VictorJuiz/thesis huggingface dataset:
Time-resolved studies of photoinduced dynamics using fast imaging sensors

In this thesis, the three-dimensional, multi-mass, and covariance imaging capabilities of the Pixel Imaging Mass Spectrometry (PImMS) camera has been demonstrated in a range of velocity-map imaging (VMI) experiments.
The development of an experimental configuration for VMI experiments allows for three-dimensional imaging with high velocity resolution along the time-of-flight axis. This was demonstrated by recording the full three-dimensional velocity distributions of CO and S photofragments, following the photodissociation of OCS, with the PImMS camera. The resultant velocity distributions are sufficiently well resolved to express as an expansion of spherical harmonics. This was further emphasised through the investigation of a system with no axis of cylindrical symmetry and therefore unsuitable for simple conventional VMI experiments.
The ultraviolet (UV) photoexcitation dynamics (λ = 267 nm) of 2(5H)-thiophenone were studied by ultrafast time-resolved Coulomb explosion imaging. The Coulomb explosion of the system was probed separately via strong-field and inner-shell ionisation. The velocity-dependent ion channels arising from an intense non-resonant infrared (IR) (λ = 801 nm) probe provide information on the photoexcitation dynamics of thiophenone. The channels derived from Coulomb explosions are supported through covariance analysis. The photoexcitation scheme and delaydependent covariance analysis are tentatively attributed to a prompt ring-opening of thiophenone, within 300 fs. The UV photoexcitation of thiophenone probed via XUV ionisation revealed many ion correlations were revealed through time-of-flight covariance analysis, supported by angular covariance. The velocity-dependent ion yields are notably different to the UV-IR which is unsurprising given the nature of ionisation.
Coulomb explosion imaging experiments of OCS were performed induced by an intense IR pulse at varying laser intensities. The rich and complicated Coulomb explosion dynamics were determined through various covariance analyses. Through these analyses, minor channels and branching ratios were identified.

Keywords: velocity map imaging
chemical dynamics
multi mass imaging
covariance analysis
Advisor: Brouard, M
The many faces of autonomy: The normalised dynamics of claiming 'autonomy' through a creative policy game

Hungarian ethnic minority elites in Romania and Slovakia have vouched for autonomy arrangements as possible institutional solutions to deal with ethnic diversity. Yet, in the post-EU accession period, explicit claims to autonomy in Slovakia have essentially dropped off the radar of Hungarian minority elites since 2008. By contrast, most Hungarian political actors in Romania have had their own territorial autonomy plan since 2014. What accounts for these different trajectories of “autonomy” claims in Romania and Slovakia? The project uses elite interviews, party documents and newspaper archives in the original Hungarian language. It draws on qualitative text analysis to unpack how claims to autonomy unfold.
Autonomy claim-making occurs through a “creative policy game” composed of two elements. First, elites frequently engage in a “word-play” which changes the discourse on autonomy to also include “self-governance”, “regionalisation” and “decentralisation”. In contrast to differentiations in the scholarly literature, these terms are interchangeable to elites. Second, elites claim autonomy through reforms across a range of policy areas such as education, administration and regional development which provide de facto autonomy for the ethnic minority.
The thesis identifies how particular starting parameters – demographic concentrations, historical legacies and policy frameworks – are more constraining in the case of Slovakia and more enabling in Romania. Moreover, the thesis shines light on the varying nature of intra-group competition and of different claiming strategies which use either a “small steps” or “big claims” logic. The kin-state and European institutions act as financial enablers for autonomy claims, particularly at the local level when the national level is static or blocked. These research findings enrich the comparative politics and conflict studies literature by providing a detailed empirical analysis of how autonomy claiming is part and parcel of “normalised” domestic politics and is not linked to ethnic conflict and secession.

Keywords: Hungarians
ethnic conflict
autonomy
institutions
ethnic minorities
Central Europe
Advisor: Sasse, G
Development of late-stage difluoromethylation strategies

In the last decades, the introduction of the difluoromethyl group has attracted many interests in drug discovery. This thesis discusses the development of novel strategies for the late-stage introduction of the difluoromethyl group in the context of photochemistry and F-18 radiochemistry. The relevance of the difluoromethyl group and an introduction to the field of late-stage difluoromethylation is described in Chapter 1. In Chapter 2, a novel methodology for the photochemical late-stage hydrodifluoromethylation of alkenes with difluoroacetic acid is discussed. Chapter 3 describes the expansion of this methodology to the hydrochlorofluoromethylation and hydrobromofluoromethylation of alkenes. Radiochemistry and its applications to positron emission tomography are introduced in Chapter 4. Chapter 5 describes our recent efforts for the synthesis of an [18F]difluorocarbene reagent for the 18F-difluoromethylation of phenols, thiophenols and N-heterocycles. Experimental data for the work described in this thesis is given in Chapter 6.

