VictorJuiz/thesis huggingface dataset:
Chemical scanning probe lithography and molecular construction

The initiation and high resolution control of surface confined chemical reactions would be both beneficial for nanofabrication and fundamentally interesting. In this work, spatially controlled scanning probe directed organometallic coupling, patterned functional protein immobilisation and highly localised reversible redox reactions on SAMs were investigated.
Catalytically active palladium nanoparticles were mounted on a scanning probe and an appropriate reagent SAM was scanned in a reagent solution. This instigated a spatially resolved organometallic coupling reaction between the solution and SAM-phase reagents. Within this catalytic nanolithography a spatial resolution of ~10nm is possible, equating to zeptomole-scale reaction. The methodology was applied to reactions such as Sonogashira coupling and local oligo(phenylene vinylene) synthesis. By altering the experimental protocols, relating probe scan velocity to reaction yield and characterising the nanopattern, a PVP matrix model describing a proposed mechanism of catalytic nanolithography, was presented. Though ultimately limited by probe deactivation, calculations indicated that activity per immobilised nanoparticle is very high in this configuration.
For biopatterning, surface nanopatterns defined by carboxylic functionality were generated from methyl-terminated SAMs by local anodic oxidation (LAO) initiated by a conductive AFM probe. By employing suitable linker compounds, avidin and Stefin-A quadruple Mutant (SQM) receptive peptide aptamers were patterned at sub-100nm resolution. The multiplexed sensing capability of an SQM array was demonstrated by reacting generated patterns with single or a mixture of multiple antibodies.
The reversible redox conversion and switching of reactivity of hydroquinone-terminated SAMs was electrochemically demonstrated prior to an application in redox nanolithography. In this methodology, spatially controlled probe-induced in situ "writing" and "erasing" based on reversible redox conversion were conducted on hydroquinone terminated SAM. In combination with dip-pen nanolithography, a novel method of redox electro-pen nanolithography was designed and the method’s application for lithography was examined.

Keywords: self assembled monolayer
AFM
scanning probe lithography
biopatterning
nanofabrication
nanolithography
Advisor: Davis, J
Characterisation of 2-oxoglutarate- and fe(II)-dependent oxygenases targeting the protein synthesis apparatus

Members of the 2-oxoglutarate (2OG)- and Fe(II)-dependent oxygenase (2OG oxygenase) superfamily catalyse a wide range of oxidative reactions in biology. 2OG oxygenases require Fe(II) and atmospheric oxygen for their activity, and couple substrate oxidation with the decarboxylation of 2OG into succinate and carbon dioxide. There are more than sixty known 2OG oxygenases in the human genome; they modify small molecules, nucleic acids and proteins implicated in diverse biological processes.
Importantly, the seemingly disparate functions of 2OG oxygenases often converge to regulate gene expression. 2OG oxygenases have been shown to affect epigenetic reprogramming, chromatin remodelling, transcription factor activity and mRNA splicing. Emerging evidence indicates that 2OG oxygenases are also involved in the translational control of gene expression. Oxygenases TYW5, ALKBH8, ALKBH5 and FTO were found to catalyse modifications of tRNA and mRNA. The work in this thesis extends these observations by demonstrating that 2OG oxygenase-catalysed protein hydroxylations also play an important role in protein synthesis. The catalytic activities of two oxygenases belonging to the JmjC-only family, NO66 and JMJD4, are described. NO66 catalyses the histidinyl hydroxylation of 60S ribosomal subunit protein L8. NO66 is part of a conserved group of ribosomal protein hydroxylases that can be traced back to prokaryotes. JMJD4 is a lysyl hydroxylase of eRF1, the eukaryotic release factor responsible for translation termination. The hydroxylation of eRF1 takes place on a conserved NIKS motif important for release factor activity, and promotes effcient translational termination. JMJD4 is further implicated in cell growth and cancer, though the link between its activity and tumourigenesis remains to be determined. These results highlight the potential of 2OG oxygenases as regulators of protein synthesis, and further extend the scope of 2OG oxygenase function. The small molecule inhibition of 2OG oxygenases presents a novel therapeutic possibility targeting translational control in cancer and other diseases.

