VictorJuiz/thesis huggingface dataset:
Twistor actions for gauge theory and gravity
Keywords: twistor theory
gauge theory
general relativity

We first consider four-dimensional gauge theory on twistor space, taking as a case study maximally supersymmetric Yang-Mills theory. Using a twistor action functional, we show that gauge theory scattering amplitudes are naturally computed on twistor space in a manner that is much more efficient than traditional space-time Lagrangian techniques at tree-level and beyond. In particular, by rigorously studying the Feynman rules of a gauge-fixed version of the twistor action, we arrive at the MHV formalism. This provides evidence for the naturality of computing scattering amplitudes in twistor space as well as an alternative proof of the MHV formalism itself.
Next, we study other gauge theory observables in twistor space including gauge invariant local operators and Wilson loops, and discuss how to compute their expectation values with the twistor action. This enables us to provide proofs for the supersymmetric correlation function / Wilson loop correspondence as well as conjectures on mixed Wilson loop - local operator correlators at the level of the loop integrand. Furthermore, the twistorial formulation of such observables is naturally algebro-geometric; this leads to novel recursion relations for computing mixed correlators by performing BCFW-like deformations of the observables in twistor space.
Finally, we apply these twistor actions to gravity. Using the on-shell equivalence between Einstein and conformal gravity in de Sitter space, we argue that the twistor action for conformal gravity should encode the tree-level graviton scattering amplitudes of Einstein's theory. We prove this in terms of generating functionals, and derive the flat space MHV amplitude as well as a recursive version of the MHV amplitude with cosmological constant. We also include some discussion of super-connections and Coulomb branch regularization on twistor space.
Quaternary nanocrystal solar cells
Keywords: photovoltaics.
nanocrystal
quaternary

This thesis studies quaternary chalcogenide nanocrystals and their photovoltaic applications. A temperature-dependent phase change between two distinct crystallographic phases of stoichiometric Cu2ZnSnS4 is investigated through the development of a one pot synthesis method. Characterisation of the Cu2ZnSnS4 nanocrystals was performed using absorption spectroscopy, transmission electron microscopy (TEM) and powder X-ray diffraction (XRD). An investigation was conducted into the effects of using hexamethyldisilathiane (a volatile sulphur precursor) in the nucleation of small (<7nm), mono-dispersed and solution-stable quaternary Cu2ZnSnS4 nanocrystals.
A strategy to synthesize high quality thermodynamically stable kesterite Cu2ZnSnS4 nanocrystals is established, which subsequently enabled the systematic study of Cu2ZnSnS4 nanocrystal formation mechanisms, using optical characterization, XRD, TEM and Raman spectroscopy. Further studies employed scanning transmission electron microscopy (STEM) energy dispersive x-ray (EDX) mapping to examine the elemental spatial distributions of Cu2ZnSnS4 nanocrystals, in order to analyse their compositional uniformity. In addition, the stability of nanocrystals synthesised using alternative ligands is investigated using Fourier transform infrared spectroscopy, without solution based ligand substitution protocol is used to replace aliphatic reaction ligands with short, aromatic pyridine ligands in order to further improve Cu2ZnSnS4 colloid stability.
A layer-by-layer spin coating method is developed to fabricate a semiconductor heterojunction, using CdS as an n-type window, which is utilised to investigate the photovoltaic properties of Cu2ZnSnS4 nanocrystals. Finally, three novel passivation techniques are investigated, in order to optimise the optoelectronic properties of the solar cells to the point where a power conversion efficiency (PCE) of 1.00±0.04% is achieved. Although seemingly modest when compared to the performance of leading devices (PCE>12%) this represents one of the highest obtained for a Cu2ZnSnS4 nanocrystal solar cell, fabricated completely under ambient conditions at low temperatures.
Role of R-loops in pause-dependent transcriptional termination of RNA polymerase II
Keywords: RNA polymerase II
R-loops
termination
pause

