VictorJuiz/thesis huggingface dataset:
Electron paramagnetic resonance studies of artificial supramolecular structures and biological systems
Keywords: hyperfine interaction
ENDOR
triplet state
EPR
protein structure
radical cation
DEER
porphyrins
HYSCORE

The research described in this thesis employs a variety of Electron Paramagnetic Resonance (EPR) techniques for the study of the electronic and structural properties of artificial supramolecular porphyrin systems and of protein complexes of biological relevance.
The electron delocalisation in the cationic radical and photoexcited triplet states of linear and cyclic Π-conjugated multiporphyrin arrays was investigated. In the radical cations, information on the extent of delocalisation can be inferred from the measurement of hyperfine couplings, either indirectly from the continuous wave EPR spectrum or directly using pulsed hyperfine EPR techniques. The results of room temperature EPR experiments showed complete delocalisation of the electron on the timescale of the EPR experiments, but frozen solution EPR measurements revealed localisation onto mainly two to three porphyrin units in the larger porphyrin systems.
Information on the delocalisation of the triplet state in the same porphyrin systems is contained both in the hyperfine couplings and in the zero-field splitting (ZFS) interaction. The results outlined in this thesis show that the hyperfine couplings provide a much more accurate estimate of the extent of delocalisation. The trends in proton and nitrogen hyperfine couplings with the size of the porphyrin systems indicate uneven spin density distributions over the linear arrays, but complete delocalisation in the cyclic systems. Time-resolved EPR and magnetophotoselection experiments have shown a reorientation of the zero-field splitting tensor between a single porphyrin unit and longer linear arrays, resulting in alignment of the main optical transition moment and the Z axis of the ZFS tensor.
Continuous wave and pulsed dipolar EPR techniques were employed for the determination of the structure of two different protein complexes, the homomultimeric twin-arginine translocase A (TatA) protein channel and the ferredoxin-P450 complex of the electron transport chain in Novosphingobium aromaticivorans. The interaction between nitroxide spin labels introduced at different positions of the TatA monomer was investigated in the complex reconstituted in detergent micelles by analysing the dipolar broadening of the EPR spectra and the results of three- and four-pulse Double Electron-Electron Resonance (DEER) measurements. In combination with results from NMR and molecular dynamics calculations, a structure for the channel complex was proposed.
The structure of the ferredoxin-cytochrome P450 complex was investigated by orientation-selective DEER between nitroxide labels introduced on the cytochrome P450 protein and the iron-sulfur cluster of the ferredoxin. The distance and orientation information contained in the experimental DEER data was interpreted in terms of a structural model of the protein complex by orientation-selective DEER simulations combined with a modelling approach based on protein-protein docking.
Single photon generation and quantum computing with integrated photonics
Keywords: integrated optics
boson sampling
quantum computing
quantum optics
heralded single photon source

Photonics has consistently played an important role in the investigation of quantum-enhanced technologies and the corresponding study of fundamental quantum phenomena. The majority of these experiments have relied on the free space propagation of light between bulk optical components. This relatively simple and flexible approach often provides the fastest route to small proof-of-principle demonstrations. Unfortunately, such experiments occupy significant space, are not inherently phase stable, and can exhibit significant scattering loss which severely limits their use. Integrated photonics offers a scalable route to building larger quantum states of light by surmounting these barriers.
In the first half of this thesis, we describe the operation of on-chip heralded sources of single photons. Loss plays a critical role in determining whether many quantum technologies have any hope of outperforming their classical analogues. Minimizing loss leads us to choose Spontaneous Four-Wave Mixing (SFWM) in a silica waveguide for our source design; silica exhibits extremely low scattering loss and emission can be efficiently coupled to the silica chips and fibers that are widely used in quantum optics experiments. We show there is a straightforward route to maximizing heralded photon purity by minimizing the spectral correlations between emitted photon pairs. Fabrication of identical sources on a large scale is demonstrated by a series of high-visibility interference experiments. This architecture offers a promising route to the construction of nonclassical states of higher photon number by operating many on-chip SFWM sources in parallel.
In the second half, we detail one of the first proof-of-principle demonstrations of a new intermediate model of quantum computation called boson sampling. While likely less powerful than a universal quantum computer, boson sampling machines appear significantly easier to build and may allow the first convincing demonstration of a quantum-enhanced computation in the not-distant future. Boson sampling requires a large interferometric network which are challenging to build with bulk optics, we therefore perform our experiment on-chip. We model the effect of loss on our postselected experiment and implement a circuit characterization technique that accounts for this loss. Experimental imperfections, including higher-order emission from our photon pair sources and photon distinguishability, are modeled and found to explain the sampling error observed in our experiment.
Town and Gown: Amateurs and Academics.
Keywords: intellectual history
local societies Underhill
Oxford
social
British prehistory
lanternslides
amateur archaeology

