VictorJuiz/thesis huggingface dataset:
Modelling columnar and equiaxed growth

A novel computer model of the evolution of columnar and equiaxed microstructure during alloy solidification has been developed. A control volume finite difference model of conduction heat transfer is applied to a two-dimensional domain bounded by a relatively cold mould. The initial condition is that of superheated liquid, and nucleation occurs either at the mould wall, leading to columnar dendritic growth, or within the bulk liquid, leading to the growth of equiaxed dendrites. The columnar front or the equiaxed grain boundaries are represented by computationally sharp interfaces, which separate liquid from partially solid alloy. Interpolation between discrete computational markers is employed to describe these interfaces, and a front-tracking technique is used to predict the evolution of the grain structure, via movement of the markers, across the fixed grid. The front velocity is determined via considerations of the kinetics of dendrite growth. The heat equation is fully coupled to the front-tracking algorithm by means of source terms which represent the evolution of latent heat due to the dendritic growth (advancing tips and thickening mushy zone). The model, applied to binary Al-Cu alloys, is computationally efficient. It predicts the variation of the extent of liquid undercooling ahead of the growing columnar front, and new metrics have been established to determine the likelihood of the formation of an equiaxed zone here. The employment of these metrics to establish the influence of heat extraction rate and alloy composition agrees with reports from the literature. The model does not distinguish between individual grains of the columnar zone, but it is shown that this is not an important limitation for most metal casting applications. Direct simulation of the nucleation and growth of multiple equiaxed crystals has been carried out, in which the nucleation and growth of individual grams can be observed via animation, and the influence of melt superheat and heat extraction rate on equiaxed solidification has been determined.

Advisor: Hunt, J
The at-sea behaviour of the Manx shearwater

Seabirds are vulnerable to a wide range of impacts at sea and function as important indicators of ocean health. A detailed understanding of their movements and distributions at sea, as well as the types of behaviour in which they engage and the extent to which those activities make them vulnerable to different impacts is critical in effective conservation planning. But their elusive lifestyles and mobility have hampered studies of their at-sea behaviour. Using miniature data loggers deployed on Manx shearwaters Puffinus puffinus this thesis explores the movements, distribution and behaviour of a small-medium pelagic, procellariiform seabird during foraging trips at sea.
Foraging distributions were most variable during the pre-laying period when females departed the colony to build their egg. Females foraged close to the colony when local resources were adequate, but more typically foraged in distant shelf edge waters. Males returned frequently to the colony during this period and typically foraged close by, but also in shelf edge waters when local resources were poor.
During incubation and chick-rearing the foraging movements of birds tracked from up to four colonies showed considerable inter-annual variability, but were largely constrained to the Irish and Celtic Seas and the inshore waters of west Scotland. Birds from each of the colonies foraged in waters local to their own colony, but also in more distant locations, including the productive Western Irish Sea and Western Irish Sea Front where birds from multiple colonies co-foraged, presumably at high densities.
At-sea behaviour was organized into three principal activities representing: (1) sustained direct flight, (2) sitting on the sea surface, and (3) foraging, comprising tortuous flight interspersed with periods of immersion and diving in pursuit of prey. Foraging was highly constrained to daylight hours during which birds engaged in bouts of diving separated by periods of flight or rest on the surface. Most dives were up to 6 m deep, lasting up to 13 s, but some much deeper dives (maximum 55.5 m) were also made.
During chick-rearing the use of short and long duration trips may allow parents to control provisioning effort and their own body condition. However, reducing parents’ requirement to provision their chick (by supplemental chick feeding) did not appear to alter the at-sea movements and behaviour of parents, suggesting that at-sea behaviour probably is controlled more by foraging conditions and prey distributions than by the nutritional demands of the chick.

Keywords: animal behaviour
biologging
seabird
foraging
Advisor: Guilford, T
The rank-one rotating mass matrix hypothesis: a general and a model specific study