Transcription termination of RNA polymerase II (Pol II) in mammals requires a functional poly(A) signal and either downstream pause sites or co-transcriptional cleavage (CoTC) sequences together with 3’transcript degradation by the nuclear 5’-3’ exonuclease Xrn2. However the molecular mechanism of pause-dependent transcriptional termination is not yet fully understood. This thesis investigates the molecular role of R-loop structures in pause-dependent transcriptional termination of mammalian genes. The results described in Chapters 3 and 4 indicate that nascent transcripts form RNA/DNA hybrid structures (R-loops) behind elongating Pol II and are especially prevalent over G-rich pause sites positioned downstream of gene poly(A) signals. Senataxin, a helicase protein and the human homologue of the yeast Sen1, acts to resolve these R-loop structures and by so doing allows access of Xrn2 at 3’ cleavage poly(A) sites. This ultimately leads to efficient Pol II termination. In effect R-loops formed over G-rich pause sites, followed by their resolution by senataxin, are required for efficient pause-dependent transcriptional termination. In addition to this, the 3’ end processing factor, Pcf11 is also involved in this process. Experiments presented in the final part of this study reveal a link between R-loops and RNAi-dependent H3K9me2 formation over G-rich termination regions. Overall my results suggest that R-loop structures and the H3K9me2 repressive mark over pause regions are important features of Pol II pause-dependent transcriptional termination of mammalian genes.
Data driven approaches to improve the drug discovery process: a virtual screening quest in drug discovery
Keywords: virtual screening
drug discovery
computational chemistry

Drug discovery has witnessed an increase in the application of in silico methods to complement existing in vitro and in vivo experiments, in an attempt to 'fail fast' and reduce the high attrition rates of clinical phases. Computer algorithms have been successfully employed for many tasks including biological target selection, hit identification, lead optimization, binding affinity determination, ADME and toxicity prediction, side-effect prediction, drug repurposing, and, in general, to direct experimental work.
This thesis describes a multifaceted approach to virtual screening, to computationally identify small-molecule inhibitors against a biological target of interest. Conformer generation is a critical step in all virtual screening methods that make use of atomic 3D data. We therefore analysed the ability of computational tools to reproduce high quality, experimentally resolved conformations of organic small-molecules. We selected the best performing method (RDKit), and developed a protocol that generates a non-redundant conformer ensemble which tends to contain low-energy structures close to those experimentally observed.
We then outline the steps we took to build a multi-million, small-molecule database (including molecule standardization and efficient exact, substructure and similarity searching capabilities), for use in our virtual screening experiments. We generated conformers and descriptors for the molecules in the database. We tagged a subset of the database as `drug-like' and clustered this to provide a reduced, diverse set of molecules for use in more computationally-intensive virtual screening protocols.
We next describe a novel virtual screening method we developed, called Ligity, that makes use of known protein-ligand holo structures as queries to search the small-molecule database for putative actives. Ligity has been validated against targets from the DUD-E dataset, and has shown, on average, better performance than other 3D methods. We also show that performance improved when we fused the results from multiple input structures. This bodes well for Ligity's future use, especially when considering that protein structure databases such as the Protein Data Bank are growing exponentially every year.
Lastly, we describe the fruitful application of structure-based and ligand-based virtual screening methods to Plasmodium falciparum Subtilisin-like Protease 1 (PfSUB1), an important drug target in the human stages of the life-cycle of the malaria parasite. Our ligand-based virtual screening study resulted in the discovery of novel PfSUB1 inhibitors. Further lead optimization of these compounds, to improve binding affinity in the nanomolar range, may promote them as drug candidates.
In this thesis we postulate that the accuracy of computational tools in drug discovery may be enhanced to take advantage of the exponential increase of experimental data and the availability of cheaper computational power such as cloud computing.
Cavity expansion theory and its application to the analysis of pressuremeters
Keywords: pressuremeter

