VictorJuiz/thesis huggingface dataset:
Supramolecular control of synthesis and electronic structure of porphyrin oligomers

The work described in this thesis demonstrates the use of supramolecular chemistry in the template-directed synthesis of porphyrin nanorings and as a tool to control conformation and topology of π-conjugated porphyrin oligomers. Particular emphasis is placed on changes to the electronic structure of these oligomers depending on their conformation.
Chapter 1 gives an overview of π-conjugated porphyrin oligomers and conjugated macrocycles in general, followed by an introduction into supramolecular cooperativity and small angle X-ray scattering in solution.
Chapter 2 describes advances in the synthesis, solution structure elucidation and optoelectronic properties of a fully conjugated cyclic porphyrin hexamer. The high rigidity and symmetry of this nanoring as well as its bent π-system lead to a significant decrease in its HOMO-LUMO gap. The resulting near-infrared emission was exploited in the fabrication of light emitting diodes, demonstrating the use of a bent topology for minimizing aggregation in thin films.
The synthesis of a [12]porphyrin nanoring using a hexadentate template is presented in Chapter 3. The concept of Vernier templating is introduced as a general strategy for the synthesis of large monodisperse macrocycles. The nanoring is characterized and its cooperative binding to two template molecules is studied. In Chapter 4 a bidentate ligand is used in the cooperative formation of a sandwich complex beween two nanorings.
Chapter 5 provides an analysis of the rigidity of the butadiyne linked porphyrin oligomers used throughout this thesis. A linear chain is significantly more flexible in solution than on a surface where it is confined within two dimensions. Analysis of the persistence length indicates that a porphyrin nanoring with more than around 20 units would not be significantly strained.
The supramolecular binding of linear porphyrin oligomers to carbon nanotubes is analyzed in Chapter 6. The binding strength increases sharply with oligomer length and binding is strongest with (8,6) and (7,5) tubes. The energy level alignment in these porphyrin CNT complexes appears to be favorable for an application in photovoltaics.
In Chapter 7 bisamidine-carboxylate salt bridges together with zinc-nitrogen coordination chemistry are used to access a variety of topologies in assemblies based on carboxylic acid functionalized porphyrin dimers.

Keywords: OLED
pi-Conjugation
Self-Assembly
Porphyrin
Template
Supramolecular Cooperativity
SAXS
Advisor: Anderson, H
The development and implementation of a beam position monitoring system for use in the FONT Feedback System at ATF2

Feedback On Nanosecond Timescales (FONT) is a feedback system being developed to correct the beam position jitter in the extraction line and final focus system at the Accelerator Test Facility (ATF2), Tsukuba, Japan. FONT5 is currently being tested and is used to correct the intra-train jitter for a 3-bunch train; the bunch spacing is 154ns. This system measures the position of an electron bunch, using beam position monitors (BPMs). From this measurement, digital feedback electronics calculate the required correction, and sends a pulse to a feedback kicker. The feedback kicker then deflects the next bunch in the train in order to correct its position. Stripline BPMs are used at ATF2, and analogue processors manipulate the BPM signals before they are interpreted by the feedback electronics.
The BPM system has been modelled and tested so that it can be parameterised and optimised. The BPMs are calibrated regularly, and the resolution of the system measured. Both of these properties have been analysed and modelled. This has allowed the resolution to be minimised. The resolution is an important factor which limits the achievable feedback correction. Several other factors have also been investigated; these include the feedback gain and the bunch-bunch correlation.
To allow the feedback electronics to be controlled remotely, several data acquisition systems (DAQs) have been developed to allow data flow both to and from the digital board. The DAQs have been designed specically for the firmware on the FONT digital board.