In this thesis we investigate whether a rank-one rotating mass matrix extended to solve the strong CP problem can, through the mass leakage mechanism, account for fermion masses, mixing angles and a thetaCP
term of order unity. In the first part we find restrictions placed on the rotation of the rank-one mass matrix by experimental data. We demonstrate that a smooth rotation of the mass matrix can reproduce the experimentally determined fermion masses and mixing angles and give thetaCP
= 1.45 radians. We then fit the speed of rotation at high (>1
GeV) scales. Using this rotation we make predictions for Higgs branching ratios for a range of Higgs masses, finding a suppression of Gamma(Hightarrowcarc)
compared to the standard model and significant flavour violating branching ratios.
In the second part we study the framed standard model (FSM). We calculate the strong framon one-loop contribution to the rotation of its rank-one mass matrix and account for the non-trivial metric on its internal symmetry space. We find that the FSM can reproduce the hierarchy seen in the fermion masses and the CKM matrix, fit thetaCPsim0.3
radians and find |Umu3|sim0.8
. Similar results are found if QCD running is included, except that |Umu3|>0.95
. We compare the FSM rotation to the rotation found in first part and find they are in good agreement above mu=mc
. We go on to show that the predictions for Higgs decay are comparable to those found in the general study.
In the final part we calculate the framon mass spectrum of the FSM in the hermitian gauge and find that, as expected, it agrees with the calculation performed in the triangular gauge. We find that none of the framons are massless.

Advisor: Tsou, S
Imidazolium- and triazolium-based interlocked structures for anion recognition and sensing

This thesis describes the synthesis and investigation of novel anion templated interlocked structures which incorporate the positively charged imidazolium and triazolium binding motifs for applications in anion recognition and sensing.
Chapter One introduces the fields of anion supramolecular chemistry and mechanically interlocked structures, focusing on topics of particular relevance to this thesis, including anion recognition, anion sensing and the templated synthesis of interlocked architectures.
Chapter Two details the incorporation of the imidazolium motif into the axle components of anion templated rotaxane hosts to achieve selective anion recognition by virtue of their interlocked binding cavities. The effects of exploiting imidazolium motifs with contrasting hydrogen bond donor arrangements and reducing the macrocycle size on the anion recognition properties of such systems were investigated using 1H NMR spectroscopy.
Chapter Three reports the work undertaken to utilise fluorescent reporter groups as stoppers in the synthesis of anion sensing rotaxanes. Imidazolium- and triazolium based systems containing either luminescent ruthenium(II) bipyridyl complexes or the organic fluorophore anthracene were prepared and their anion sensing behaviours explored using fluorescence spectroscopy. Synthetic efforts to construct suitable photo-active rotaxanes are detailed.
Chapter Four describes investigations of the novel naphthalimide triazolium motif both for use in interlocked molecular motion systems, and for fluorescence sensing applications. The preparation of a naphthalimide triazolium rotaxane, capable of selective, anion-induced, uni-directional shuttling which was investigated extensively using 1H NMR spectroscopy and optically signalled by perturbations in the UV/Vis spectrum, is detailed. Preliminary research studies into the potential to exploit this motif for surface based fluorescence sensing devices are also included.
Chapter Five presents research into the utilisation of acyclic receptors displaying considerable binding induced conformational changes for fluorescence anion sensing. The recognition properties of a series of imidazolium-based receptors were studied, whilst the ability of a pyrene appended analogue to signal anion complexation via changes in excimer emission is reported. The control of interpenetrated assembly formation using anion-induced conformational changes within the threading component of a pseudorotaxane is also discussed.
Chapter Six provides the experimental procedures and characterisation details for the compounds synthesised in this thesis.
Chapter Seven is a summary of conclusions from Chapters Two, Three, Four and Five.
Supplementary information relating to titration protocols, crystallographic data and surface studies is provided in the Appendices.

Keywords: sensing
molecular recognition
template synthesis
supramolecular
anions
rotaxane
Advisor: Beer, P
Investigation of the bend transition in Pi-cell devices

The Pi-cell is known to have the fastest response time amongst commercialised nematic LCD applications due to the bend configuration. The Bend configuration can be obtained when a high voltage is applied to a Pi-cell initially treated to have a splay configuration, but transition is complex because the splay and the bend states are topologically not identical. Although two possible mechanisms (anchoring breaking and order reconstruction) can explain the bend transition, it is still difficult to be certain of the mechanism in some cases. In this thesis, therefore, the bend transition mechanism in the Pi-cell is investigated.
Whichever mechanism is present, the bend transition speed is expected to increase when a high voltage is applied to the cell. However, in some cases, the application of a higher voltage reduces the bend transition speed. These phenomena are discussed based on various experimental results, and the reasons are also discussed. Four different regimes are suggested depending on the bend transition speed change. From these results, it is possible to understand the best way to obtain the bend state quickly in a TFT-LCD in the Pi-cell mode.
During the experiments, unexpected light leakage was observed in the extinction position. It was proved that the light leakage came from the residual twist angle caused by the manufacturing process. In addition, two new methods were suggested for measuring the residual twist angle from the light leakage. One of the methods, the analytic method, was extended to the TN-cell.
Allowing for the residual twist angle in the Pi-cell, the reason for lower CR compared to other LCD modes is discussed, and methods are suggested in this thesis to improve the CR of Pi-cell devices.