The successful application of in-situ testing of soils heavily depends on development of methods of interpretation of the tests. The purpose of this thesis is to develop a consistent theoretical basis for the interpretation of pressuremeter tests in cohesive and frictional materials. The research programme is based on cavity expansion theory with additional details provided by a large strain finite element analysis. A unified analytical solution is developed for the expansion and contraction of both cylindrical and spherical cavities in dilatant elastic-plastic soils. For the first time, explicit solutions for the pressure-expansion and pressure-contraction relationships are derived without any restriction being imposed on the magnitude of the deformation. In addition, the finite element method is adopted for solving the cavity expansion problem. This is mainly due to the fact that only in special cases when simple material models and boundary conditions are involved has it been possible to solve the problem analytically. A finite element analysis of the cone-pressuremeter test in sand is described. A series of two-dimensional finite element calculations on both the self-boring pressuremeter test and the cone-pressuremeter test is performed. In modelling the penetration process of cone-pressuremeter tests, the stresses evaluated by the cavity expansion theory are used as the starting condition for the finite element analysis. Emphasis is placed on quantifying the effects of pressuremeter geometry on derived deformation and strength parameters. In the finite element formulation, a special effort is devoted to developing a lower order finite element suitable for analysing axisymmetric elastic-plastic problems which involve incompressibility constraints. The formulation of a new six-noded isoparametric displacement finite element is presented. To account for large strain (rotation) effects, an Eulerian description of deformation is adopted and the Jaumann stress rate is used in the soil constitutive equations. The suitability of the conventional interpretation methods for pressuremeter tests is critically assessed in the light of the finite element results. Based on the numerical results, improved procedures for obtaining in-situ soil parameters from pressuremeter tests in both clay and sand have been proposed.
The role of class 1 KNOX genes in sporophyte evolution
Keywords: evolution
land plants.
development
KNOX

Land plants are characterized by the alternation of two generations: the haploid gametophyte and the diploid sporophyte. As land plants evolved from bryophytes to vascular plants, the sporophyte became the dominant generation in the life cycle. The sporophytes of bryophytes are developmentally simple structures characterized by determinate growth. In contrast, the sporophytes of vascular plants diverged to become highly variable and often complex structures with indeterminate growth.
KNOTTED1-LIKE HOMEOBOX (KNOX) genes encode homeodomain containing transcription factors that are key regulators of sporophyte development. KNOX genes are divided into two subclasses, class 1 and class 2. The critical role of class 1 KNOX genes in the apical growth of all extant land plants studied to date, suggests that modifications to class 1 KNOX gene function may have played an important role in sporophyte evolution. However, the nature of any such modifications is largely unknown. In this study, a number of cross-species complementation experiments were carried out to determine the extent to which class 1 KNOX gene function is conserved between different land plant groups. The role of KNOX genes in hornworts was also investigated because hornworts are believed to be the sister group to vascular plants.
The work presented in this thesis demonstrates that the function of class 1 KNOX genes is conserved between lycophytes and angiosperms. In contrast, the function of class 1 KNOX genes appears to have diversified between bryophytes and vascular plants. Collectively, these results indicate increased complexity of class 1 KNOX gene function during the evolution of land plants.
Investigations into the effects of neuromodulations on the BOLD-fMRI signal
Keywords: General Linear Modelling
Information Theory
Pre-clinical imaging
Functional Magnetic Resonance Imaging
Anaesthetics
Electroencephalography
fMRI
DCM
Neurovascular coupling
BOLD
EEG
Generative Embedding
Dynamic Causal Modelling
GLM
Blood Oxygen Level Dependent

