VictorJuiz/thesis huggingface dataset:
Impact of tidal turbine support structures on realizable turbine farm power
Keywords: CFD
tidal

This thesis discusses the importance of tidal turbine support structures through analytical and computational modelling. A head-driven analytical channel model was first developed to determine the sensitivity of the flow to the presence and type of support structures. It showed that there was a significant potential reduction in farm power output even when only considering approximate force coefficients for rotor and support structure. To confirm these findings, computational simulations were performed on a full-scale turbine to obtain more accurate force coefficients considering full rotor-support structure interactions.
The flow interaction effects between the rotor and its support structure were studied using Computational Fluid Dynamics (CFD) for different support structure shapes for a range of tidal velocities including the power-capping zone. The integrated rotor force coefficients were higher in the presence of the cylindrical support structure than the elliptical support due to the higher opposing thrust from the cylinder in the channel redirecting the flow and increasing the flow velocity over the top half of the rotor. The presence of rotor caused a drop in the stream-wise forces on the support structure. The amplitude of the stream-wise sectional forces along the support structure height was lower in the case of an elliptical than a circular cylinder due to more streamlined shape of the ellipse.
At device scale, the computational model was used to study the turbine performance in the power-capping zone by pitching the blades to feather. The influence of pitch-to- feather power-capping strategy was examined by studying the forces and angle of attack on the turbine blades, and the wake at three different blade pitch angles. Increasing blade pitch angle resulted in a significant drop in the average load on the blade. Also since the tidal channel flow has a shear in its velocity profile, the influence of shear on turbine performance was studied by comparing it to the same turbine in a uniform flow.
The analytical channel flow model was used to investigate the characteristics of tidal stream energy extraction for large tidal farms deployed in tidal channels with specific focus on the limitations to realizable farm power due to turbine support structure drag and constraints on volume flow rate reduction. The force coefficients dataset from computational modelling was used to obtain a better estimate of the farm power output. Support structures were seen to contribute significantly to the overall resistive force in the channel and thus reduce the overall flow rates in the channel, leading to losses in realizable power. Over a wide range of channel characteristics, realistic levels of support structure drag lead to up to a 10% reduction in realizable power, and an associated reduction in the number of turbines that can be economically installed.
Conservation planning in Europe: ecological, financial, and political challenges
Keywords: Species Distribution Modelling
Conservation
Europe
Biodiversity
Environmental framework agreements

Conservation of biodiversity and sustainable resource use are central aims within ecology. This thesis focuses on the current data and environmental frameworks used to support these aims across different states in Europe. In particular, it examines the impact of geo-political boundaries on data-use, funding and planning for temporal movement of species in response to climate change. It also examines the current environmental framework agreements in Europe and their capacity to deal with trans-boundary aspects of biodiversity change.
Through examination of European biodiversity datasets, undertaking species distribution modelling of forest taxa, examining economic data, palaeo-ecological data, and assessing international environmental framework agreements, this thesis identifies a number of important knowledge gaps. Probably unsurprisingly, the distribution of biodiversity in Europe mostly does not match political entities, all of which have individual aims, financial resources, and biodiversity management regimes in place. All have a significant impact on biodiversity conservation planning because i) the use of geo-politically truncated data influences modelling predictions, ii) financial commitment to biodiversity conservation varies between countries influencing success outcomes, iii) biodiversity persistence in current and future climate change does not recognise geo-political boundaries, and iv) many of the key environmental frameworks are implemented within countries and do not considering trans-boundary issues.
Overall these findings significantly improve the understanding of conservation and resource management in Europe and fill a number of important knowledge gaps. They highlight the importance of appropriate trans-boundary ecological datasets and the need for more consistency across Europe in financial resources for biodiversity conservation. They also highlight the need for appreciation of areas of high-persistent biodiversity regardless of geo-political boundaries and environmental framework agreements that support cross-border conservation measures.
Systems within systems – free and open source software licences under German and United States law
Keywords: Open Source Software
FOSS
United States Law
FOSS Licensing
Free Software
German Law

Free and Open Source Software (FOSS) licences channel the exclusionary and individualising force of copyright to establish a qualitatively different, somewhat subversive, system for the exploitation of software. This thesis examines how it is that FOSS licences establish this 'system within a system' under both German and United States law. The inquiry begins with a detailed examination of FOSS licence templates as the instruments which transform code from its default position as the 'res' of proprietary relations to its status as 'open' or 'free'. The thesis then considers whether FOSS licence templates, as the legal basis for this subversive move, are valid and enforceable under domestic law. In addressing this question, the thesis undertakes a critical analysis of the leading case law in each jurisdiction. Going beyond the immediate case law, the thesis considers the broader systemic effects of FOSS licence enforcement. It highlights how building a system within a system foments certain tensions and contradictions within the law, in turn giving rise to unintended consequences and legal uncertainty. By highlighting these tensions, the thesis argues that the questions of FOSS licence enforcement in Germany and the United States may not be as settled as some may think.
iASPP in the balance between tolerance and autoimmunity
Keywords: P53
iASPP
Apoptosis

