to store ions in and shuttle them between many independent traps which serve as potential interaction sites.
The core of the work described in this thesis is the experimental evaluation of a microfabricated segmented ion trap, built by Sandia National Laboratories ("Sandia trap"). These experiments required construction of a wholly new optical setup including laser and detection systems, a vacuum system and control electronics. Among our experimental achievements were: successful loading of single and pairs of ions in the microscale trap, measurement of ion storage lifetime, measurement of the motional heating rate with a time-resolved Doppler-cooling method — which showed above than average heating, and implemented a single-ion shuttling method — which reliably transferred the ion through a distance of 360 μm (two DC electrode widths away) and back. These results have been used to improve the next version of the Sandia trap design.
We also used computer modelling to study several aspects of ion traps: a mesoscopic ion trap designed for fast ion separation, simulated ion loading to quantify requirements for successful trapping in small and shallow traps, and analyzed a precise shuttling method — where the time dependence of the trapping potential is engineered such that there is minimal motional heating.
The results show that ion trap arrays at the 100 μm distance scale are feasible and suggests that such multiple trap designs merit further study.

Keywords: Simulation
Laser
Calcium
Matlab
Ion trap
Advisor: Steane, A
The uses and abuses of referendums

Referendums, especially referendums with constitutional content, are often treated as exceptional acts. They are treated as exceptional in a democratic sense, because they are thought to go beyond the usual democratic processes and institutions. Since referendums are thought to be exceptional in a democratic sense they are treated as exceptional in a constitutional sense too. The political and legal significance attributed to votes in referendums far surpasses that of elections, protests, or votes in legislatures. The aim of this thesis is to challenge this approach to referendums. I will argue that referendums, even referendums with constitutional content, are democratic processes like any other. This thesis interrogates the treatment of referendums in theory and practice. It challenges the ideas that inform the view of referendums as exceptional democratic processes. This is not an argument against the use of referendums. Far from it. Instead, it is an argument for the normalization of referendums. To argue for the normalization of referendums is to say that referendums are not higher-order decision-making processes that operate on a distinct democratic plane. Referendums are just one of many ways that direction is given to representatives in a democracy. Certain features of referendums distinguish them from other democratic processes. In particular, they give more specific direction to representatives than elections do. There are features of referendums that are significant and distinctive, but nothing places them above –or apart from– other democratic processes.

Advisor: Green, L
Many-sided sympathy and the science of religion in George Eliot, Vernon Lee, and Edna Lyall

Discourse on sympathy in mid-to-late nineteenth-century Britain took place in many intellectual contexts, including philosophy, aesthetics, evolutionary science, and physiological psychology. Concomitantly, the science of religion was a rising enterprise that largely transferred the study of religion from theologians to philologists, cultural evolutionists, and anthropologists as it sought to produce a comparative, systematic account of the growth and nature of religious belief. This thesis contends that these ostensibly disparate aspects of the intellectual climate overlapped in the literary marketplace as women writers combined the popular and specialized researches of each, both in answer to public anxieties these discourses fostered and in an effort to wield their fiction to ethical, social, and political purpose. It considers the fiction of three women with very various backgrounds, intellectual pursuits, and writing styles – that of George Eliot (1819–1880), Vernon Lee (1856–1935), and Edna Lyall (1857–1903) – and sets their work side by side to discern a common thread running through their oeuvres: a pattern of fictional ‘many-sided’ male sympathetic figures arranged to balance broad tolerance with specific function and achieve a form of modern spirituality for the benefit of the reader and society at large. Translated from the German Vielseitigkeit in the 1830s, the term ‘manysidedness’ initially entered the lexicon to describe the multi-faceted mind of Johann Wolfgang von Goethe (1749–1832), whose influence sat at the heart of much of the science of religion initiative. By mid-century it became a conduit for thinking about sympathy via its close association with positions of tolerance, impartiality, and acculturation. Intentionalist in nature and experimenting with ‘surface reading’ as methodology, this research has resulted in a fruitful exploration of sympathy both as a form of ‘doubling’ and as a continual intellectual and emotional unfolding akin to the interpretation of manysidedness as a model of self-cultivation. Each author is examined in light of her affinity with a male thinker: Eliot is paired with the philologist and scholar of comparative religion, Friedrich Max Müller (1823–1900); Lee is viewed in relation to the aestheticism of her friend Walter Pater (1839–1894); Lyall is explored through her compassionate response to the suffering of the freethinker Charles Bradlaugh (1833–1891).