Keywords: Difluoromethylation
Radical
Radiochemistry
Carbene
Advisor: Gouverneur, V
Davis, B
Silyl radical-mediated late-stage hydrofunctionalisation of alkenes

In the last decades, photochemistry has been at the forefront of organic chemistry as a modern tool for the synthesis of organic compounds in early- and late-stage functionalisation. This thesis consists of the development of novel methodologies for the late-stage hydrofunctionalisation of alkenes under visible light activation. Specifically, the reactivity of the tris(trimethylsilyl)silyl radical is harnessed for the activation of different organohalides. A general introduction to photochemistry, silyl radicals and hydrofunctionalisation of alkenes is described in Chapter 1. In Chapter 2, the development of an operationally simple and cost-effective protocol for the late-stage hydrosulfamoylation of electron-deficient alkenes using sulfamoyl chlorides as radical precursors is described. The success of this transformation relies on the generation of a sulfamoyl radical by direct chlorine atom abstraction from a silyl radical. In Chapter 3, a facile and robust protocol for the hydrosulfonylation of alkenes is presented. The reaction is amenable to scale-up and allows for the preparation of relevant building blocks for drug discovery in batch and in continuous flow. Chapter 4 discusses the generation of the fluoromethyl radical from fluoroiodomethane under visible light activation. The application of this protocol has been validated on the 18F-hydrofluoromethylation of alkene-containing biologically active molecules. Chapter 5 provides experimental data and analysis for the work described in this thesis.

Keywords: photochemistry
radical
sulfone
sulfonamide
alkene
fluorine
Advisor: Gouverneur, V
Circadian regulation of Hepatitis B virus.

Whilst the role that circadian rhythm plays in human disease is emerging rapidly, its role in infection is only beginning to dawn. HBV affects over 350 million people globally with no cure and limited treatment options. Currently available interventions will not curb this epidemic. Every living organism on earth has evolved a circadian rhythm, whereby key systemic processes including metabolism, growth and immunity undergo seismic changes on a daily basis to maximise energy conservation. In order to achieve organism wide control, there are a myriad of individual cellular functions like autophagy that receive cues from a central pacemaker to optimise their functioning. The HBV replication cycle is known to be dependent on a competent autophagic pathway. It is unknown if HBV is being modulated by circadian rhythm and whether such overarching regulation would include autophagy as an intermediate process. The work presented here shows that the HepaRG cell line is permissive to HBV infection and is capable of sustaining an endogenous circadian rhythm. The NTCP receptor -key for HBV entry- is shown to be regulated by REV-ERBα. Separately, autophagosome maturation is shown to be delayed by HBV replication through the use of a dual fluorophore LC3 reporter. Both autophagy and HBV are shown for the first time to be pharmacologically modulated by an agonist of REV-ERB called SR9009, in addition to known autophagy regulators, thereby suggesting an intersecting point of governing pathways. I present evidence that HBV transcription, translation of HBsAg and HBeAg as well as mature virion release are susceptible to modulation by SR9009. Finally, I describe how an in vivo murine HBV model shows decreased HBV pgRNA and HBeAg following treatment with SR9009.
Whilst the broader potential role of chrono-medicine in human pathogenesis is emerging rapidly, its place in infection is in its infancy. It is anticipated that these results could be a starting point for understanding and utilising the role of circadian rhythm in HBV replication for treatment development.

Advisor: McKeating, J
Zhuang, A
Matthews, P
Two studies on branching processes

We consider two branching processes: a Galton-Watson process and a branching Brownian motion.
In Chapter 2 we study behaviour of a minimax recursion defined on Galton-Watson trees. This recursion corresponds to a two-player combinatorial game. The value associated to the root of a tree truncated at some level 2n
corresponds to the probability that the first player wins a game played on such a truncated tree. We study convergence of the value at the root as n→∞
, in particular we give distributional limits under suitable rescaling in various cases. We address also a question of endogeny, which can be seen as a property that holds if the game can be played close to optimally for large n
by inspecting only the initial section of the tree.
In Chapter 3 we consider a branching Brownian motion in 𝓡d. We prove that there exists a random subset Θ of 𝕊d-1 of full measure such that the limit of the derivative martingale exists simultaneously for all directions in Θ almost surely. This allows us to define a random measure on 𝕊d-1 whose density is given by the derivative martingale. We argue that this measure should correspond to the distribution of the direction of the furthest particle and we prove this claim in dimension one.
In Chapter 4 we present conclusions and further research directions, in particular we discuss a conjecture on the form of the extremal point process of the multidimensional BBM.

