VictorJuiz/thesis huggingface dataset:
Stochastic population oscillators in  ecology and neuroscience

In this thesis we discuss the synchronization of stochastic population oscillators in ecology and neuroscience. Traditionally, the synchronization of oscillators has been studied in deterministic systems with various modes of synchrony induced by coupling between the oscillators. However, recent developments have shown that an ensemble of uncoupled oscillators can be synchronized by a common noise source alone.
By considering the eﬀects of noise-induced synchronization on biological oscillators, we are able to explain various biological phenomena in ecological and neurobiological contexts - most importantly, the long-observed Moran eﬀect. Our formulation of the systems as limit cycle oscillators arising from populations of individuals, each with a random element to its behaviour, also allows us to examine the interaction between an external noise source and this intrinsic stochasticity. This provides possible explanations as to why in ecological systems large-amplitude cycles may not be observed in the wild. In neural population oscillators, we were able to observe not just synchronization, but also clustering in some pa- rameter regimes.
Finally, we are also able to extend our methods to include coupling in our models. In particular, we examine the competing eﬀects of dispersal and extrinsic noise on the synchronization of a pair of Rosenzweig-Macarthur predator-prey systems.
We discover that common environmental noise will ultimately synchronize the oscillators, but that the approach to synchrony depends on whether or not dispersal in the absence of noise supports any stable asynchronous states. We also show how the combination of correlated (shared) and uncorrelated (unshared) noise with dispersal can lead to a multistable steady-state probability density. Similar analysis on a coupled system of neural oscillators would be an interesting project for future work, which, among other future directions of research, is discussed in the concluding section of this thesis.

Keywords: stochastic processes
mathematical neuroscience
mathematical ecology
dynamical systems
Advisor: Bressloff, PC
Goriely, A
Palladium-catalysed enolate arylation in the synthesis of isoquinolines

Chapter 1. Introduction
Scientific background on the development of homogeneous palladium-catalysed cross coupling reactions, focusing on the α-arylation reaction of enolates and its application to the synthesis of heteroaromatic compounds. The classical syntheses of isoquinolines are discussed, followed by an account of modern methods for their synthesis, including the recent α-arylation-based methodology developed by the Donohoe group.
Chapter 2. Results and Discussion
2.1 Studies towards the development of a palladium-catalysed, C–H activation-based α arylation reaction of ketones, resulting in a C–H bromination/α-arylation sequence for the synthesis of isoquinolines and isoquinoline N-oxides.
2.2 The one-pot, four component coupling of a ketone, an acetal protected ortho-bromobenzaldehyde or ketone, an electrophile, and an ammonia source is described. This protocol, which ultimately provides C4 functionalised isoquinolines, is later extended to a novel α,α heterodiarylation protocol to furnish C4-aryl isoquinolines.
2.3 It is shown that the synthesis of 3 aminoisoquinolines can be achieved via the α arylation of nitriles. tert-Butyl cyanoacetate can act as a substitute for primary alkyl nitriles, with sequential α-arylation, in situ functionalisation, decarboxylation and cyclisation reactions provide C4 functionalised 3 aminoisoquinolines.
2.4 The synthetic utility of the α arylation based methodology for isoquinoline synthesis is exemplified by the total synthesis of the alkaloid berberine in 68% yield over five steps. This is followed by syntheses of pseudocoptisine, palmatine, dehydrocorydaline, and an unnatural fluorine containing analogue, in yields of 46%, 73%, 60% and 37%, respectively.
2.5 Finally, preliminary investigations demonstrate the utility of palladium-catalysed enolate arylation in the synthesis of β-carbolines.

Keywords: palladium catalysis
protoberberines
natural products
total synthesis
isoquinolines
alpha-arylation
alkaloids
synthesis
Advisor: Donohoe, T
Measurement and analysis of bubble pump and Einstein-Szilard single pressure absorption refrigeration system

The increasing demand for the domestic refrigeration system urges the development of greener form of refrigeration. The eighty-year-old single pressure absorption refrigeration system invented by Albert Einstein and Leo Szilard is attractive as it has no mechanical moving parts and can be driven by heat alone. However, the literature on either the refrigeration system or its components is scarce. The bubble pump is the crucial component of the refrigeration system, but it is poorly understood as its mass flow rate cannot be readily predicted. Two new time correlations in the mass flow rate prediction are presented to increase the accuracy when heat losses occur in the bubble pump. These time correlations are verified with the experimental results. When either the heat input or submergence ratio increases, the accuracy of the prediction increases. The percentage of error for the high heat input or submergence ratio is within ±10%. Working conditions and system dimension have a direct influence to the bubble pump performance. For instance, the bubble pump experimental results show that the mass flow rate of the bubble pump increases when either the submergence ratio or the concentration of ammonia increases. However, the performance of the bubble pump drops when the tube diameter or the system pressure increases.
The Einstein refrigeration system has only been rebuilt once since it invention. In order to redesign and rebuilt a practical Einstein refrigeration system, some challenges are revealed. With the combination of the good features of the designs of Einstein and Delano, a new prototype has been rebuilt and tested. The practical results obtained from the five experimental setups are the first set of experimental result that has ever been presented. The highest cooling capacity and coefficient of performance (COP) obtained are 5 W and 0.04 respectively.