Keywords: Pi-cell
anchoring breaking
order reconstruction
bend transition speed
Advisor: Elston, S
Raynes, P
Population structure and dynamics of Campylobacter populations carried by wild birds and chickens reared in a free-range woodland environment

Ingestion of contaminated chicken meat is a major cause of Campylobacteriosis in Europe and the USA. The environment, including wild birds, is considered to be an important reservoir for chicken colonization. The aims of this study were to determine the population structure of Campylobacter amongst chicken and wild bird sources on a single farm, and to establish the extent to which genotypes flow between them and ultimately infect humans, using MLST and antigen sequence typing.
A pilot study amongst farm animals and wild birds in Lancashire demonstrated that Campylobacter genotypes from human disease were common on the farm and could be isolated from more than one animal source. Between 30-50% of wild geese and Starlings were shedding Campylobacter, with a seasonal peak in shedding rate in Spring. Genotypes were divergent from those previously isolated from human disease, retail meat and farm animal sources, with the majority being restricted to the host source. The carriage rate of Campylobacter was between 70- 100% amongst 78 free-range poultry flocks tested at 56 days of age. Up to seven genotypes were found to co-exist within a flock, and genotypes varied throughout the year on a random basis.
Some Campylobacter strains were isolated from one farm site only, but a small percentage of them had spread nationally and were stable over a period of a decade. A total of 23% of Campylobacter isolates from free-range chickens were indistinguishable to those from human disease, and 5% were indistinguishable from wild birds. A total of 6% of genotypes isolated from wild birds were indistinguishable from those isolated from human disease. Wild birds could not be completely disregarded as a potential reservoir of Campylobacter for both humans and poultry, but their role is likely to be limited.

Advisor: Maiden, M
Genetics of chronic otitis media: a mouse to man approach

Chronic otitis media (OM) is an archetypal complex disease, which is particularly prevalent in childhood. Epidemiological data suggest high heritability for disease susceptibility, but previous genetic association studies have had methodological flaws, and none have specifically focused on chronic OM phenotypes.
Mouse models represent one way to ascertain candidate loci for human association testing. A number of mouse models of middle ear inflammation have been reported, but many susceptibility loci remain undiscovered. I demonstrate that oto-endoscopy is a robust and scalable phenotyping platform for OM in the mouse, and discuss its value in new model discovery.
Chronic OM is also a feature of trisomy HSA21 (Down Syndrome). Through an interrogation of the mouse library of segmental trisomy models of Down Syndrome, I identify a critical trisomic region for chronic otitis media. This region may underlie OM susceptibility in Down Syndrome, but could also contribute to disease susceptibility in non-syndromic disease.
Mouse models can also be used to interrogate disease mechanisms. Our previous work has shown that the chronically inflamed middle ear is hypoxic, and that hypoxia signalling is a potential therapeutic target. Exploiting the Junbo mouse model, I demonstrate that surgical ventilation of the Junbo ear improves inflammation, and that this is associated with loss of hypoxia signalling. I present preliminary results from transcript analyses of human middle ear effusions showing marked upregulation of hypoxia signalling.
A systematic review of existing mouse models suggests that the loci FBXO11, EVI1, SMAD2, and TGIF1 are good candidates genes for human association testing. I detail recruitment and collection of DNA from families in the UK where a child is undergoing grommet insertion. Association testing using a variant of the transmission disequilibrium test shows susceptibility associated with polymorphisms at FBXO11, and possibly also SMAD2 and TGIF1.

Keywords: mouse
otitis media
hypoxia
genetics
Down syndrome
Advisor: Burton, M
Brown, S
Renormalisation of random hierarchial systems

This thesis considers a number of problems which are related to the study of random fractals. We define a class of iterations (which we call random hierarchical systems) of probability distributions, which are defined by applying a random map to a set of k independent and identically distributed random variables. Classical examples of this sort of iteration include the Strong Law of Large Numbers, Galton-Watson branching processes, and the construction of random self-similar sets.
In Chapter 2, we consider random hierarchical systems on ℝ, under the condition that the random map is bounded above by a random weighted mean, and that the initial distribution is bounded below. Under moment conditions on the initial distribution we show that there exists almost sure convergence to a constant.
In Chapters 3 to 5 we consider the asymptotics of some examples of random hierarchical systems, some of which arise when considering certain properties of random fractal graphs. In one example, which is related to first-passage percolation on a random hierarchical lattice, we show the existence of a family of non-degenerate fixed points and show that the sequence of distributions will converge to one of these. The results of some simulations are reported in Chapter 7.
Part III investigates the spectral properties of random fractal graphs. In Chapter 8 we look at one example in detail, showing that there exist localised eigenfunctions which lead to certain eigenvalues having very high multiplicity. We also investigate the behaviour of the Cheeger constants of this example. We then consider eigenvalues of homogeneous random fractal graphs, which preserve some of the symmetry of deterministic fractals. We then use relationships between homogeneous graphs and more general random fractal graphs to obtain results on the eigenvalues of the latter. Finally, we consider a few further examples.
Climate-related disaster risk in mountain areas: the Guatemalan highlands at the start of the 21st Century