Keywords: branching processes
branching Brownian motion
derivative martingale
Galton-Watson trees
Advisor: Martin, J
Berestycki, J
Structural analogues of complex magnetic phases

This thesis studies the phase behaviour of a variety of complex solid structures. The principal approach taken is to develop a suitable coarse graining of the degrees of freedom in order to allow a representation in terms of interaction models.
Chapter 3 concerns the polytypism of layered AB2 compounds. We develop a simple interaction model that has at its ground states many of the key experimentally determined structural phases. At phase boundaries we identify complex disordered states that we show sometimes provide a more convincing descriptor of the polytypism than established models. These results allow us to question the existence of previously characterised phases and new undocumented phases are put forward as perhaps more chemically sensible alternatives.
Continuing on the theme of layered materials, Chapter 4 maps the stacking disorder present in the layered inorganic material Ni(CN)2 onto a model containing continuous degrees of freedom. Moreover, the model can also take the form of the Heisenberg XXZ model used to describe interacting chains of quantum spins, and as such, we have identified a system realising the classical analogue of a 1D quantum chain.
Chapter 5 maps complex magnetic phases onto structural degrees of freedom by focusing on topological defects within chiral magnets. Here we show that these degrees of freedom can be related to quadrupolar orientations of molecules within a chiral framework, and can create analogous topological defects in chiral MOFs. This result expands the field of data storage by highlighting potential materials not normally associated with emergent phenomena.
This thesis ends with two appendices containing experimental work carried out during the DPhil, which had to be put on hold due to constraints set up by the ongoing COVID-19 pandemic. Both these studies tie into the theme of statistical mechanical models and structural disorder, with the first centring on the extent to which ice like disorder manifests in the compositionally disordered cyanospinel KRb[Zn(CN)4]. The second study focuses on the stacking disorder present in the solid solution K[AgxAu1-x(CN)2] which varies as a function of composition and temperature. The larger aim of both these studies is to see how correlated disorder may selectively effect the phononic properties of materials.

Keywords: Modelling
1D materials
Disorder
Statistical mechanical models
Crystallography
Advisor: Goodwin, A
National Trails in chalk landscapes – an under-utilised tool for conservation?

Lowland calcareous grassland (chalk grassland) has suffered extensive habitat loss and fragmentation in the UK over the past century. Outside of Salisbury Plain – the largest remnant area of chalk grassland in Europe – most patches of chalk grassland are now small and spatially isolated, with the median patch size currently less than two hectares. Extensive habitat restoration is needed if we are to conserve species-rich chalk grassland communities. However, this will be difficult to achieve in the densely-populated and intensively-farmed chalk landscapes of Southern England. Therefore, innovative solutions for restoring chalk grassland need to be identified and implemented. In this thesis, I suggest focusing restoration efforts within and along National Trails could be one such approach. In Chapter 2, I identify a number of characteristics of National Trails that make them suitable as a target for conservation resources. I concentrate on three National Trails (The Ridgeway, North Downs Way and South Downs Way) that extend through the chalk landscapes of Southern England – finding that these trails are important for reducing the isolation of remnant fragments of chalk grassland and that increasing the width of well-managed verge habitat along these trails could increase habitat connectivity. In Chapter 3, I drone-map and survey the verges of The Ridgeway. Using this data, I find that the trail currently has an important role in maintaining chalk grassland connectivity and that small areas of targeted habitat restoration along the trail could drive large increases in connectivity. In Chapter 4, I examine a range of management interventions that could be used to restore grassland verges along National Trails. I find that a mixture of simple management approaches can restore species-rich chalk grassland verges within a short timeframe. Overall, these results suggest that focusing conservation efforts along National Trails could improve the connectivity of chalk landscapes while simultaneously delivering a range of public benefits.

Keywords: Habitat Restoration
National Trails
Linear Landscape Features
Habitat Connectivity
Conservation Ecology
Lowland Calcareous Grassland
Chalk Grassland
Ecology
Dispersal Ecology
Advisor: Turnbull, L
Kirby, K
Mapping the glycan shields of enveloped viruses