Keywords: bubble pump
absorption refrigeration
refrigeration
single pressure absorption refrigeration
Einstein-Szilard refrigerator
Advisor: McCulloch, M
Predicting archaeo-colluvium on the Berkshire Downs

A new and relatively unexplored source of archaeological and environmental information on the Chalkland are the sediments of dry valleys. From relatively recent studies these deposits have been shown to be the product of ancient land use and soil loss and a rich repository of both primary and archaeological material. There have, however, been no attempts to determine the spatial distribution of this class of ancient valley deposit - for the purpose of this project termed archaeo-colluvium.
The study focuses on the north-west part of the Berkshire Downs (58km2), a landscape of both chalk and superficial drift deposits, which together with relict ancient fields, lynchets and settlement features offered a suitable area in which to develop and test a method for predicting the distribution of these deposits.
The project uses a multi-disciplinary approach which combines the traces of ancient arable (Celtic fields), some topographic parameters and assumptions about past soils, erosion regimes, and colluvial preservation in the development a GIS-based predictive model for the distribution of archaeo-colluvium within this study region.
Following the production of a map of predicted sites, archaeo-colluvium was checked in the field by an extensive auger and trench survey of the main valleys and tributaries. Dry valley sequences were assembled and dated, both for the purposes of evaluating the accuracy of the model and to draw some archaeological implications from the nature and distribution of these deposits. A synthesis of local soils, colluvium and wider archaeological observations suggested a three-stage chronology for prehistoric and Romano-British land use on the Berkshire Downs, centred around earliest arable use at Seven Barrows with later shifts to surrounding catchments of mixed chalk and clay soils.
The results of the field program were encouraging with the predictive model verified at 71% of target sites. A number of field observations were contrary to the original model, notable among these were that thicker sequences were common in landscapes of heavier soils as was evacuation of valley sediments from open chalk landscapes. This feedback allowed some modified principles to be briefly tested on three other Chalkland landscapes.
Protein-ligand interactions of arylamine N-acetyltransferase from Mycobacterium smegmatis

Tuberculosis is the world's largest cause of death from an infectious agent. Treatment is by an extended period of combination chemotherapy. Drug resistance is an increasing problem in tuberculosis therapy, particularly to the frontline anti-tubercular drug isoniazid (INH). Recombinant arylamine N-acetyltransferase (NAT) of Mycobacterium tuberculosis N-acetylates INH using the cofactor Acetyl Coenzyme A. NAT from M. tuberculosis is a polymorphic enzyme and also acetylates INH in vivo. Acetylated INH is inactive therapeutically against M. tuberculosis both in vivo and in vitro. The acetylation of isoniazid in the mycobacterial cell may compete with the activation of INH by the catalase-peroxidase, katG, and hence contribute to INH resistance in clinical isolates. Inhibition of NAT in M. tuberculosis may thus increase the efficacy of INH therapy.
A novel assay based around the detection of free Coenzyme A released during the acetylation reaction was used to determine the substrate specificity of recombinant NAT from the related Mycobacterium M. smegmatis (MSNAT). A relationship was observed between the lipophilicity of simple arylamine substrates and the rate of acetylation by MSNAT. Several MSNAT substrates possess antibacterial activity. The assay could also be used to screen compound libraries for MSNAT inhibitors.
Synthesis of seventeen thiazolidinedione sultams in collaboration with Dr.Vickers (Dyson Perrins), identified as weak inhibitors of MSNAT, gave a minimum competitive inhibitory constant of 14μM. Screening a library of 5,074 drug-like compounds for inhibition of MSNAT identified thirteen compounds with semi-maximal inhibition constants (IC50) of below 10μM. Based on this, fifteen maleimides were synthesised and were irreversible inhibitors of MSNAT with submicromolar potency. Similarly, ninety-six aminothiazoles were synthesised by Dr. Vickers and were uncompetitive inhibitors of MSNAT with a minimum IC50 of 1.5μM. The most potent aminothiazole showed no effect on the growth of M. smegmatis or M. bovis BCG or the sensitivity of the bacteria to isoniazid. However the aminothiazoles were shown not to penetrate the cells.