Advisor: Ballaster, R
Shuttleworth, S
A multi-country study of dengue vaccination modelling using econometric and GIS approaches in three dengue-endemic countries: Vietnam, Thailand, and Colombia

The overall theme of this thesis is to generate innovative health-economic outcomes which are needed prior to the introduction of population-level dengue immunization programs in three dengue-endemic countries: Vietnam, Thailand, and Colombia. This thesis consists of six chapters which are distinctive but inter-related. Following the introductory chapter, where the existing literature search is carried out, in Chapter 2 I begin by conducting a multi-country study of the economic burden of dengue fever based on standardized field studies in the three dengue-endemic countries.
In Chapter 3, an Early Warning Signal (EWS) model is developed based upon climate and non-climate factors. In particular, this chapter adopts a theory of elasticity, which is not common in the field of health economics but which is a key notion in economics, to predict geographically-dispersed dengue outbreaks in Colombia.
The econometric technique used in the third chapter is further extended to the mixed-effects modeling work in Chapter 4 where high-risk areas for dengue fever are identified at the 5 km by 5 km geographical unit, and the number of dengue vaccine doses is estimated at the population-level in Vietnam, Thailand, and Colombia. The concepts and methodologies applied in both Chapter 3 and 4 are unconventional but clearly underscore the needs for innovative approaches in order to respond to existing public health problems.
Based on the findings from Chapter 1 to Chapter 4, the vaccination impacts and cost-effectiveness of dengue vaccination strategies are estimated in the three dengue-endemic countries in Chapter 5. Vaccination impact is derived from a spatially explicit, individual-based meta-population transmission model developed by the Oxford/Exeter group for the WHO Strategic Advisory Group Experts (SAGE) working group exercise. In addition, country-specific health economic parameters are taken from the economic burden field studies in the second chapter of the thesis. In particular, Chapter 5 is designed to reflect the most up-to-date information on the dengue vaccine development: including controversial debates over CYD-TDV, introducing a new vaccine candidate (NVC) with no safety concern identified in CYD-TDV.
Lastly, Chapter 6 summarizes the roles of the four core chapters as a country-specific investment case, and underscores the importance of an evidence-based decision-making process prior to implementing vaccination campaigns at the population-level.

Keywords: immunization
vaccines
Advisor: Farlow, A
Gupta, S
Lourenco, J
‘How many miles doth your hand travell!’: Women’s textual journeys in seventeenth-century England

The seventeenth century is often called the first truly global era, but worldly adventures did not require physical movement abroad. Despite the limitations placed on women’s physical movement that were prevalent in early modern English culture, their textual habits reveal global curiosity. My thesis uncovers the ways in which some English women, many of whom had neither the means nor opportunity to travel, experienced this era of exploration through their own reading and writing. By recognising cases of virtual travel, as well as the numerous ways of interpreting and influencing the foreign, this study introduces an often-overlooked yet vital discourse concerning imagined travels. When it comes to women’s recorded experiences of the world beyond their own, scholarship has tended to focus on individual female writers who physically travelled abroad, and their creation of some kind of travelogue. Unless we consider the varied and frequent series of exchanges between English travellers and women at home in England, I argue, we ignore the complexly gendered transnational dialogues negotiating global information. Women left textual traces of their worldly journeys across print and manuscript – including, but not limited to, sermons, poems, conduct literature, almanacs, petitions, wage receipts, powers of attorney, commonplace books, letters, and diaries. I consider examples of each mode to see how genres were specifically chosen to cater to the author’s purpose and intended audience, as well as being inextricably connected to their social position and levels of education. My thesis therefore advances the study of non-elite women’s literary and historical resources, most of which have not received sufficient scholarly attention. I explore the processes of piecing together stories through sometimes fragmented or anecdotal sources, considering how we might interpret the signs that are left, which are often slight when dealing with this demographic. To speak of these engaged women helps to further our understanding of how travel is a multi-faceted concept, and stimulates new ways of thinking about women’s textual contributions during a period of profound global discoveries.

Advisor: Williams, A
Smyth, A
Mathematical modelling of silicon furnaces

Silicon is a widely utilised material, with use in the production of semiconductors, textiles, and metallic alloys. It is produced by feeding quartz rock and carbon into huge furnaces, which are heated by electrodes. In this thesis, we develop mathematical models to better understand furnace behaviour. Of particular interest is crust formation, a phenomenon whereby a blockage emerges, preventing the raw materials from falling naturally under gravity to the lower, hotter part of the furnace where the necessary chemical reactions occur.
We begin by developing a continuum model for the evolution of chemical concentrations, temperature, and gas flow in a vertical cross-section of the furnace. This model is analysed in the context of 'pilot furnace' experiments, which are smaller, cylindrical furnaces heated in laboratory conditions. Numerical simulations of our model are shown to compare well with these experiments. We further perform parameter sweeps of our model, to give recommendations for operating strategies.
Next, we undertake an asymptotic analysis of this model, to identify the dominant chemical and thermal behaviour within the pilot furnace. We determine chemical balances in different spatial and temporal regions by imposing a temperature profile. We also obtain a simplified thermo-chemical furnace model, which captures the main behaviour of our original model, but comprises only two partial differential equations.
We then present a model of crust formation, in which furnace crust is treated as a single fluid of thermally-dependent viscosity, located between two moving boundaries. Numerical simulations show that solutions of this model can either tend towards a steady state, indicative of crust formation in practice, or the raw materials can fall indefinitely. The latter case is desirable in real furnaces, although it may not always be feasible. We discuss bifurcations between these two behaviours in our model, and the significance of such bifurcations to avoiding the build-up of crust.
Finally, we focus on the reaction between solid carbon particles and silicon monoxide gas. This motivates us to develop a homogenised model for reactions between solid particles and gas, which has many possible applications. We comment on simplifications of this model for both diffusion-limited and chemically-limited reactions.