This investigation into the origin of a collection of nineteenth century lanternslides revealed evidence of the social, intellectual and cultural importance of various scientific societies in Oxford, and the contributions made by those involved, particularly the creator of the lanternslides, H. M. J. Underhill, (1855–1920). Evidence gathered from primary sources showed a fluidity of relationships between the supposed ‘town and gown’ in late nineteenth century Oxford which consisted of a community of citizens, amateurs and academics, all of whom were linked by a growing interest in the real and mythological British past. Following a discussion of the key intellectual and social influences in Britain during the latter half of the nineteenth century, including the implications of the emerging evidence of an ancient human past, the thesis focuses on individual case studies. They illustrate the roles of overlooked or neglected individuals whose work contributed to the growth of today’s discipline of British prehistory. Several people, now forgotten, including Underhill were contemporaries of Arthur Evans and Edward Tylor whose social circumstances made it easier for them to become prominent academics. The results of this research indicate that a new approach is required in the history of archaeology; one that would draw attention to the vital contributions made by forgotten or overlooked individuals, societies and popular publications. Further attention to these issues will shed new light on the way that prehistoric archaeology moved from an antiquarian pastime to an academic discipline between 1850 and 1900.
Boundary properties and construction techniques in general topology
Keywords: cohesion
analytic topology
elementary submodels
general topology
boundary properties

The aim of this thesis is twofold. First, we investigate spaces defined by asserting that their nowhere dense subsets have certain properties. Secondly, we develop some techniques for the construction of topological spaces.
We consider spaces where the nowhere dense sets are asserted to have some property P, calling such spaces boundary-P. We show that if there are no Lusin spaces then every compact boundary-metrizable space is metrizable. Boundary-separability is also studied and we show that if there are no L-spaces then every boundary-separable space is separable.
By adapting the absolute dimension function of Arhangel'skii, we define the new concept of cohesion. We show that every compact cohesive and every Hausdorff, sequential cohesive space is scattered. However, we construct regular, crowded spaces of all finite cohesions though there are no regular spaces of transfinite cohesion. We consider too the preservation of cohesion under various mappings and under the formation of products.
Turning to construction, we consider the class of compact monotonically normal spaces. It is well-known that it contains the class of spaces which are the continuous images of compact ordered spaces but it is still open as to whether they are actually distinct classes. Using Watson's resolutions, we give a method for constructing monotonically normal spaces. Though this also preserves continuous images of arcs, we show that it is because of a powerful result of Cornette rather than any trivial observation.
We also examine more closely monotone normality in images of compact ordered spaces using the Collins-Roscoe structuring mechanism. From this, we extract a strong instance of the mechanism, linear chain (F), which is held by all images of ordered compacta and all proto-metrizable spaces and implies Junnila's concept of utter normality.
Elementary submodels are an important tool in the construction of topological spaces. We develop a general method for applying them in varying circumstances and illustrate it by constructing three examples: Balogh's Q-set space, Rudin's normal but not collectionwise Hausdorff space and Balogh's small Dowker space.
Universal moduli of parabolic sheaves on stable marked curves
Keywords: moduli spaces
parabolic bundles
algebraic geometry
geometric invariant theory
parabolic sheaves
marked curves