Advisor: Sim, E
Using non-linear vibration techniques to detect damage in concrete bridges

There has been much work published in recent years on the use of vibration characteristics to detect damage in bridges. Almost all of this work has been based on the assumption that the vibration is linear, i.e. the natural frequencies are not dependent on the amplitude of oscillation. The aim of the work presented here was to investigate the possibility of using changes in the non-linear vibration characteristics to detect damage in reinforced concrete bridges. These changes in the non-linear vibration characteristics were studied by conducting impact excitation vibration tests o reinforced concrete beams. The non-linearities were detected by examining the changes in fundamental frequency over time (and hence over amplitude of vibration). Several time-frequency distribution estimation tools are discussed including the discrete Fourier Transform moving window, the auto-regressive model moving window, harmonic wavelets and examples of the Cohen class of bilinear time-frequency distributions. A detailed investigation into these various distribution predictors was conducted to assess which is most suitable for analysing the vibration signals to detect changes in frequency with time. To understand the non-linearities in the vibration characteristics, a time-stepping model was described. The model is capable of including damage in the form of a moment-rotation relationship over the cracked region. It was validated for linear vibrations against theoretical values and the representation of a non-linear mechanism using the model was compared with experimental data. Static load tests were also conducted on the beams at various damage levels. They involved the use of vibrating wire strain gauges to investigate the moment-rotation behaviour over the cracked region. Several possible non-linear crack mechanisms are discussed and two of them are assessed using the vibration and the static load tests. Future experimental work is proposed to study the possible non-linear mechanisms further. The beam tests demonstrated that there is a change in non-linear vibration behaviour with damage. The change is greatest at low levels of damage and after the beam has been loaded to 30% of the failure load in three-point loading there is a reversal in the trend and a slight reduction in non-linearity with further damage.

Keywords: dynamics
concrete
Advisor: McFadden, P
Williams, M
The consolidation behaviour of gassy soil

The consolidation behaviour of gassy soil has been studied in a programme of experimental and theoretical research. This research is of particular importance to the offshore geotechnical industry as the presence of gas in the seabed can have a dramatic effect on the material properties of a marine sediment. Initial numerical modelling based on existing unsaturated soil theory combining the gas and the water phase into a compressible fluid in the pores of compressible soil skeleton failed to simulate the soil behaviour previously observed experimentally at Oxford. Therefore, there was scope for further study in this field. Chapters 2 to 4 describe the experimental preparation, consolidation technique and experimental results of the two series of tests on artificially prepared gassy soil samples. The results of these tests indicated that the gas appeared to be affected by the total stress rather than the pore water pressure, with the saturated soil matrix outside the gas voids being controlled by the consolidation stress. Chapter 5 presents the one-dimensional numerical modelling of the experimental results. Poor simulations were again made using compressible fluid theory. Treating the gas as compressible solid inclusions embedded in a saturated soil matrix, however, resulted in excellent simulations of the observed pore water pressures and settlements. Chapter 6 attempts to explain the results of the experimental and numerical modelling in terms of elastic and plastic soil behaviour. This includes the introduction to the double compressibility model in which the deformation behaviour of the saturated matrix is governed by changes in consolidation stress, whereas that of the gas is governed by changes in total stress. Chapter 7 presents the development of the governing gassy soil consolidation equations under both plane strain and axisymmetric conditions. Chapter 8 describes the approximation of the governing consolidation equations using the Galerkin finite element method in terms of nodal displacements and pore water pressures. The resulting finite element approximation is subsequently formulated for rectangular elements under plane strain and axisymmetric conditions in Chapter 9. The remainder of the thesis describes the structure of the finite element model DCFEM2 and the constitutive relationships that are required for such a model. The code is verified with existing analytical solutions and then is used to simulate the observed gassy soil behaviour under laboratory and field conditions.

