VictorJuiz/thesis huggingface dataset:
Structures and mechanisms for synthetic DNA motors
Keywords: Kinetics
Nanotechnology
DNA origami
DNA
Toehold-mediated strand displacement
DNA tension
DNA motors
Molecular motors
Strand displacement
Mismatches
Self assembly

DNA provides an ideal substrate for nanoscale construction and programmable dynamic mechanisms. DNA mechanisms can be used to produce DNA motors which do mechanical work, e.g. transportation of a substrate along a track.
I explore a method for control of a DNA mechanism ubiquitous in DNA motor designs, toehold-mediated strand displacement, by which one strand in a duplex can be swapped for another. My method uses a mismatch between a pair of nucleotides in the duplex, which is repaired by displacement. I find that displacement rate can be fine-tuned by adjusting the position of the mismatch in the duplex, enabling the design of complex kinetic behaviours.
A bipedal motor [1, 2] is designed to walk along a single-stranded DNA track. Previously the motor has only taken a single step, due to a lack of designs to extend the single-stranded track. I present a novel design for track held under tension using a 3D DNA origami tightrope, and verify its assembly. The bipedal motor design is adapted and a method to specifically place motors on tightropes is demonstrated. Motor operation is investigated on truncated tracks and tightrope tracks by electrophoresis and spectrofluorometry. The motor does not accumulate appreciably at the track end; this is tentatively attributed to rearrangement of the motor between track sites without interaction with fuel.
Tightrope origami can hold single-stranded DNA under pN tension. I use tightropes to study hybridization kinetics under tension and find dramatic, non-monotonic changes in hybridization rate constants and dissociation constants with tension in the range &Tilde;0-15 pN. Extended tracks for a 'burnt-bridges' motor which destroys its track as it moves [3] are created on the inside of DNA nanotubes, which can be polymerised to create tracks up to a few mm in length, and on tiles which I attempt to join in a specific order. Crossing of the motor between tubes is verified, and microscopy experiments provide some evidence that track is being cleaved by the motor, a requirement for movement along the track. Tile based tracks are imaged by super-resolution DNA PAINT [4], providing proof-of-principle for track observation to infer motor movement.
Mathematical modelling and optimisation of Venturi-enhanced hydropower
Keywords: Optimisation
Fluid mechanics
Optimal control
Applied mathematics
Mathematical modelling

In this thesis we study a novel type of hydropower generation which uses a Venturi contraction to amplify the pressure drop across a turbine, allow- ing for cost-effective hydropower generation in situations where the head drop is small, such as in rivers and weirs. The efficiency is sensitive to how the secondary flow, which passes through the turbine, mixes with the accelerated primary flow, which is diverted around the turbine, within the confines of a closed geometry. In particular, it is important to understand the behaviour of the turbulent shear layers between the primary and sec- ondary flows, which grow downstream, mixing the flows together. The behaviour of the shear layers in the expanding part of the Venturi con- traction is strongly dependent on the shape of the channel. An important consequence of the channel shape, and hence the flow behaviour, is the degree of pressure amplification across the turbine, which determines the amount of generated power.
We focus on mathematically modelling the mixing of the flows in turbu- lent shear layers, and we investigate two different ways to increase pres- sure amplification: optimising the shape of the channel, and using swirl to enhance mixing. The channel shape optimisation reveals an interest- ing balance between the effects of mixing and wall drag. Wide channel expansion tends to accentuate non-uniform flow, causing poor pressure amplification, whilst shallow expansion creates enhanced wall drag, which is also detrimental to pressure amplification. We show how the maximum power is generated with a channel shape that strikes a balance between these two effects. We find that swirl enhances mixing by increasing shear layer growth rates, but it produces large pressure losses in doing so, and for large amounts of swirl a slowly recirculating region can form along the channel centreline. Whilst swirl does not improve efficiency, there may be some inevitable swirl present in the flow, and we show how this affects the optimum channel shape. We also establish the criteria for the existence of such a recirculation region so that it may be avoided.
Creative reading: using books in the vernacular context of Anglo-Norman England
Keywords: Materiality
Manuscript
Reading
Book History
early Middle English
Medieval
Poema Morale