Mountains are hazardous places. Framed in political ecology and disaster theory in geography, this research set out to answer the overarching question of how the risk of climate-related disasters has changed in mountain areas of Guatemala at the start of the century. It involved four main related activities that examined key elements of disaster risk: 1) the trigger, assessing extreme rainfall trends based on daily records; 2) the hazards, through an evaluation of the relevance of land use and cover (LUC) to slope failure; 3) elements of social vulnerability, looking at its geography and trend at the turn of the century, and also exploring the role of globalisation in specific communities; and 4) an assessment and mapping of disaster risk in two sites, including an estimation of exposure levels to hazards. Methods range from statistical analysis of quantitative data (rainfall, landslide, and vulnerability chapters), GIS-based modelling (risk mapping), and qualitative analysis including interviews.
The main findings state that: increasing annual and extreme rainfall has contributed to higher disaster risk only in a few areas; LUC change from forest to annual crops has increased risk in a few locations but it has not done so in most of the volcanic highlands either because there has been only minor LUC change or because LUC does not seem to have an effect on slope failure in certain types of geology. Disaster risk has decreased overall because vulnerability has become lower in the vast majority of mountain areas but risk may be higher as a result of increased exposure to hazards either in mountain communities or in marginal areas of the capital and surrounding municipios. The analysis of risk helped identify four mountain zones where risk is very likely to have increased. Further research questions are mostly related to studying the evolution of climate-related disaster risk in those areas.

Keywords: social vulnerability
extreme rainfall
disaster risk
Guatemala
hazards
mountains
landslides
Advisor: Liverman, D
Signal processing methods for cerebral autoregulation

Cerebral autoregulation describes the clinically observed phenomenon that cerebral blood flow remains relatively constant in healthy human subjects despite large systemic changes in blood pressure, dissolved blood gas concentrations, heart rate and other systemic variables. Cerebral autoregulation is known to be impaired post ischaemic stroke, after severe head injury, in patients suffering from autonomic dysfunction and under the action of various drugs. Cerebral auto-regulation is a dynamic, multivariate phenomenon. Sensitive techniques are required to monitor cerebral auto-regulation in a clinical setting. This thesis presents 4 related signal processing studies of cerebral autoregulation. The first study shows how consideration of changes in blood gas concentrations simultaneously with changes in blood pressure can improve the accuracy of an existing frequency domain technique for monitoring cerebral autoregulation from spontaneous fluctuations in blood pressure and a transcranial doppler measure of cerebral blood flow velocity. The second study shows how the continuous wavelet transform can be used to investigate coupling between blood pressure and near infrared spectroscopy measures of cerebral haemodynamics in patients with autonomic failure. This introduces time information into the frequency based assessment, however neglects the contribution of blood gas concentrations. The third study shows how this limitation can be resolved by introducing a new time-varying multivariate system identification algorithm based around the dual tree undecimated wavelet transform. All frequency and time-frequency domain methods of monitoring cerebral autoregulation assume linear coupling between the variables under consideration. The fourth study therefore considers nonlinear techniques of monitoring cerebral autoregulation, and illustrates some of the difficulties inherent in this form of analysis. The general approach taken in this thesis is to formulate a simple system model; usually in the form of an ODE or a stochastic process. The form of the model is adapted to encapsulate a hypothesis about features of cerebral autoregulation, particularly those features that may be difficult to recover using existing methods of analysis. The performance of the proposed method of analysis is then evaluated under these conditions. After this testing, the techniques are then applied to data provided by the Laboratory of Human Cerebrovascular Physiology in Alberta, Canada, and the National Hospital for Neurology and Neurosurgery in London, UK.

Keywords: maximal overlap discrete wavelet transform
signal processing
cerebral autoregulation
near infrared spectroscopy
hilbert wavelet
non-parametric correlation analysis
gaussian copula analysis
Advisor: Gavaghan, D
Payne, S
Whiteley, J