Keywords: ATF2
CLIC
BPM
ILC
feedback
FONT
Advisor: Burrows, P
Automatic error detection in non-native English

This thesis describes the development of Dapper (`Determiner And PrePosition Error Recogniser'), a system designed to automatically acquire models of occurrence for English prepositions and determiners to allow for the detection and correction of errors in their usage, especially in the writing of non-native speakers of the language. Prepositions and determiners are focused on because they are parts of speech whose usage is particularly challenging to acquire, both for students of the language and for natural language processing tools. The work presented in this thesis proposes to address this problem by developing a system which can acquire models of correct preposition and determiner occurrence, and can use this knowledge to identify divergences from these models as errors. The contexts of these parts of speech are represented by a sophisticated feature set, incorporating a variety of semantic and syntactic elements. DAPPER is found to perform well on preposition and determiner selection tasks in correct native English text. Results on each preposition and determiner are discussed in detail to understand the possible reasons for variations in performance, and whether these are due to problems with the structure of DAPPER or to deeper linguistic reasons. An in-depth analysis of all features used is also offered, quantifying the contribution of each feature individually. This can help establish if the decision to include complex semantic and syntactic features is justified in the context of this task. Finally, the performance of DAPPER on non-native English text is assessed. The system is found to be robust when applied to text which does not contain any preposition or determiner errors. On an error correction task, results are mixed: DAPPER shows promising results on preposition selection and determiner confusion (definite vs. indefinite) errors, but is less successful in detecting errors involving missing or extraneous determiners. Several characteristics of learner writing are described, to gain a clearer understanding of what problems arise when natural language processing tools are used with this kind of text. It is concluded that the construction of contextual models is a viable approach to the task of preposition and determiner selection, despite outstanding issues pertaining to the domain of non-native writing.

Keywords: determiners
prepositions
learner English
error detection
Advisor: Pulman, S
2-tactics in the Choquet game, and the filter dichotomy

This thesis is comprised of two parts. The first part (Chapter 1) concerns a problem born from descriptive set theory, and is motivated by the desire to understand a particular topological game, in the presence of examples which exhibit interesting (arguably counterintuitive) behaviour. The work develops an understanding of the limits of this behaviour, and indicates where one might look for interesting examples. While set-theoretic techniques may appear in the analysis here, the focus is mostly topological.
The second part (Chapter 2) is much more set-theoretic. The work there developed from an interest in characterising closed subsets of βω, and focuses on developing tools which are promising for generalising the current relative consistency proofs of a duality principle for closed subsets of βωω. Knowledge of forcing comparable to that contained in Kunen and Jech is assumed.
The appendices contain results which are worthy of inclusion, and help provide additional perspective on the rest of the text. The results there are probably all already known, if not all recorded in the literature.

Keywords: choquet game
forcing
morasses
filter dichotomy
Advisor: Knight, R
Koenigsmann, J
Validation of lymphoma-associated antigens identified using autoantibody profiling and protein arrays

Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoma subtype with heterogeneous clinical outcome and a significant number of patients still die of their disease. Characterising lymphoma patients’ autoantibody repertoires represent one approach to improve the understanding of their disease biology. Our hypothesis was that characterisation of antigens eliciting humoural immune responses in lymphoma patients may provide insights into mechanisms of lymphomagenesis and identify novel diagnostic/therapeutic targets.
HIP1R was validated as a novel B-NHL autoantigen by immunoblotting with patients’ sera. No response was identified to the related HIP1 protein. Consistent with this finding, more widespread expression of HIP1R, compared to HIP1, was observed in lymphoma cell lines. Expression studies, at both transcript (qRT-PCR and analysis of microarray datasets) and protein levels (blotting and immunolabelling), identified abundant HIP1R in normal B cells and low level expression in a poor prognosis activated B-cell (ABC)-like DLBCL subtype. Upregulation of HIP1R expression was observed in activated non-malignant B cells at both transcript and protein levels, suggesting that downregulation of HIP1R expression in ABC-DLBCL might be a disease-related process. Despite its potential for DLBCL subtyping, HIP1R protein expression was not statistically significantly associated with patients’ survival in a series of 256 DLBCL. Short FOXP1 isoforms were identified as one mechanism repressing HIP1R transcription in an ABC-DLBCL cell line. Phenotypic analysis of HIP1R-depleted B-cell lymphoma cells indicated that HIP1R silencing could increase the surface levels of B-cell receptor (BCR) components such as IgM and CD79b.
HIP1R represents a novel lymphoma autoantigen and cell-of-origin marker for distinguishing germinal centre- versus ABC-DLBCL subtypes. As ABC-DLBCL survival is dependent on chronic BCR signalling, future studies will address whether HIP1R silencing plays a fundamental role in disease pathogenesis by promoting BCR signalling.