Glycosylation is a ubiquitous post-translational modification responsible for a multitude of crucial biological roles. As obligate parasites, viruses exploit host-cell machinery to glycosylate their own proteins during replication. Viral envelope proteins form a myriad of human pathogens including HIV-1, influenza virus, Lassa virus, coronaviruses, Zika virus, dengue virus, and Ebola virus have evolved to be glycosylated to varying degrees. These host cell derived glycans facilitate diverse structural and functional roles during the viral life-cycle ranging from aiding glycoprotein folding to enhancement of immune cell infection. As the primary focus of the humoral immune response, vaccine development efforts often concentrate on the viral glycoproteins that protrude from the virion envelope.
This thesis primarily focuses on immune evasion of viruses by molecular mimicry and glycan shielding. The work presented here reveals how viral glycan shields from evolutionarily distinct pathogens share conserved features, namely clusters of underprocessed oligomannose-type glycans. Furthermore, this thesis explores how an anti-HIV-1 antibody, 2G12, that targets oligomannose-type glycans cross-reacts and neutralises more recent influenza strains, as they have evolved to accrete N-linked glycosylation sites on their respective hemagglutinins, which result in the formation of oligomannose clusters. These findings provide a potential avenue for the development of a broad class of antivirals, that can target conserved features of viral glycosylation.
Comparisons of several viral glycan shields are also carried out which probes the rules governing glycan processing and the disparate efficacies of them. Given the prominence of N-linked glycosylation on viral glycoprotein surfaces, it is suggested that the compositional and structural data presented here can aid vaccine development and therapeutic efforts to combat these diseases.

Keywords: Glycosylation
Viruses
Coronavirus
Influenza
Glycans
Lassa
Advisor: Crispin, M
Bowden, T
Wormald, M
The political, cultural, and dynastic history of the Farnese family: between the end of the Western Schism and the outbreak of the Italian wars, 1417-1494

This thesis investigates the strategies for the extension and perpetuation of power employed by the Farnese in Quattrocento Italy. It argues the preconditions of their success lay in their internal organisation, active government of their patrimony, and in the adoption of solutions to overcome the perils of partible inheritance. It addresses the decisions that governed the creation of dynastic and pseudo-dynastic ties and, above all, how the Farnese strengthened and maintained their kinship network. This network provided the basis for interactions in the political sphere on a peninsular level and within the Papal States. The argument is forwarded that the Farnese were at the heart of developments which saw an increase in political connections established across state boundaries, forcing historians to rethink the current consensus on state formation in Italy. Of particular relevance were the Farnese’s ties to the Medici in Florence, ties that grew in importance as the century progressed. Within the Papal States, the Farnese followed a policy of support for pontifical power, a policy as much perceived as a political tradition inherited from their ancestors as a practical approach to finding a working relation with the newly-established papacy in Rome after the end of the Western Schism, suggesting that traditional notions of papal-noble antagonism need to be replaced by a model that stresses collaboration. Moreover, the Farnese were among the first to profit from the growth in number of curial offices as they increasingly focused their ambitions on placing sons in the Church, ultimately leading to Alessandro Farnese’s nomination as cardinal. Finally, the Farnese’s patronage on Isola Bisentina and the creation of a family mausoleum, Franciscan friary, and sacred landscape are revealing of mid-century developments in devotional practices and illuminate the Farnese’s self-perception as a dynasty rooted in space and time, and their fabrication of dynastic memory.

Advisor: Parrott, D
Pattenden, M
A critical analysis of current debates in natural law: a theo-cultural engagement with John Finnis, Jean Porter, & John Milbank 

This thesis argues that natural law – when construed as an epistemological and trans-cultural lingua franca, adjudged capable of legitimating the rational intelligibility and universal applicability of specific Christian moral principles within contemporary “secular” discourse – has failed. Through a detailed analysis of the contributions of three prominent natural law theorists who are located within a shared philosophical-theological tradition, namely, John Finnis, Jean Porter, and John Milbank, the thesis illuminates the extent to which this failure is as much intramural as it is extramural. The contribution of this thesis is borne out of a two-fold realisation: (1) that despite renewed levels of inter-disciplinary interest within the academy, the discourse has become increasingly fragmented and will continue to fragment in the absence of a critical analysis of the deeper theo-cultural assumptions and aporias that animate current debates in natural law; (2) that by illuminating and attending to the theological and methodological “unsaid(s)” that have, heretofore, been seldom acknowledged, one can begin to appreciate how the fragmentation of the discourse is inexorably linked to the fragmentation of the secular mythos. Once this two-fold realisation has been critically substantiated, the thesis develops its contribution to knowledge by exploring how new horizons open up for natural law if the theological “unsaid(s)” are allowed to surface and the disremembering power of the secular mythos is overcome. The thesis addresses one such horizon as a gateway to further research — that the theoretical fulcrum of the natural law lies not in its perceptual self-evidence or in its immanent secularity; but rather in its subtle provision of an immanent eschatology. This insight not only provides an immanent critique of current debates in natural law but is also theologically generative and subversive. More specifically, I argue that natural law is a theory of dialogical anamnesis — a “work of memory”.

Keywords: Jacques Derrida
John Milbank
Plato
John Finnis
Natural Law
Post-Modern
Deconstruction
Jurisprudence
Anamnesis &amp; Eschatoloy
Jean Porter
Advisor: Hanvey, J
Riordan, P