Keywords: gas
clay
consolidation
Advisor: Sills, G
Fear and greed: financial crisis in the novel since 1850

The financial crisis of 2008 has been the most significant global economic phenomenon of the new century. Sudden and largely unanticipated, this crisis nonetheless marks the latest in a series of financial panics that forms a welldocumented feature of finance capitalism stretching back to the Dutch Tulip Bubble of 1637 and beyond, including such notorious crises as the South Sea Bubble of 1720, the Railway Shares panics of 1837 and 1847, the Wall Street Crash of 1929, and Black Monday in 1987. These and other crises have fostered a complex and diverse intellectual response - particularly since the South Sea Bubble - that has included interventions not only from economists and economic historians, but poets, dramatists, novelists, and others. This raises the question of whether the novel’s contribution to our wider understanding of financial crises has been fully acknowledged and assessed. In this thesis, the complex and shifting relationship between literary and non-literary responses to financial crisis is explored through an examination of the ideas of political economists, philosophers, journalists, financiers, and others, including Adam Smith, David Ricardo, Lord Overstone, Walter Bagehot, Herbert Spencer, Thorstein Veblen, Joseph Schumpeter, and J.M. Keynes, that situates their theories alongside readings of novels of financial crisis from the 1850s onward...
Abstract truncated for record page display

Keywords: Financial Crisis
Novel
Literature and Economics
Bellow
Norris
Dickens
Dreiser
DeLillo
F. Scott Fitzgerald
Trollope
H.G. Wells
Amis
Advisor: Small, H
Pratt, L
Texture determination from ultrasound for HCP and cubic materials

Crystallographic texture in polycrystalline HCP and cubic materials, often developed during thermomechanical deformations, has profound effects on properties at the macroscopic or component level. Given the respective natures of current detection techniques, a non-destructive, three-dimensional bulk texture detection method for these materials has not yet been developed. This thesis aims to achieve this goal through systematic studies on the relationship between ultrasonic wave velocity and texture.
The feasibility of such development is firstly reviewed via the combination of computational and experimental studies on exemplary HCP materials. Numerical results obtained via a representative volume element (RVE) methodology reveal that the wave speed varies progressively and significantly with changing texture, and experimental ultrasound studies combined with EBSD characterisation demonstrate distinguished velocity profiles for samples with different textures. Thus the possibility of the development is demonstrated from these combined results.
A novel convolution theorem is then presented, which couples the single crystal wave speed (the kernel function) with polycrystal orientation distribution function to give the resultant polycrystal wave speed function. Firstly developed on HCP and then successfully extended to general anisotropic materials, the theorem expresses the three functions as harmonic expansions thus enabling the calculation of any one of them when the other two are known. Hence, the forward problem of determination of polycrystal wave speed is solved for all crystal systems with verifications on varying textures showing near-perfect representation of the sensitivity of wave speed to texture as well as quantitative predictions of polycrystal wave speed. More importantly, the theorem also presents a solution to the long-standing inverse problem for HCP and cubic materials, with proof of principle established where groups of HCP and cubic textures are recovered solely from polycrystal wave velocities through the theorem and the results show good agreements with the original textures. Therefore the theorem opens up the possibility of developing a powerful technique for bulk texture measurement and wave propagation studies in HCP, cubic materials and beyond.

Keywords: cubic
wave propagation
crystallographic texture
ultrasound
HCP
non-destructive testing
Advisor: Dunne, F
Siviour, C
Time-of-flight secondary ion mass spectrometry - fundamental issues for quantitative measurements and multivariate data analysis

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a powerful technique for the analysis of organic surfaces and interfaces for many innovative technologies. However, despite recent developments, there are still many issues and challenges hindering the robust, validated use of ToF-SIMS for quantitative measurement. These include: the lack of metrology and fundamental understanding for the use of novel cluster primary ion beams such as C60n+ and Ar2000+; the need for validated and robust measurement protocols for difficult samples, such as those with significant micron scale surface topography; the lack of guidance on novel data analysis methods including multivariate analysis which have the potential to simplify many time-consuming and intensive analyses in industry; and the need to establish best practice to improve the accuracy of measurements. This thesis describes research undertaken to address the above challenges. Sample topography and field effects were evaluated experimentally using model conducting and insulating fibres and compared with computer simulations to provide recommendation to diagnose and reduce the effects. Two popular multivariate methods, principal component analysis (PCA) and multivariate curve resolution (MCR), were explored using mixed organic systems consisting of a simple polymer blend and complex hair fibres treated with a multi-component formulation to evaluate different multivariate and data preprocessing methods for the optimal identification, localisation and quantification of the chemical components. Finally, cluster ion beams C60n+ and Ar500-2500+ were evaluated on an inorganic surface and an organic delta layer reference material respectively to elucidate the fundamental metrology of cluster ion sputtering and pave the way for their use in organic depth profiling. These studies provide the essential metrological foundation to address frontier issues in surface and nanoanalysis and extend the measurement capabilities of ToF-SIMS.

Keywords: principal component analysis
topography
instrumentation
cluster ions
SIMS
secondary ion mass spectrometry
ToF-SIMS
organic depth profiling
multivariate analysis
sputtering
Advisor: Grovenor, C
Gilmore, I