This thesis responds to a lack of information regarding reading practice in literature in early Middle English. Here, reading is often used as a metaphorical or symbolic act—representing piety, devotional practice, or intellectualism—but how reading took place, how users engaged with books, is rarely figured. Other seams of evidence are therefore needed to access the reading process. The corpus of manuscripts on which I focus consists of thirty-three multilingual books containing English, Latin, and French produced in England between 1066 and c. 1300. Using this corpus, and inspired by the work of Leah Price, Juliet Fleming, Kathryn Rudy, and others, I seek to test the boundaries of what has previously been considered permissible evidence for reading, thereby adjusting and expanding current conceptions of the range of activities and practices high medieval book use entailed.
The thesis begins with a case study of some important readers: scribes. In chapter one, using the seven surviving copies of Poema Morale as a corpus I read against current critical considerations of variance in manuscript transmission as a sign of ‘scribal authorship’ in order to establish practices of scribal reading. Chapters two and three go on to demonstrate how these ‘scribal readers’ prefigured a work’s use as they copied, particularly when they chose to introduce or exclude textual apparatus in the form of titles, capitals, or paraph marks. The final part of the thesis examines the retrospective evidence of use left by readers who marked and altered their books to determine the extent to which readers conformed to the practices imagined by manuscript producers.
As a whole, then, the thesis showcases the variegated nature of reading practice—from critical analysis to nugatory scanning—and the alternative uses for books in English in this period. It shows that vernacular reading was a work of ‘embodied intellectual labour’ that benefitted from the material form of the book, and that engagement and manipulation of this form was not just tolerated, but expected, and perhaps actively encouraged.
Algorithms for decision making
Keywords: decision making
optimisation
optimal control

We investigate algorithms for different steps in the decision making process, focusing on systems where we are uncertain about the outcomes but can quantify how probable they are using random variables. Any decision one makes in such a situation leads to a distribution of outcomes and requires a way to evaluate a decision. The standard approach is to marginalise the distribution of outcomes into a single number that tries in some way to summarise the value of each decision. After selecting a marginalisation approach, mathematicians and decision makers focus their analysis on the marginalised value but ignore the distribution. We argue that we should also be investigating the implications of the chosen mathematical approach for the whole distribution of outcomes.
We illustrate the effect different mathematical formulations have on the distribution with one-stage and sequential decision problems. We show that different ways to marginalise the distributions can result in very similar decisions but each way has a different complexity and computational cost. It is often computationally intractable to approximate optimal decisions to high precision and much research goes into developing algorithms that are suboptimal in the marginalised sense, but work within the computational budget available. If the performance of these algorithms is evaluated they are mainly judged based on the marginalised values, however, comparing the performance using the full distribution provides interesting information: We provide numerical examples from dynamic pricing applications where the suboptimal algorithm results in higher profit than the optimal algorithm in more than half of the realisations, which is paid for with a more significant underperformance in the remaining realisations.
All the problems discussed in this thesis lead to continuous optimisation problems. We develop a new algorithm that can be used on top of existing optimisation algorithms to reduce the cost of approximating solutions. The algorithm is tested on a range of optimisation problems and is shown to be competitive with existing methods.
The Eoan Group and the politics of coloured opera in apartheid South Africa
Keywords: Race
Opera
Apartheid
Eoan Group
South Africa

The Eoan Group, founded in 1933 in Cape Town, was South Africa’s first and only all-coloured opera, dance and theatre company. Its 1956 production of La Traviata was the first opera produced by non-white people in South Africa, and initiated an operatic career that spanned twelve opera seasons and ten operas. The group was under the administration of white directors and received funding from the apartheid government. In return, they agreed to honour the regime’s racial laws by performing for segregated audiences. Their acquiescence to segregation and their complicity in the promotion of apartheid ideology caused political problems: they were ostracised by their own community and boycotted by members of the white and coloured racial groupings. After the group’s operatic activities came to a permanent halt in 1980, their history sank into obscurity, despite their importance in the establishment of an operatic culture in the country. The memorialisation of South Africa’s cultural-political past continues to maintain a binary of complicity and resistance, with those who are remembered grouped neatly into either of these categories. These labels, however, do not map tidily onto the Eoan Group, with its bewildering narrative of self-empowerment-through-collusion. Consequently, their story presents a problem for the writing of South African music history.
Drawing extensively on material from the Eoan Group Archive, this dissertation considers the socio-political ambiguities of the Eoan narrative from musicological and post-colonial theoretical angles, to show how the group’s operatic activities disrupted the cultural and material determinism of apartheid’s racialised ideology. It calls for a disavowal of the Manichean ethics by which subaltern agency is measured, and proposes instead a turn to Njabulo S. Ndebele’s ‘politics of the ordinary’. From the sonic and material residue of the Eoan Group’s productions, this project forges a newly conceived decolonial writing of apartheid operatic history.
Singular representation
Keywords: Representation
Contextualism
Attitude reports
Knowing which
Reference
Singular thought
Aboutness
Acquaintance