Keywords: DLBCL
Lymphoma
HIP1R
Advisor: Banham, A
Studies of crystalline organic molecular materials under extreme conditions

This thesis describes investigations into the properties of -phase BEDT-TTF charge transfer salts. Charge transfer salts are mainly studied as they are very useful test beds for fundamental physics due to the tuneability of their proper- ties and ground states. The effects of temperature and pressure on such systems have been studied, as these allow access to a wide range of different states and properties. Transport properties of these systems have been studied to obtain information about the Fermi surface and effective mass, and the effect of deuter- ation and also change of pressure media will be discussed. The interaction of infrared radiation with these systems has also been investigated and simultaneous pressure and temperature measurements will be presented, something not greatly studied due to the large technical challenges. The techniques and approaches for overcoming these are also discussed.
Chapter 1 provides an introduction to the organic materials themselves with particular emphasis on the actual compounds studied.
Chapter 2 provides the necessary theoretical background for studying organic charge transfer salts using magnetic quantum oscillations and their infrared re- ectivity.
Chapter 3 covers the experimental techniques and also discusses some of the challenges encountered and their solutions to aid others working in this area. Chapter 4 describes an investigation into the transport properties of - (ET)2Cu(SCN)2 by studying Shubnikov-de Haas oscillations using both deuter- ated and normal samples and using two different pressure media, and comparing it to work done using a third.
Chapter 5 presents an investigation into the pressure dependence of selected phonon modes in -(ET)2Cu(SCN)2 using infrared radiation on a deuterated sam- ple.
Chapter 6 presents what is believed to be the first pressure and temperature dependent infrared study of an organic molecular material. In this case the or- ganic molecular material is d8--(ET)2Cu[N(CN)2]Br, but the techniques should be readily transferable to other materials.

Keywords: charge transfer salts
TMTSF2PF6
Shubnikov-de Haas
high pressure
FFT spectrometer
low temperature
organic supercondutor
magnetoresistance
Fourier transform spectrometer
IR
piston cylinder cell
extended Drude model
phonon modes
helium gas pressure cell
infrared reflectivity
quasi 2D Fermi surface
deuterated kappa phase BEDT-TTF copperthiocyanate
BEDT-TTF
diamond anvil pressure cell
Advisor: Singleton, J
Klehe, AK
Blundell, S
Structure and activity of factor D̄ of the alternative pathway of human complement

1. A method for the purification of the serine protease,factor D,was developed using conventional chromatographic procedures. The final product was homogeneous as judged by SDS/polyacrylamide gel electrophoresis, its migration as a single component in ion exchange and gel filtration media, and its amino acid sequence analysis. The molecule had an apparent molecular weiyht of 24,000. It contained <1.5% (w/w) reducing sugars as judged by periodic acid/Schiff staining, and existed as a monomer in buffers containing either EDTA or calcium ions.
2. Approximately 84% of the amino acid sequence was established unequivocally by automated sequence analysis of the intact molecule and peptides derived by digestion with CNBr, o-iodosobenzoic acid, trypsin and V8 protease. Carboxypeptidase-Y digestion was used to establish the C-terminal amino acid. The peptides were aligned either by homology with other serine proteases, or by the overlap of sequences obtained from peptides derived by different fragmentation procedures. The molecule nad a typical serine protease-type sequence with isoleucine as the Nterminal amino acid. The active site serine and aspartic acid and the surrounding sequences were conserved as well as the sequence around the position of the active site histidine, although this residue itself was not identified.
3. The possibility of the existence of a factor D̄ zymogen which can be activated by trypsin was reinvestigated, but no evidence for a precursor was found. No enzymic activity towards a number of p-nitroanilide substrates and arginyl and lysyl esters was observed with factor D̄,but it was found to release p-nitrophenol from p-nitrophenyl-p'-guanidinobenzoate. Factor D̄ was inhibited by diisopropylphosphofluoridate and p-nitrophenyl-p'-guanidinobenzoate, but a variety of other non-protein and protein inhibitors including α2-macroglobulin, c1 inhibitor and inter-α-trypsin inhibitor had no effect on enzymic activity.