The topic of this thesis is the moduli theory of (parabolic) sheaves on stable curves. Using geometric invariant theory (GIT), universal moduli spaces of semistable parabolic sheaves on stable marked curves are constructed: `universal' indicates that these are moduli spaces of pairs where the underlying marked curve may vary as well as the parabolic sheaf (as in the Pandharipande moduli space for pairs of stable curves and torsion-free sheaves without augmentations).
As an intermediate step in this construction, we construct moduli spaces of semistable parabolic sheaves on flat families of arbitrary projective schemes (of any dimension or singularity type): this is the technical core of this thesis. These moduli spaces are projective, since they are constructed as GIT quotients of projective parameter spaces. The stability condition for parabolic sheaves depends on a choice of polarisation and is derived from the Hilbert-Mumford criterion. It is not quite the same as traditional stability with respect to parabolic Hilbert polynomials, but it is closely related to it, and the resulting moduli spaces are always compactifications of moduli of slope-stable parabolic sheaves. The construction works over algebraically closed fields of arbitrary characteristic.
Neoliberalism and education in Russia: global and local dynamics in Post-Soviet education reform
Keywords: Russian education
neoliberalism
education reform
neoliberal globalisation

This dissertation examines the socio-cultural underpinnings of neoliberal educational reforms vis-à-vis the national educational settings in Russia.
By drawing upon NVivo-aided Discourse and Frame analysis as a methodological path, this study critically examines a corpus of state laws on education and official government statements from 1991 to 2012 in contrast to contemporary societal discourse on education, where novel and indigenous educational meanings have been contested and re-negotiated. This thesis shows how the conceptual mélange of global neoliberal ideas has been interpreted, institutionalised and resisted in Russia by exploring the semantics of key neoliberal reform ideas - ‘quality assurance,’ ‘educational standards,’ and ‘commercial educational service’ - at the micro-level of policy texts, political debates and public discussions.
This thesis shows that having heralded an educational revolution, the official reform narrative rhetorically endorsed neoliberal orthodoxy, while continuing in practice to discursively draw on pedagogical and administrative frameworks which it previously renounced as outdated. In communicating the spirit of radical neoliberal modernisation, the Russian government rhetoric has collectively embraced a number of contradictory concepts, slogans and directives that have never been harmonised in a unified reformatory framework.
The study also argues that the public interpretation of neoliberal concepts has been radically different from the intended conceptualisations offered by the global international stakeholders and conveyed by the Russian educational elite. It shows how, when interpreted through the lens of local pedagogical values, the semantics of global modernisation templates, such as ‘educational quality’ and ‘educational standardisation,’ took on unexpected, culturally-specific, meanings. It also finds that the newly introduced principles of entrepreneurship, self-interest, consumer choice, self-responsibility and competition, which underlie the neoliberal economic reform, remained in opposition to fundamental principles of Russian culture, such as communalism, egalitarianism, state paternalism and anti-monetarism. By unpacking opposing ideological and pedagogical frames, this thesis explains the cultural aspects of the widespread public resistance to post-1991 education reform in Russia.
This dissertation seeks to enhance the understanding of the policy formulation process and interpretation of global neoliberal ideas from both top-down and bottom-up perspectives. By advancing a culturalist approach to policy analysis, the present study addresses an overlooked piece of the long-standing puzzle of perceived post-Soviet educational crisis, supplementing the broader scholarly discussion on the successes and failures of neoliberal reforms in the post-Soviet space.
A functional approach to backward stochastic dynamics
Keywords: semimartingales
functional differential equations
backward stochastic dynamics