The blood oxygen level dependent functional MRI (BOLD-fMRI) signal is an indirect measure of the neuronal activity that most BOLD studies are interested in. This thesis uses generative embedding algorithms to investigate some of the challenges and opportunities that this presents for BOLD imaging.
It is standard practice to analyse BOLD signals using general linear models (GLMs) that assume fixed neurovascular coupling. However, this assumption may cause false positive or negative neural activations to be detected if the biological manifestations of brain diseases, disorders and pharmaceutical drugs (termed "neuromodulations") alter this coupling. Generative embedding can help overcome this problem by identifying when a neuromodulation confounds the standard GLM. When applied to anaesthetic neuromodulations found in preclinical imaging data, Fentanyl has the smallest confounding effect and Pentobarbital has the largest, causing extremely significant neural activations to go undetected. Half of the anaesthetics tested caused overestimation of the neuronal activity but the other half caused underestimation. The variability in biological action between anaesthetic modulations in identical brain regions of genetically similar animals highlights the complexity required to comprehensively account for factors confounding neurovascular coupling in GLMs generally. Generative embedding has the potential to augment established algorithms used to compensate for these variations in GLMs without complicating the standard (ANOVA) way of reporting BOLD results.
Neuromodulation of neurovascular coupling can also present opportunities, such as improved diagnosis, monitoring and understanding of brain diseases accompanied by neurovascular uncoupling. Information theory is used to show that the discriminabilities of neurodegenerative-diseased and healthy generative posterior parameter spaces make generative embedding a viable tool for these commercial applications, boasting sensitivity to neurovascular coupling nonlinearities and biological interpretability. The value of hybrid neuroimaging systems over separate neuroimaging technologies is found to be greatest for early-stage neurodegenerative disease.
The effect of light elements on metal/silicate partitioning
Keywords: Metal/Silicate partitioning

The accretion of the Earth was marked by the high-pressure segregation of most of its core, accompanied by dissolution of about 10% of one or more “light” elements into the metallic phase. Various light elements have been proposed including S, Si, C and O, with each having an effect on the partitioning behaviour of the trace elements. Metallurgical data indicate that dissolution of even small amounts of light elements in liquid Fe can have profound effects on the activities of some trace components. For instance, significant partitioning of Si into the core of the growing Earth should have affected the observed Mo content of the mantle (Ono-Nakazato et al., 2007).
Here, I use the epsilon model of non-ideal interactions in Fe liquids (ε. I present interaction parameters (ε, derived from 1.5GPa, 1550-1650oC metal-silicate equilibration experiments, for W, Ni, Co and Mo in liquid Fe alloyed with C, and W, Ni, Co, Mo, Cu, Mn, Ag, Sb, Cd, In, Tl, Pb, Ga, Ge, Cr, V and Zn in liquid Fe alloyed with S. Additional epsilon values were taken from the steelmaking sourcebook when necessary.
I used this new data in conjunction with published metal–silicate partitioning results to develop a model of continuous accretion and core segregation taking explicit account of the partitioning of Si (this study) and O (from Ozawa et al., 2008) between metal and silicate and their effects on metal–silicate partitioning of siderophile elements. The best model for explaining the Earth’s formation including the Mo:W ratio of the silicate Earth posits that the Earth’s oxidation state increased in steps from 1 to 6.26% FeO, increasing Si in the Earth’s core and the light elements C and S being added to the planet in the last ~20% of accretion material.
Shape analysis in mammograms
Keywords: breast density
shape analysis
Breast cancer
computer aided diagnosis