Keywords: Reaction Kinetics
Heat Transfer
Silicon Production
Mathematical Modelling
Advisor: Please, C
Van Gorder, R
Information-theoretic foundations of thermodynamics in general probabilistic theories

In this thesis we study the informational underpinnings of thermodynamics and statistical mechanics. To this purpose, we use an abstract framework— general probabilistic theories—, capable of describing arbitrary physical theories, which allows one to abstract the informational content of a theory from the concrete details of its formalism. In this framework, we extend the treatment of microcanonical thermodynamics, namely the thermodynamics of systems with a well-defined energy, beyond the known cases of classical and quantum theory. We formulate two requirements a theory should satisfy to have a well-defined microcanonical thermodynamics. We adopt the recent approach of resource theories, where one studies the transitions between states that can be accomplished with a restricted set of physical operations. We formulate three different resource theories, differing in the choice of the restricted set of physical operations.
To bridge the gap between the objective dynamics of particles and the subjective world of probabilities, one of the core issues in the foundations of statistical mechanics, we propose four information-theoretic axioms. They are satisfied by quantum theory and more exotic alternatives, including a suitable extension of classical theory where classical systems interact with each other creating entangled states. The axioms identify a class of theories where every mixed state can be modelled as the reduced state of a pure entangled state. In these theories it is possible to introduce well-behaved notions of majorisation, entropy, and Gibbs states, allowing for an information-theoretic derivation of Landauer’s principle. The three resource theories define the same notion of resource if and only if, on top of the four axioms, the dynamics of the underlying theory satisfy a condition called “unrestricted reversibility”. Under this condition we derive a duality between microcanonical thermodynamics and pure bipartite entanglement.

Keywords: general probabilistic theories
quantum thermodynamics
sharp theories with purification
quantum foundations
purification
quantum information theory
majorisation
Advisor: Barrett, J
Tales from topological oceans

Functional relationships between variables can offer great illumination to hard problems. In geophysical fluid dynamics these often arise via alignment of gradients, in which case the functional relationship is multivalued; its branches are determined by a topological analysis of the connectedness of level sets, accomplished by the Reeb graph.
The neutral tangent plane, along which mixing in the ocean predominantly occurs, is defined by ∇nρ = ρp ∇n p, thus a multivalued function relates the in-situ density ρ and the pressure p. With topological analysis, a new approximately new surface is presented, called a topobaric surface. This surface possesses an exact geostrophic stream function, namely the exact geostrophic stream function for neutral surfaces, which ΜcDougall (1989) proved must exist. A closed form expression for this stream function is presented.
For a steady, inviscid, buoyancy conserving fluid, a multivalued function relates the potential vorticity Q and the Bernoulli potential B on buoyancy surfaces. In the Antarctic Circumpolar Current (ACC), level sets of B are dominated by one circumpolar contour, so Q is studied as a single-valued function of B. A tight linear relationship is discovered. Its slope, appropriately non-dimensionalised, provides information about the degree of PV homogenisation on a buoyancy surface, and about the shear stability of the flow regime via Arnol'd's stability theorems.
The real ocean does not obey these assumptions, and Q is not exactly materially conserved. In the time-mean ACC, it is found that Q can vary along streamlines by up to 50%. The causes for these fluctuations are studied, revealing a balance between two large and opposite-signed forcings---mean vertical advection and eddy interfacial form stress---with friction significant near topography. Variation of Q along B contours adds complexity on top of a background state defined by constant Q along B contours.