In this thesis, we consider a class of stochastic dynamics running backwards, so called backward stochastic differential equations (BSDEs) in the literature. We demonstrate BSDEs can be reformulated as functional differential equations defined on path spaces, and therefore solving BSDEs is equivalent to solving the associated functional differential equations. With such observation we can solve BSDEs on general filtered probability space satisfying the usual conditions, and in particular without the requirement of the martingale representation. We further solve the above functional differential equations numerically, and propose a numerical scheme based on the time discretization and the Picard iteration. This in turn also helps us solve the associated BSDEs numerically.
In the second part of the thesis, we consider a class of BSDEs with quadratic growth (QBSDEs). By using the functional differential equation approach introduced in this thesis and the idea of the Cole-Hopf transformation, we first solve the scalar case of such QBSDEs on general filtered probability space satisfying the usual conditions. For a special class of QBSDE systems (not necessarily scalar) in Brownian setting, we do not use such Cole-Hopf transformation at all, and instead introduce the weak solution method, which is to use the strong solutions of forward backward stochastic differential equations (FBSDEs) to construct the weak solutions of such QBSDE systems. Finally we apply the weak solution method to a specific financial problem in the credit risk setting, where we modify the Merton's structural model for credit risk by using the idea of indifference pricing. The valuation and the hedging strategy are characterized by a class of QBSDEs, which we solve by the weak solution method.
Burning water - the state, irrigation technology and the production of scarcity in Spain
Keywords: La Mancha
environmental degradation
Spain
irrigation politics
colonisation
technology
groundwater

Through studying the adoption of groundwater abstraction technology in the twentieth century in La Mancha, this research investigates the historical role of the state in the development of modern groundwater-fed irrigation in Spain between the 1940s and 1985. By focusing on the Mancha Occidental aquifer and the Las Tablas de Daimiel wetland, this study also scrutinizes how the adoption of groundwater abstraction technology led by the state fed back into the environment through ecosystem degradation and groundwater scarcity at the local and regional level.
By examining the historical links between technology adoption, statecraft and ecological change, this study explores the different ways through which the state has taken a prominent role in producing groundwater-fed irrigation socio-ecologies. Additionally, it traces the socio-political mechanisms involved in the progressive desiccation of the Las Tablas de Daimiel wetland and its transformation into a burning dryland.
Synthesis and reactivity of titanium hydrazido(2-) complexes
Keywords: hydrazide
hydrazido(2-)
hydrazido
titanium

This Thesis describes the synthesis and characterisation of titanium hydrazido(2-) complexes and their reactivity towards unsaturated molecules. Exploration of the bonding in titanium hydrazido(2-) complexes is performed through structural and computational studies.
Chapter 1 introduces current Group 4 hydrazido chemistry and describes its relevance with comparison to Group 4 imido and mid/late metal hydrazido examples.
Chapter 2 describes the synthesis and characterisation of new titanium hydrazido(2-) half-sandwich complexes. A general route to new titanium hydrazido(2-) chemistry is described and suppression of dimerisation pathways common to Group 4 alkyl hydrazido(2-) chemistry is investigated.
Chapter 3 describes the synthesis, bonding and preliminary reaction chemistry of a new titanium hydrazido(2-) sandwich complex. Through structural and computational techniques, the bonding in the sandwich complex Cp2Ti(NNPh2)(py) (14) is explored and the implications to the reactivity of this complex considered.
Chapter 4 describes the synthesis of new titanium hydrazido(2-) synthons which is extended to the synthesis of new titanium hydrazido(2-) complexes with diamide-amine type ligands. The bonding of the hydrazido(2-) ligand is explored through structural and computational study of these complexes.
Chapter 5 describes the novel reaction chemistry of a diamide-pyridyl titanium hydrazido(2-) complex Ti(N2Npy)(NNPh2)(py) (23). Novel reactivity of both the Ti=Nα and Nα-Nβ bonds is presented with the mechanisms of some of these transformations probed by density functional theory (DFT) calculations.
Chapter 6 presents full experimental procedures and characterising data for the new complexes reported.
CD Appendix contains .cif files for all new crystallographically characterised complexes described.
Evolution and taxonomy of myrmecophytes with particular reference to Myrmecodia and Hydnophytum
Keywords: epiphytes
taxonomy