Advisor: Reid, K
Photogrammetric techniques for characterisation of anisotropic mechanical properties of Ti-6Al-4V

The principal aims of this research have been the development of photogrammetric techniques for the measurement of anisotropic deformation in uniaxially loaded cylindrical specimens. This has been achieved through the use of calibrated cameras and the application of edge detection and multiple view geometry. The techniques have been demonstrated at quasi-static strain rates, 10^-3 s^-1, using a screw-driven loading device and high strain rates, 10^3 s^-1, using Split Hopkinson Bars. The materials that have been measured using the technique are nearlyisotropic steel, anisotropic cross-rolled Ti-6Al-4V and anisotropic clock-rolled commercially pure Zr.
These techniques allow the surface shapes of specimens that deform elliptically to be completely tracked and measured in situ during loading. This has allowed the measurement of properties that could not have been recorded before, including true direct stress and the ratio of transverse strains in principal material directions, at quasi-static and elevated strain rates, in tension and compression. The techniques have been validated by measuring elliptical prisms of various aspect ratios and independently measuring interrupted specimens using a coordinate measurement machine.
A secondary aim of this research has been to improve the characterisation of the anisotropic mechanical properties of cross-rolled Ti-6Al-4V using the techniques developed. In particular, the uniaxial yield stresses, hardening properties and the associated anisotropic deformation behaviour along the principal material directions, have all been recorded in detail not seen before. Significant findings include: higher yield stresses in-plane than in the through-thickness direction in both tension and compression, and the near transverse-isotropy of the through-thickness direction for loading conditions other than quasi-static tension, where significant anisotropy was observed.

Keywords: Yield surface
Zirconium
anisotropic
roughness
extensometer
material behaviour
high strain rate
R-ratio
surface
image processing
Ti-6Al-4V
displacement
strain
3D reconstruction
edge detection
Steel
optical
Split-Hopkinson bar
ellipse
Advisor: Siviour, C
Petrinic, N
Nabokov and play

In December 1925, Vladimir Nabokov said that "everything in the world plays" and that "everything good in life - love, nature, the arts and domestic puns - is play." This thesis argues that, after December 1925, play was Nabokov's leading idea. Previous critics have spoken of Nabokov as a playful writer but have not drawn on the untranslated early Russian texts; have rarely discussed the actual games depicted in his novels; and have been vague on what it means to call Nabokov a playful writer. This thesis argues that Nabokov's novels after 1925 are all playful or game-like in different ways related to the games they depict, and become ever more radically so. It provides a chronological narrative of play as the evolving subject and style of Nabokov's writing.
The first chapter discusses the sources of Nabokov's idea of aesthetic play in Kant, Schiller, and Nietzsche. The second chapter traces the emergence of play in Nabokov's earliest writings, from 1918 to 1925, isolating the themes of play of self, play as make-believe, and play as violence. The third chapter looks at how in King, Queen, Knave (1927) and The Luzhin Defense (1930), Nabokov adopted the scheme of Lewis CarrolPs two Alice books, first using cards as an image of play and freedom, then chess as an image of rule and game. The fourth chapter shows that in the 1930s Nabokov wrote about play in contrast to work, and deals with Glory (1931), Despair (1934), Invitation to a Beheading (1935-6), and The Gift (1937-8; 1952). The fifth chapter is about free play in Nabokov's American writing, and emphasises the influence of Joyce's Finnegans Wake. It covers Bend Sinister (1947), Speak, Memory (1951; 1967), Lolita (1955) and Ada (1969). The sixth chapter argues that Pale Fire (1962) belongs to the genre of the literary game, and is in complex intertextual relation to a previous literary game, Pope's Dunciad.