This thesis is a study of aboutness. It defends the claim that we have singular thoughts about ordinary objects and argues that an essential part of how we do so is by maintaining singular representations. This proposal allows us to avoid traditional, unsatisfying conceptions of the scope of singular thought while restoring the sense in which such thought is a distinctively epistemic achievement. Reconnecting the study of aboutness with epistemology promises to alleviate the sense of directionlessness in the contemporary literature, offering a firmer grip on the phenomenon along with new, systematic resources for its investigation.
Chapters 1–2 explore the effects of contextualist machinery on orthodox views about singular thought. It is widely thought that if there is to be a plausible connection between the truth of a de re attitude report about a subject and that subject’s possession of a singular thought, then there can be no acquaintance requirement(s) on singular thought. Chapter 1 shows that this view rests on a faulty picture of how we talk about attitudes. Indeed, the truth of a de re attitude report cannot be taken to track the singular/non-singular distinction without collapsing it. A new, contextualist picture is needed. That there must be a distinction between singular and non-singular intentionality is emphasized in Chapter 2, where a key explanatory role for singular thought—brought out by a thought experiment due to Strawson—is examined. I show that the role does not call for any distinctive kind of mental content.
Once we abandon the two widespread views questioned in Chapters 1–2, our grip on the phenomenon of singular aboutness is loosened: it is not constitutively tied to the kinds of attitude-reporting data or mental content by which it is often assumed to be revealed. Where are we to look for insight? What makes something the object of a singular thought?
According to Russell, it is a datum of intuition that singular thought involves a kind of knowledge; a theory of aboutness will precisify the intuitive notion of ‘knowing which thing one is thinking about’ in order to capture this demand in a philosophically revealing way. If Russell is right, teasing out this connection to knowledge will allow us to see what it takes for a particular thing to be the immediate subject matter of thought. Chapter 3 discusses Evans’s theory of this kind. Chapter 4 examines recent work by Dickie. While serious concerns emerge in each case, insights recovered are used to precisify Russell’s requirement, leading to a novel picture of singular representation and the epistemic character of this achievement.
While the chapters follow a narrative, providing an extended rationale for the proposal in Chapter 4, each may be read in isolation by those familiar with the philosophical issues. For those who are not, the Introduction provides sufficient background.
The stability of host-pathogen multi-strain models
Keywords: pathogen
invasion
random forest
influenza
rotavirus
multi-strain

Previous multi-strain mathematical models have elucidated that the degree of cross-protective responses between similar strains, acting as a form of immune selection, generates different behavioural states of the pathogen population. This thesis explores these multi-strain dynamic states, to examine their robustness and stability in the face of pathogenic intrinsic phenotypic variation, and the extrinsic force of immune selection. This is achieved in two main ways: Chapter 2 introduces phenotypic variation in pathogen transmissibility, testing the robustness of a stable pathogen population to the emergence of an introduced strain of higher transmission potential; and Chapter 3 introduces a new model with a possibility of immunity to both strain-specific and cross-strain (conserved) determinants, to investigate how heterogeneity in the specificity of a host immune response alters the pathogen population structure. A final investigation in Chapter 4 develops a method of reverse-pattern oriented modelling using a machine learning algorithm to determine which intrinsic properties of the pathogen, and their combinations, lead to particular disease-like population patterns. This research offers novel techniques to complement previous and ongoing work on multi-strain modelling, with direct applications to a range of infectious agents such as Plasmodium falciparum, influenza A, and rotavirus, but also with a wider potential for other multi-strain systems.
Finite element analysis of short-term and long-term building response to tunnelling
Keywords: Constitutive models
Immediate settlement &amp; consolidation
Tunnels &amp; tunnelling
Finite element analysis
Building damage assessment
Masonry structures
Soil-structure interaction

Tunnelling in urban areas causes short-term and long-term ground movements under existing buildings. Finite element analysis provides a useful option for assessing the likely extent of damage induced in these buildings. Although finite element analysis is suggested to be used in the later phases of the building damage assessment procedures employed in practice, only the effect of short-term ground movements is typically considered and there are no detailed guidelines on the specification and complexity of the modelling. This thesis addresses the tunnel-soil-building interaction problem and the effect of long-term consolidation, as well as demonstrating the application of 3D finite element analysis with appropriate simplifications for practical assessment purposes.
Finite element models are developed to quantify the effect of shallow tunnelling on an example masonry building founded on strip footings, considering both single- and twin-tunnel scenarios in a typical London soil profile. Total stress and effective stress analyses are adopted with specific modelling procedures to focus on the short-term and long-term response respectively. The analyses use a non-linear model for the masonry, and allow slippage and gapping at the soil-footing interface. Two advanced constitutive models for the soil (the extended Mohr-Coulomb model and the modified two-surface kinematic hardening model) are implemented with customized stress update schemes.
The finite element results present the interaction between the soil and the building by comparing with the greenfield ground response. The horizontal coupling between the foundation and the ground is shown to be relatively weak. The dominant deformation mode of the building varies with the tunnel configuration (i.e. single or twin tunnels) and the tunnel eccentricity. Strain localization is found around the explicitly modelled window and door openings. The long-term consolidation is sensitive to the permeability of the tunnel lining. The building response to long-term ground movements is further affected by the tunnel-tunnel interaction in the case of twin-tunnel configuration.
Performing 3D analysis of a single facade and foundation provides useful damage predictions, without the need to model a complete building. The proposed result processing methods such as characteristic strain and damage bar chart are practical tools for assessment. The study highlights some limitations of the elastic beam assessment method, which is often adopted in the early phase of the damage assessment process.
The politics of the public sphere: English-language and Yoruba-language print culture in colonial Lagos, 1880s-1940s
Keywords: civil society
West Africa
Nigeria
media history
print culture
newspapers

