VictorJuiz/thesis huggingface dataset:
Supramolecular control of synthesis and electronic structure of porphyrin oligomers
Keywords: OLED
pi-Conjugation
Self-Assembly
Porphyrin
Template
Supramolecular Cooperativity
SAXS

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.
The development and implementation of a beam position monitoring system for use in the FONT Feedback System at ATF2
Keywords: ATF2
CLIC
BPM
ILC
feedback
FONT

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.
Automatic error detection in non-native English
Keywords: determiners
prepositions
learner English
error detection

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.
2-tactics in the Choquet game, and the filter dichotomy
Keywords: choquet game
forcing
morasses
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.
Validation of lymphoma-associated antigens identified using autoantibody profiling and protein arrays
Keywords: DLBCL
Lymphoma
HIP1R

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.
Studies of crystalline organic molecular materials under extreme conditions
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

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.
Photogrammetric techniques for characterisation of anisotropic mechanical properties of Ti-6Al-4V
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

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.
K+ channels: gating mechanisms and lipid interactions
Keywords: small molecule docking
phosphatidyl inositol phosphates
ion channel gating
complex bilayers
Ion channels
homology modelling
molecular dynamics simulations
potassium ion channel
membrane proteins

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.
Improved understanding of combustor liner cooling
Keywords: film cooling
Combustor Liner
heat transfer
impingement

Heat management is an essential part of combustor design, as operating temperatures within the combustor generally exceed safe working temperatures of the materials employed in its construction. Two principal methods used to manage this heat are impingement and film cooling.
Impingement heat transfer refers to jets of impinging fluid delivered by orifices integrated into internal structures in order to remove undesired heat. This mode of heat transfer has a relatively high effectiveness, making it an attractive method of heat management. As such, a considerable number of studies have been done on the subject providing a substantial body of useful knowledge. However, there are innovative cooling configurations being used in gas turbines which generate compressibility and temperature ratio effects on heat transfer which are currently unexplored. Presented here are data showing that these effects have a significant impact on heat transfer and new correlations are presented to account for temperature ratio and Mach number effects for a range of conditions. These findings are significant and can be applied to impinging flows in other areas of a gas turbine engine such as turbine blades and vanes.
Film cooling refers to the injection of coolant onto a surface through an array of sharply angled holes. This is done in a manner that allows the coolant to remain close to the surface where it provides an insulating layer between the hot gas freestream and the cooler surface. In order to improve turbine efficiency, research efforts in film cooling are directed at reducing film cooling flow without decreasing turbine inlet temperatures.
Both impingement cooling and film cooling are heavily utilized in combustor liners. Frequently, cooling air first impinges against the back side of the liner, then the spent impingement fluid passes through film cooling holes. This arrangement combines the convective heat transfer of the impinging jets convection as the coolant passes through the film cooling holes and the benefits that come from having a thin film of cool air between the combustor wall and the combustion products.
In order to improve the understanding of internal cooling in gas turbine engines, the influence of previously unexplored physical parameters such as compressible flow effects and temperature ratio in impingement flows and variable blowing ratio in a film cooling array must be examined. Prior to this work, there existed in the available literature only an extremely limited exploration of compressibility effects in impingement heat transfer and the results of separately examining the effects of Mach number and Reynolds number. The film cooling literature provides no information for a full array of film cooling holes along a contraction at high blowing ratios. Exploring these effects and conditions adds to the body of available data and allows the validation of numerical predictions.
Acoustic anemometry on the surface of Mars
Keywords: Transducer
Atmosphere
Planetary
Acoustic
Sensor
Electronics
Electrostatic
Mars
MEMS
Layer
Surface
Boundary
Anemometry
Wind

There is a need for wind sensors with high accuracy and measurement frequency for deployment on the surface of Mars. The wind data obtained to date have been adversely affected by thermal contamination and calibration issues. Improved data would not only help to constrain and validate theoretical models, but also increase safety and longevity of lander operations. The mechanical and thermal wind sensing techniques used on previous missions, whilst sufficient for basic meteorology, are wholly inadequate for measuring fundamental phenomena such as dust and volatile transport. Two promising technologies, optical and acoustic anemometry, could permit precise and high-frequency measurement of three-dimensional wind speeds on the Martian surface. Ultrasonic acoustic anemometry, which relies on time-of-flight measurements, was ultimately chosen for its lower processing requirements and ability to measure the speed of sound; and therefore temperature. Capacitive transducers were selected for their low impedance and high sensitivity, to maximise signal transmission through the rarefied Martian atmosphere. These transducers, which consist of a metallised polymer film oscillating on top of a contoured metal backplane, were evaluated for their suitability as anemometers on the Martian surface. A theoretical framework was assembled to model transducer performance and determine which factors are the most important in determining received signal amplitude. A pair of transducers were designed and manufactured to allow for testing of a wide range of parameters including thickness of the oscillating membrane and diameter. Tests were carried out on the assembled transducers to investigate the dependence on these parameters, and their behaviour was generally found to fit the assembled theoretical framework well. Transducer performance was highly dependent on roughness depth of the backplanes, as expected. The frequency response of the transducers was dominated by the backplane roughness at atmospheric pressure but by film thickness at low pressures. Cross-correlation of the sent and received signals was confirmed as the most reliable signal detection method at low signal amplitudes. The transducers were tested under simulated Martian conditions (a low-pressure carbon dioxide atmosphere with airborne dust), and found to be capable of accurately and reliably measuring the incident wind speed. The cumulative deposition of airborne dust noticeably reduced received signal amplitude, but further testing is required to determine the effect of significant amounts of dust on transducer performance. The impact of the transducer heads impeding the incident fluid flow was found to be very significant in wind tunnel testing. Preliminary computational models were found to accurately predict these effects, but a more comprehensive modelling campaign and experimental validation would be required to ensure accurate instrument calibration.