Advisor: Professor Hermione Lee, A
K+ channels: gating mechanisms and lipid interactions

Computational methods, including homology modelling, in-silico dockings, and molecular dynamics simulations have been used to study the functional dynamics and interactions of K+ channels. Molecular models were built of the inwardly rectifying K+ channel Kir2.2, the bacterial homolog K+ channel KirBac3.1, and the twin pore (K2P) K+ channels TREK-1 and TRESK. To investigate the electrostatic energy profile of K+ permeating through these homology models, continuum electrostatic calculations were performed. The primary mechanism of KirBac3.1 gating is believed to involve an opening at the helix bundle crossing (HBC). However, simulations of Kir channels have not yet revealed opening at the HBC. Here, in simulations of the new KirBac3.1-S129R X-ray crystal structure, in which the HBC was trapped open by the S129R mutation in the inner pore-lining helix (TM2), the HBC was found to exhibit considerable mobility. In a simulation of the new KirBac3.1-S129R-S205L double mutant structure, if the S129R and the S205L mutations were converted back to the wild-type serine, the HBC would close faster than in the simulations of the KirBac3.1-S129R single mutant structure. The double mutant structure KirBac3.1-S129R-S205L therefore likely represents a higher-energy state than the single mutant KirBac3.1-S129R structure, and these simulations indicate a staged pathway of gating in KirBac channels. Molecular modelling and MD simulations of the Kir2.2 channel structure demonstrated that the HBC would tend to open if the C-linker between the transmembrane and cytoplasmic domain was modelled helical. The electrostatic energy barrier for K+ permeation at the helix bundle crossing was found to be sensitive to subtle structural changes in the C-linker. Charge neutralization or charge reversal of the PIP2-binding residue R186 on the C-linker decreased the electrostatic barrier for K+ permeation through the HBC, suggesting an electrostatic contribution to the PIP2-dependent gating mechanism. Multi-scale simulations determined the PIP2 binding site in Kir2.2, in good agreement with crystallographic predictions. A TREK-1 homology model was built, based on the TRAAK structure. Two PIP2 binding sites were found in this TREK-1 model, at the C-terminal end, in line with existing functional data, and between transmembrane helices TM2 and TM3. The TM2-TM3 site is in reasonably good agreement with electron density attributed to an acyl tail in a recently deposited TREK-2 structure.

Keywords: small molecule docking
phosphatidyl inositol phosphates
ion channel gating
complex bilayers
Ion channels
homology modelling
molecular dynamics simulations
potassium ion channel
membrane proteins
Advisor: Sansom, M
Tucker, S
Short-term effects of cigarette smoking

In spite of Health Education campaigns the majority of smokers continue to smoke. This thesis presents some evidence concerning the factors underlying the maintenance of cigarette smoking, in terms of the short term effects of cigarette smoking on a variety of physiological measures of arousal.
Both stimulant, depressant and mixed effects of cigarette smoking were demonstrated on a number of physiological variables (EEG, electrodermal and EMG). No consistent effect was found on respiration rate or irregularity. Heart rate was invariably increased by cigarette smoking.
Sham smoking accounted for approximately 50% of all effects in both directions (.stimulant or depressant), with the exception of cigarette induced tachycardia which appeared to be entirely accounted for by tobacco smoke inhalation and by implication nicotine.
The pre-smoking 'starting-state' of the subject had important consequences as regards the magnitude and direction of smoking effect, stimulant versus depressant. Cigarette smoking tended to produce stimulant effects in subjects with low levels of presmoking physiological arousal CEEG, electrodermal) and depressant effects in subjects exhibiting high levels of pre-smoking arousal.
The vigour of smoking style (puffing rate, puff duration and pressure, inhalation) increased during stress and also increased with low nicotine delivery cigarettes.
These results are interpreted as supporting an 'Arousal Modulation' model of cigarette smoking, i.e. smokers can use cigarette smoking as a device for controlling their level of arousal towards an 'optimum' by virtue of the biphasic stimulantdepressant dose response of nicotine and to some extent, by virtue of the effects of smoking behaviour in the absence of nicotine.