This thesis studies print culture in colonial Lagos against the background of the public sphere, and brings together a variety of English-language and Yoruba-language newspapers. Such an approach allows for highlighting the practicalities of newspaper production and foregrounding the work accomplished by newspapermen in a changing ‘information environment’ and political context. It offers insights into Lagos politics, contributes to the history of the educated elite, and to more global histories of communication. Using newspapers as well as archival records, and focussing on events that strikingly reveal dynamics in the public sphere, this thesis narrates a nuanced history of a discursive field which was, amongst other things, central for Lagos politics.
This thesis complicates a Habermasian notion of the public sphere as an open discursive space, and not only highlights that the public sphere was an arena of contested meanings, but also illustrates axes along which the composition of this social structure was negotiated. When newspapers emerged in the late nineteenth-century, discussions in the press were largely restricted to the elite. The economy of recognition that was at play in the public sphere was to change in the 1920s. This thesis highlights how newspapermen and contributors sought to carve out niches for themselves in the public sphere in new ways and how their becoming a speaker in this discursive field was challenged and contested. It highlights the nuanced ways in which newspapermen and contributors convened publics through their papers: how they did so around particular issues, in distinction from each other, and how they adapted the convening of publics to new political dynamics in the 1940s. This thesis gives insight into the complex relationship between English-language and Yoruba-language newspapers, and moreover illustrates how the practicalities of the newspaper business were coming to bear on dynamics in the public sphere.
Development and pre-clinical evaluation of HIV-1 vaccines
Keywords: HIV-1
Vaccines

Infants born to HIV-1 positive mothers are at risk of acquiring the infection through pro-longed breastfeeding due to the presence of HIV-1 cell-free RNA and cell-associated DNA in breast milk. However, there is limited focus on vaccines to prevent mother-to-child transmission (MTCT) via breastfeeding. Mycobacterium tuberculosis (M. tuberculosis) the causative agent of Tuberculosis (TB) is the most common cause of AIDS-related deaths. Most infants in Africa receive Bacillus Calmette-Guérin (BCG) at birth or soon after birth and it is the only licensed vaccine for TB. The development of a dual platform vaccine against HIV-1 and TB would be a logical effort to combat these two deadly diseases. Thus, rBCG expressing an HIV-1 derived immunogen may induce HIV-1 responses at birth and these responses can be boosted at adolescence, by a heterologous vector such as modified vaccinia Ankara (MVA) or Chimpanzee adenovirus serotype 63 (ChAdV63). In the first study, I assessed BCG-based vaccines derived from BCG Danish SSI-1331 (BCG1331), expressing an HIV-1 immunogen HIVconsv either by an episomal plasmid (BCG.HIVconsv401epi) or integrated into the BCG chromosome (BCG.HIVconsv401int) in a prime-boost regimen. BALB/c mice were immunised with the different prime-boost regimens. rBCG alone was unable to induce detectable HIV-1-specific T-cell responses, however, when used in a prime-boost strategy, elevated HIV-1-specific T-cell responses were observed.
In the second study, I aimed to construct marker-less mycobacterium-vectored HIV-1 vaccines using the operator-repressor titration (ORT®) system as an alternative system for antibiotic resistance gene free vaccines. This rBCG vaccine would express the HIVconsv immunogen. I first constructed plasmids carrying the lac operator lacO and tetracycline operator tetO to enable use in ORT Escherichia coli (E.coli) and Mycobacterium strains, respectively. The ORT system was successful in E. coli and not in mycobacterium. I also constructed plasmids carrying mycobacterium essential genes that would allow for genetic manipulation in Mycobacterium and the use of ORT in mycobacterium. Although the plasmid construction was successful, in the end, genetic manipulations in Mycobacterium and the production of an ORT based BCG (ORT-VAC) was not successful.
Finally, I evaluated the immunogenicity of conventional DNA plasmid pTH.HIVconsv compared to Semliki Forest virus replicon DREP.HIVconsv in rhesus macaques. Immunisations were done in a prime-boost strategy with heterologous vectors MVA or ChAdV63 delivering the same immunogen, HIVconsv. It was found that DREP.HIVconsv which was at least 20-fold lower dose than pTH.HIVconsv was capable of inducing comparable T-cell responses and in some experiments, the responses were superior to the conventional DNA plasmid pTH.HIVconsv.