Those epiphytes which are inhabited by ants are reviewed; they comprise nine genera in four families. All are tropical and most are from the Far East. They probably all gain mineral nutrients from material brought by the ants. This contrasts with myrmecophytic trees and shrubs which are defended against insect herbivores by ants collecting food produced by the plant.
five of the nine genera of ant-epiphytes belong to the Rubiaceae; two of these, Hydnophytum and Myrmecodia are highly diversified and specialized. They are found throughout the tropical Far East in a range of habitats, but are most abundant in open canopies. Ants (Iridomymex cordatus and I. cf. scrutator) occupy cavities in the enlarged hypocotyl.
The 'tuber' cavities and other unusual morphological features are elaborated in Myrmecodia. For instance, spines of different types are derived from adventitious roots; internodes are condensed and covered by outgrowths at each leaf-base; stipules are enlarged and differ in their splitting. The inflorescence rachis is progressively reduced in Hydnophytum, and the flowers sunk in the stem in Myrmecodia. These structural changes possibly benefit the ants, but may have reduced the frequency of crosspollination, though some heterostyly is present. The morphology of the satellite genera (Myrrnephytum, Anthorhiza and Squamellaria) shows some parallels with that of Myrmecodia.
The five genera are united as a subtribe - the Hydnophytinae. Detailed taxonomic treatment of Myrmecodia and the satellite genera, but not Hydnophytum, is given. Myrmecodia is reduced from 43 to 18 species. One is a variable, widespread, lowland species which is divided into informal categories. One is polytypic with three subspecies, four are variable, but not divided, and the rest are monotypic, geographically restricted, mostly montane species. The pattern of variation is often reticulate, and a hierarchy or infrageneric grouping was not identified.
Myrmecodia and the satellite genera appear to have evolved independently from Hydnophytum-like ancestors. Structures probably advantageous to the ants have arisen repeatedly, but may also have led to inbreeding and taxonomic difficulty. The more sophisticated symbiosis in Myrmecodia may be reflected by the more mesomorphic nature of that genus, and is a prime example of coevolution between higher plants and animals.
The study of DNA methylation anomalies in chronic lymphocytic leukaemia
Keywords: malignancy
epigenetics
methylation
chronic lymphocytic leukaemia

Many haematological malignancies are associated with widespread alterations of the transcriptional and epigenetic programmes. Changes in DNA methylation provide the clearest example of epigenetic changes, but the mechanism(s) underlying such changes is unknown. To investigate this I studied DNA methylation across an ~80kb segment of the genome which is not known to be mutated in haematological malignancies. Methylation was perturbed in 35-100% of samples of DNA from individuals with a wide range of haematological malignancies but not in non-malignant haematological disorders. DNA methylation was comprehensively assessed by Southern blot analysis, classical bisulphite sequencing and using a newly developed capture bisulphite sequencing protocol. The results were also compared with analysis by MeDIP, an immunoprecipitation-based technique. These analyses provide methylation status at various levels including individual CpG resolution. This showed both gain and loss of methylation at CpG dinucleotides. Of interest, hypomethylation was most frequently seen in intergenic regions corresponding to transcription factor binding sites and areas of increased chromosome accessibility. These observations suggested that hypomethylation of the genome in haematological malignancies could arise from aberrantly expressed DNA binding proteins which, recruited to sequences in regions of open chromatin, would protect the underlying CpG dinucleotides from the methylation machinery. This, in turn, could lead to passive demethylation accumulating with increasing cell divisions. This hypothesis was tested with electrophoretic mobility shift assays using oligonucleotides representing the DNA underlying one such region. This showed that, compared to nuclear extracts from the lymphocytes of normal individuals, those from patients with CLL were enriched for a protein which binds to oligonucleotides containing the underlying sequence. Using a mass spectrometry approach, I identified a variety of proteins that may bind such regions and account for their passive demethylation in haematological malignancies.