Keywords: Potential vorticity
Rossby waves
Multivalued function
Reeb graph
Topology
Neutral surfaces
Geostrophic stream function
Southern Ocean
Instability
Advisor: Marshall, D
The effect of maternal anthropometry on newborn size and body composition

This thesis assesses how gestational weight gain (GWG) influences newborn body composition (NBC) in an ethnically diverse population and determines the modifiers on that relationship.
To answer the research question, it was important to understand what may be classified as optimal GWG. To achieve this, I carried out a systematic review of studies that produced GWG charts; this showed there was considerable heterogeneity in the quality of available GWG charts.
GWG was transformed into z-scores; this allowed analyses, which were independent of gestation length. Newborn body composition is considered a more accurate marker of neonatal size in anthropometric research when compared with birthweight. It is usually divided into body fat percentage (BF%) and fat free mass (FFM). NBC was measured using a PEAPOD® device which calculates BF% and FFM in infants up to the age of 6 months. It is considered the gold standard of measuring NBC.
My results showed that as GWG increased, both BF% and FFM increased. For each z-score unit increase in GWG, BF% increased by 1.8% and FFM by 292.7grams. The strongest modifiers on this relationship were BMI group, gender and GA at delivery. In addition, endocrine disorders and age at PEAPOD measurement affected only FFM and smoking affected only BF%.
The factors driving future morbidities are, of course, complex but GWG represents a modifiable factor that is easily measured and monitored hence its appeal. Public health issues such as childhood obesity, adulthood obesity, stunting and wasting and medical issues such as cardiovascular disease and diabetes appear to be affected by fetal environment and NBC. If it is at all possible to alter these, by influencing GWG through women’s behaviour and clinical care we provide, the benefits in both the developed and developing world in the form of preventative medicine would be invaluable.

Advisor: Hirst, J
Cheikh-Ismail, L
The marble statuettes from the Athenian Agora, first century BC to fourth century AD

This study presents the full range of marble statuettes and statuette fragments, certainly or probably carved between the first century BC and the fourth century AD, that have been found during excavations of the Athenian Agora conducted by the American School of Classical Studies at Athens. The statuettes depict gods and goddesses in the forms of well-known classical and hellenistic models: Aphrodite, Asklepios, Eros, Artemis, Herakles, Pan, Apollo, Tyche, and Hermes, among others. In addition to the close autopsy and description of individual works, the primary aim of this study is to examine the statuettes as a group of cultural artefacts that document religion, society, and artistic production in Athens and beyond. Chapter 1 introduces the material and defines it shape. Chapter 2 builds an archaeological and chronological framework that places the bulk of production in the second and third centuries AD, up until the time of the Herulian sack in AD 267. Chapter 3 considers the demands of consumers through the lens of iconographic choice revealing local Athenian ways of picturing the gods. Chapters 4 and 5 explore the display settings of statuettes in sacred and domestic spaces, ultimately arguing that most statuettes were destined for houses where they could perform roles in ritual activities. Chapter 6 shifts attention to the maker for a discussion of the techniques and processes of production, as well as patterns of trade. Chapter 7 concludes the study with focus on the mobile nature of statuettes in household settings. A brief epilogue reflects on the late-antique lives of the statuettes.

Advisor: Smith, R
Æthelwold’s Circle, Saints’ Cults, and Monastic Reform, c. 956-1006

This dissertation examines the veneration of saints at the monasteries which were refounded and funded by the English monastic reformer Æthelwold and his students between the mid-950s and 1006. Scholars have noted that monastic reformers in general— and Æthelwold in particular— invested considerable energy and resources in the veneration of saints, and this work attempts to provide the first full-scale discussion of venerating practices at the houses connected to Æthelwold. Æthelwold’s circle is worth studying because its members dominate the surviving sources and also seem to have exerted a considerable influence on contemporaries. Moreover, Æthelwold’s and his disciples’ veneration of saints reveals interesting patterns. Although Æthelwold and his monks promoted (and often achieved) ecclesiastical uniformity and standardization in many areas, they venerated different saints in various ways at their different monasteries. I argue that these practices emerged because the forms of veneration revealed in the sources were developed by monks in reaction to events and actors outside their monasteries. The timing of certain forms of veneration (as revealed in charters) and the nature of some of the saints (like Swithun, an unreformed cleric whose lifestyle contravened some of the monks’ ideals) suggest that the monks were motivated by their relationships with groups outside their monasteries. Indeed, most surviving sources pertain to forms of veneration that the monks anticipated would be viewed by groups outside the monastery. Since the social and political contexts at the circle’s monasteries varied, so did the monks’ veneration. Thus, this study illuminates how the members of Æthelwold’s circle shaped their relationship with the laity, a relationship which posed key problems for monasticism (and reformers) throughout the ages. Equally, the variety of saints at Æthelwold’s monasteries can highlight and supplement our understanding of different social, political, and geographical contexts in Anglo-Saxon England.

Keywords: Saints -- Cult
approximately 908-984
600-1500
Bishop of Winchester
Anglo-Saxons -- Religion
Church history -- Middle Ages
449-1066
Great Britain -- History -- Anglo-Saxon period
Aethelwold
Saint
Medieval History
Church renewal -- Catholic Church -- History -- To 1500
Monasteries and state -- History -- To 1500
Advisor: Abrams, L
Leyser, C