Keywords: ribosome
translational termination
post-translational modification
oxygen sensing
protein synthesis
Advisor: Ratcliffe, P
Coleman, M
A computational and experimental examination of turbine cooling flows

Film cooling by means of holes is an essential cooling technique in modern gas turbine engines. This cooling technique is employed over endwalls, as well as on the surface of blades. Thus, there is a need for film cooling predictions in a three-dimensional setting. Currently only boundary layer codes are available for design purposes and they are difficult to apply to the three-dimensional case with secondary flows. Present advanced computation prediction methods are capable of solving the complete flow field in three dimensions with coolant flow. However, the spatial resolution that these methods require eliminate them as suitable options for design tools
This study introduces a simpler description of the film cooling process which may be implemented in a code for design purposes. The parameters of turbulence enhancement, turbulence decay, and the coolant distribution at injection were optimized using existing experimental data. Finally, the code was employed in a three-dimensional setting with film cooling present.
An experimental study of the flow through cooling holes was also undertaken. Two unique geometries were later developed where a row of cooling holes exited into a vortex region where the flow was mixed before being injected from a slot. The cooling benefits of these geometries is apparent.
In vitro analysis of viral fusion and receptor binding with a focus on selected arthropod-borne viruses of the families Bunyaviridae and Togaviridae

Emerging arthropod-borne viruses, such as alphaviruses and bunyaviruses, represent a serious threat to human and animal health worldwide, and for most of them, vaccines and specific treatments are unavailable. Viral host cell entry can be divided into several entry checkpoints, and the most important checkpoints for low pH-dependent enveloped viruses, such as bunyaviruses and alphaviruses, include receptor binding at the cell surface and, followed by endocytosis, low pH dependent membrane fusion from within intracellular compartments. A more thorough understanding of the detailed mechanisms allowing the viruses to pass these checkpoints is a pre-requisite for the design of viral entry inhibitors.
This thesis reports the in vitro analysis of native alphavirus-receptor interactions, with the help of electron cryo-microscopy and icosahedral reconstruction of virus-recaptor complexes, using the prototypic alphavirus Semliki Forest virus (SFV) and the C-type lectin DC-SIGN. Together with results from collaborative work on SFV glycosylation, this study provides progress in defining the binding sites of DC-SIGN at the surface of SFV.
Second, an in vitro system for phlebovirus fusion was developed using standard fluorometry, and has been characterized with the help of electron cryo-microscopy. It was discovered that negatively charged phospholipids with a conical shape, including the late endosomal phospholipid BMP, allow efficient phlebovirus fusion in vitro, thereby providing a possible rationale for phlebovirus fusion in late endosomes. Furthermore, electron cryo-microscopy of phlebovirus-liposome complexes allowed the capture of early stage fusion intermediates and laid the basis for possible future higher resolution studies of these fusion intermediates.

Keywords: Electron cryotomography
Icosahedral reconstruction
Electron cryomicroscopy
DC-SIGN
Phlebovirus
Alphavirus
Virus entry
Semliki Forest virus
Membrane fusion
Uukuniemi virus
Bunyaviridae
Advisor: Huiskonen, JT
Gruenewald, K
A critical edition of Lope de Vega's 'San Nicolás de Tolentino' with an introductory study

This thesis presents a first critical edition of Lope de Vega’s saint’s play 'San Nicolás de Tolentino' (c. 1614) alongside an introductory study. The text is based on the sole seventeenth-century witness. The four modern re-prints/editions of the play have been consulted to help remedy defects in the 'princeps', which has been edited in accordance with the current practices of 'comedia' editors. Variants are collated in a list following the playtext. Footnotes to the text explain the important complexities and obscurities of 'San Nicolás' and some idiosyncrasies of Golden-Age literature generally.
The introductory study has six sections. The first pieces together a history of the veneration of St Nicholas in Spain, detailing the miracles and patronages that might have led Lope to compose this play of his own accord or that might have led to a commission. Internal evidence suggests strongly that any commission must have come specifically from the Discalced Augustinians. The second section examines Lope’s possible sources, concluding tentatively that Critana’s 'Vida' is the most likely source. Sections 3 and 4 present an interpretation of the protagonists – Nicolás and the 'gracioso' Ruperto. My comparison of Lope’s Nicolás with the saint depicted in the hagiographies casts into relief techniques Lope used to prevent this prodigious miracle-worker from alienating the audience. The 'gracioso' character, I argue, is intended to offer a model of Christian piety of a humbler kind: one significant factual departure from the hagiographic tradition places Ruperto at the forefront of the play’s religious purpose. However, a couple of comically lewd scenes in Act 2 (unmentioned by previous critics) make for a complex 'gracioso' struggling to resist temptation. I argue that Ruperto’s inner turmoil might reflect Lope’s own sense of unworthiness as he prepared for priestly ordination. Section 5 treats the supernatural in 'San Nicolás', demonstrating Lope’s familiarity with early modern theories of supernatural phenomenology and concluding that, despite the typically allegorical names of Ira, Carne, and Inobediencia, for example, these figures are intended, not as literary abstractions, but as real spirits, incorporeal demons. The final section presents an analysis of the play’s versification, which is largely in keeping with Lope’s usual habits.