The number of women diagnosed with the breast cancer continues to rise year on year. Breast cancer is now the most common type of cancer in the UK, with over 55000 cases reported last year. In most cases, mammography is the first step towards diagnosing breast cancer. However, it continues to have many practical limitations as compared to more sophisticated modalities such as MRI. The relatively low cost of mammography, together with the ever increasing risk of women contracting the disease, has led to many developed countries having a breast screening program. These routine breast screens are taken at different points in time and are called temporal mammograms. Currently, a radiologist tends to qualitatively assess temporal mammograms and look for any abnormalities or suspicious regions that might be of a concern. In this thesis, we develop an automatic shape analysis model that can detect and quantify such changes inside the breast. This will not only help in early diagnosis of the disease, which is key to survival, but will potentially aid prognosis and post treatment care.
The core to this thesis is the use of Circular Integral Invariants. We explore its multi-scale properties and use it for image smoothing to reduce image noise and enhance features for segmentation. We implement, modify and enhance a segmentation method which previously has been successfully used to acquire breast regions of interest.
We applied such Integral Invariants for shape description, to be used for shape matching as well as for subdividing shapes into sub-regions and quantifying the differences between two such shapes. We combine boundary information with the information from inside a shape, thus eccentrically transforming shapes before describing their structure. We develop a novel false positives reduction method based on Integral Invariants scale space.
A second aspect of the thesis is the evaluation of and emphasis on the use of breast density maps against the commonly used intensity maps or x-rays. We find density maps sufficient to use in clinical practice. The methods developed in this thesis aim to help clinicians in making diagnostic decision at the point of case. Our shape analysis model is easy to compute, fast and very general in nature that could be deployed in a wide range of applications, beyond mammography.
The analysis of offshore foundations subjected to combined loading
Keywords: offshore
foundation

This thesis is concerned with four different types of offshore foundations, namely gravity foundations, jack-up foundations, the mudmats for piled jacket structures and caisson foundations for jacket structures. In most applications, these can be idealised as circular rigid foundations. Unlike onshore foundations, offshore foundations are subjected to large horizontal and moment loads. This research used the finite element method to examine the elastic behaviour and stability of circular footings under combined loading. Due to the circular shape of the footings and the combination of vertical, horizontal and moment loads, three dimensional finite element analysis was used. In-depth analyses of the elastic behaviour of circular footings under combined loading (V,H,M) were performed. The vertical stiffness coefficient was investigated using two dimensional axi-symmetric analyses whereas three dimensional analyses were used to examine the other coefficients. Different features of offshore foundations such as footing embedment and cone angle were taken into consideration. Based on the numerical results, a set of empirical expressions for elastic stiffness coefficient was derived. For footing stability calculations, large horizontal or moment loads can cause the footing to lose contact with the soil, or cause the footing to slide relative to the soil. In finite element analyses, this loss of contact and sliding are modelled by interface elements. A new zero-thickness iso-parametric interface element was formulated for both two and three dimensional analyses. An exact close formed solution for integration of the stress-strain relationship (for the two dimensional interface element) was found. The element is then used to explore footing stability. It was shown that by using a yield criteria which allows the interface to behave as either frictional or cohesive interface, depending upon the normal stress, numerical stability is achieved. The footing stability was examined by establishing the bearing capacity envelope. The envelopes for footings on undrained clays were established for surface flat strip footings and for surface flat circular footings. The effects of soil strength varying with depth, cone angle and embedment on the bearing capacity envelope were also investigated.
Photocatalytic water splitting by utilising oxide semiconductor materials
Keywords: ZnO
oxide semiconductor
photoelectrochemical cell
band gap

This thesis reports the study of metal oxide semiconductors for the application of photoelectrochemical water splitting with a particular emphasis on both anion and cation-doped zinc oxides. A study of the mechanisms of visible light absorption in both anion and cation-doped ZnO semiconductors, the potentials of metal oxide materials modified by impurities as one of the ideal photocatalysts in harvesting solar light has been explored. X-ray photoelectron spectroscopy (XPS) and UV-Vis spectroscopes have been performed to establish the electronic structures of anion and cation-doped ZnO. Aluminium impurities in ZnO thin films reveal the relationship between the bandgap broadening and the so-called Burstein Moss effect. Both cadmium and sulphur dopants were incorporated in ZnO either as powders by the solid state synthesis or as thin films by spray pyrolysis technique. Cadmium and sulphur dopants demonstrate effective electronic bandgap reduction and an increasing absorption of visible light. Furthermore, the incorporation of cadmium and sulphur in ZnO were prepared as photoanodes and evaluated in a custom-built photoelectrochemical workstation for the measurement of photon energy conversion efficiencies.