Advisor: Thacker, J
Community, Self-Help and Mutual Aid: Friendly Societies and the Parish Welfare System in Rural Oxfordshire, 1834-1918

This thesis examines welfare provision in rural Oxfordshire after the 1834 Poor Law Amendment Act. The county had little industrial development, remained largely agricultural in nature, and the region had been perceived as a backwater of friendly society development.
This thesis rectifies that view and places Oxfordshire as an important component of the movement with its independent nature and early rejection of affiliated order branches that emanated from urbanized and industrialized areas. There is no evidence of impetus given to friendly society formation after the implementation of the new poor law with the general increase in societies continuing. However, the relationship with poor law administration changed. A case study of Stonesfield demonstrates how the friendly society became the heart of village life and was integral to self help and support for the poor.
A wider view is taken of welfare provision, with detailed assessment of a range of welfare instruments, such as coal and clothing clubs, soup kitchens, and medical clubs, together with an appraisal of their geographical spread. The range of welfare instruments available is compared to Maslow’s Hierarchy of Need, a model of human motivation. The case study of Whitchurch provides an in-depth assessment of one parish welfare system where after 1834 at least nine stands of welfare were available at all times to the poor who held a degree of selection in what was an increasingly a consumer market. The thesis is underpinned throughout by the use of extensive primary source material.

Keywords: Welfare
Oxfordshire
Clothing Club
Friendly Society
Stonesfield
Philanthropy
Welfare System
Clubs
Coal Club
Nursing Association
Social Welfare
Parish
Whitchurch
Soup Kitchen
Medical Aid Club
Friendly Societies
Advisor: Tiller, K
Plasma waveguides for high-intensity laser pulses

This thesis documents the development of plasma waveguides for high-intensity laser pulses. Initial work concentrated on the development of the discharge-ablated capillary waveguide, based on the work of A. Zigler (Zigler, A., Y. Ehrlich, C. Cohen, J. Krall and P. Sprangle, J. Opt. Soc. Am. B 13, 68). The waveguide was shown to be capable of guiding picosecond laser pulses with an intensity of 1016 W cm-2 over a length of 10 mm. The pulse energy transmission of the capillary was increased from 48% to 70% when the discharge was fired.
An interferometry-based measurement technique was developed, allowing measurement of the electron density profile formed in the capillary waveguide. These measurements were used as input to a numerical simulation that predicted the propagation of intense laser pulses through partially-ionised plasma waveguides. Numerical simulations accurately reproduced the picosecond pulse guiding results, and gave important insights into the properties and severe drawbacks of partially-ionised waveguides.
Previous work on partially-ionised plasma waveguides has not fully explored the implications of the propagation of intense pulses through the partially-ionised plasma. For polypropylene waveguides, it was shown that for pulses with an intensity of 1016 W cm-2, the waveguide is not capable of high-quality guiding. However, for pulses with an intensity of greater than 1017 W cm-2, high-quality guiding is predicted through the partially-ionised waveguide in a new regime called "quasi-matched guiding".
A novel gas-filled capillary discharge waveguide was designed and built. The device was shown to form a guiding channel inside a capillary pre-filled with gas. Interferometry measurements of the electron density profile formed in a hydrogen-filled capillary discharge waveguide showed that an approximately parabolic plasma waveguide could be formed in an essentially fully-ionised hydrogen plasma. The device was used to guide femtosecond laser pulses, with an intensity of 1017 W cm-2, over distances of 20 and 40 mm, with a pulse energy transmission of 92% and 82% respectively. For the 20 mm-long waveguide, the peak intensity in the output plane of the waveguide was 70% of that at the waveguide input. These results indicate the lowest coupling and insertion losses of any waveguide published to date.
The gas-filled capillary discharge waveguide is shown to be capable and versatile, and is suited for use as a tool in other applications. The use of the waveguide in the fields of XUV lasers and laser wakefield acceleration is discussed.
Innokenty Fedorovich Annensky and the classical ideal

Innokenty Annensky (1855-1909) was better known to his contemporaries as a classics teacher and translator than as a poet; but, with the exception of two or three obituary articles, nothing has been written on his work as a classicist. His work has often been misconstrued and he has been described as an outstanding scholar. It has not been generally appreciated that his interest in the scholarly world was not really academic; he saw classical texts as models for his own literary works, and as inspiration for the 'Slavonic renaissance' he looked forward to with F.F. Zelinsky.
This thesis covers Annensky's classical education, the essays he wrote on classical literature, and his translations of classical texts. Particular attention is given to the essays and translations which were intended to be published in Teatr Evripida, the first complete Russian version of Euripides. Annensky wrote no essay explicitly devoted to the subject of classicism. But from his essays on classical literature and the remarks on classical literature in his essays on modern literature it is possible to extrapolate his views on the nature of the classical tradition and on how he thought classical literature should be imitated. I show that Annensky's attitude to the classics was idiosyncratic and paradoxical. On the one hand, the classical world was viewed elegaically as an ideal of lost perfection; on the other, it was one of many cultural traditions on which he drew in his literary works and which was adapted in accordance with Modernist poetics.
The discussion of Annensky's views on classicism is accompanied by information about the system of classical education in Russia 1870-1910, and about the history of classical scholarship and of literary classicism in Russia. Annensky's essays are compared with those of a representative scholar, Zelinsky, and a representative Symbolist, Vyacheslav Ivanov.
Saturation methods for global model-checking pushdown systems

Pushdown systems equip a finite state system with an unbounded stack memory, and are thus infinite state. By recording the call history on the stack, these systems provide a natural model for recursive procedure calls. Model-checking for pushdown systems has been well-studied. Tools implementing pushdown model-checking (e.g. Moped) are an essential back-end component of high-profile software model checkers such as SLAM, Blast and Terminator.
Higher-order pushdown systems define a more complex memory structure: a higher-order stack is a stack of lower-order stacks. These systems form a robust hierarchy closely related to the Caucal hierarchy and higher-order recursion schemes. This latter connection demonstrates their importance as models for programs with higher-order functions.
We study the global model-checking problem for (higher-order) pushdown systems. In particular, we present a new algorithm for computing the winning regions of a parity game played over an order-1 pushdown system. We then show how to compute the winning regions of two-player reachability games over order-n pushdown systems. These algorithms extend the saturation methods of Bouajjani, Esparza and Maler for order-1 pushdown systems, and Bouajjani and Meyer for higher-order pushdown systems with a single control state. These techniques begin with an automaton recognising (higher-order) stacks, and iteratively add new transitions until the automaton becomes saturated.
The reachability result, presented at FoSSaCS 2007 and in the LMCS journal, is the main contribution of the thesis. We break the saturation paradigm by adding new states to the automaton during the iteration. We identify the fixed points required for termination by tracking the updates that are applied, rather than by observing the transition structure. We give a number of applications of this result to LTL model-checking, branching-time model-checking, non-emptiness of higher-order pushdown automata and Büchi games.
Our second major contribution is the first application of the saturation technique to parity games. We begin with a mu-calculus characterisation of the winning region. This formula alternates greatest and least fixed point operators over a kind of reachability formula. Hence, we can use a version of our reachability algorithm, and modifications of the Büchi techniques, to compute the required result. The main advantages of this approach compared to existing techniques due to Cachat, Serre and Vardi et al. are that it is direct and that it is not immediately exponential in the number of control states, although the worst-case complexity remains the same.

Keywords: temporal logic
verification
model-checking
higher-order pushdown automata
pushdown automata
Advisor: Ong, C
The city in motion

This dissertation examines the interaction between leisured movement and space in Rome from 100 BC – AD 150, primarily drawing upon archaeological evidence from Rome, central Italy and the Bay of Naples. This thesis argues that leisured movement was significant and that an examination of the relationship between leisured movement and space provides new insights into Roman architecture, gardens, attitudes to design and space. Chapter one reviews the theoretical models associated with the study of movement and space in various disciplines and utilitizes these approaches to formulate the theoretical basis for this thesis. Previous scholarship on movement and space in the Roman world is also reviewed to demonstrate the need for further study. Chapter two focuses on ancient literature and epigraphy to examine leisured movement in ancient Rome and the spaces identified as locations for leisured movement. In chapter three the Severan marble plan and the archaeological evidence for the monumental porticos and temple-porticos in Rome, the public and urban context for leisured walking, are analyzed. An examination of the relationship between leisured movement and space in high-status Roman villas and residences is undertaken in chapter four. Walking, driving, riding and boating and their spatial context played an important role in these high-status residences. Finally, chapter five examines the relationship between leisured movement and space in Pompeian houses, in order to understand how leisured movement functioned in such houses and to demonstrate that leisured movement also had a role in the lives of those below the top of Roman society. This thesis demonstrates that movement was a prominent leisure activity and that it was a complex way through which the Romans negotiated Greek culture. It also establishes that Rome’s public porticos and portico-temples, which housed leisured movement, were original contributions to the architectural canon. Movement and space were interconnected phenomena that interacted upon each other; the design of private and public gardens and porticos often created an ordered approach to movement and space. In sum, leisured movement is a productive lens through which we can study Rome, her cultural and leisure activities, approach to design and conception of space.

Keywords: gardens
archaeology
landscape architecture
architecture
Rome
Advisor: Janet, D
Nicholas, P