Maintenance of immunological homeostasis between tolerance and autoimmunity is essential for the prevention of human diseases ranging from autoimmune disease to cancer. Adaptive immune responses require both antigenicity and adjuvanticity, and cell death can critically influence immunological homeostasis by modulating the adjuvanticity it elicits. Accumulating evidence suggests that in addition to inducing apoptosis, p53 mitigates phagocytosis-induced adjuvanticity thereby promoting tolerance following physiologic tissue turnover. Here I identify Inhibitor of Apoptosis Stimulating p53 Protein (iASPP), a negative regulator of p53 transcriptional activity widely considered to be oncogenic, as a novel master regulator of immunological tolerance. Surprisingly, iASPP deficiency promoted oncogenic K-ras driven lung adenocarcinoma and pancreatic cancer tumorigenesis, while iASPP deficient mice were less susceptible to autoimmune disease. Furthermore, immune responses to iASPP-deficient tumors exhibited hallmarks of immunosuppression, including activated regulatory T cells and exhausted CD8+ T cells, and iASPP-deficient CD4+ T cells were less responsive to TCR engagement in vitro. Interestingly, iASPP-deficient tumor cells, myeloid cells, CD4+, and γδ T cells expressed elevated levels of PD-1H, a recently identified transcriptional target of p53 that promotes tolerogenic phagocytosis. These findings suggest that iASPP can inhibit p53-mediated immunosuppressive PD-1H cross-talk between malignant cells, phagocytes, and responding immune cells, thereby promoting adjuvanticity following phagocytosis. Identification of a novel iASPP/p53 axis of immune homeostasis provides an exciting therapeutic opportunity for both autoimmune disease and cancer.
RNA-based engineering of inducible CRISPR-Cas9 transcription factors for de novo assembly of eukaryotic gene circuits
Keywords: RNA engineering
CRISPR
synthetic biology
transcription factor
genome engineering

Synthetic biology in mammalian cells holds great promise for reverse engineering biological processes and rewiring cellular behaviors for therapeutic purpose. An essential aspect in our ability to reprogram the cellular code is the availability of highly orthogonal, inducible transcriptional regulators. CRISPR-based strategies employing effector-domain tethering to the single guide RNA (sgRNA)-dCas9 complex have greatly advanced this field by allowing for precise activation or repression of any gene via simple sgRNA reprograming. However, the implementation of inducible CRISPR-based transcriptional regulators (CRISPR-TRs) has so far been restricted to dCas9 protein engineering and conditional effector tethering. Although elegant, these approaches are limited by dCas9 promiscuous loading of sgRNAs, which hinders their use for the creation of independent multi-gene transcriptional programs.
To address this limitation, I have developed a modular framework for the rational design of inducible CRISPR-TR, based on simple and reversible modifications of the sgRNA sequence. At the core of this conceptual framework lies the ability to inactivate native sgRNAs by appending on their 5’-end a short RNA segment, which folds to form a spacer-blocking hairpin (SBH). Base-pairing between the extension and the sgRNA spacer prevents docking of the CRISPR-TR on-target, fully abrogating its activity. Subsequently, I have created inducible SBH variants (iSBH) by replacing the hairpin loop with conditional RNA cleaving units. Using a variety of sensing-loops, I was able to engineer a panel of switchable iSBH-sgRNAs, designed to activate specifically in the presence of protein, oligonucleotide, and small molecule inducers. Leveraging the versatility of this method, I demonstrate that iSBH-sgRNAs expression can be multiplexed to assemble synthetic gene circuits implementing parallel and orthogonal regulation of multiple endogenous gene targets. Finally, I have distilled the design principles derived throughout this project to develop a web tool that automates the creation of iSBH- sgRNAs. Already a valuable addition to the synthetic biology toolkit, iSBH-based inducibility should in theory also be applicate to all CRISPR-Cas9 derivatives (genome editing, epigenetic alteration, DNA labelling, etc.) as well as other newly characterized RNA-guide nucleases from the CRISPR family.
Cultural appropriation in Messiaen’s rhythmic language
Keywords: Traité de rythme, de couleur, et d'ornithologie
Sarangadeva
Hindu symbolism
Saṅgītaratnākara
Sept Haïkaï
Śārṅgadeva
Turangalîla-Symphony
Encyclopédie de la musique et dictionnaire du Conservatoire
decitalas
Messiaen, Olivier, 1908-1992
Technique de mon langage musical
Turangalîla-Symphonie
Non-retrogradable rhythms
Sangita Ratnakara
Greek meter
Sept Haikai
Animal symbolism
Deśītālas
Indian rhythm
Cultural Appropriation
Le Tombeau resplendissant
Harold Bloom
Les Offrandes oubliées

Bruhn (2008) and Griffiths (1978) have referred in passing to Messiaen’s use of non-Western content as an appropriation, but a consideration of its potential moral and aesthetic failings within the scope of modern literature on artistic cultural appropriation is an underexplored topic. Messiaen’s first encounter with India came during his student years, by way of a Sanskrit version of Saṅgītaratnākara (c. 1240 CE) written by the thirteenth-century Hindu musicologist Śārṅgadeva. I examine Messiaen’s use of Indian deśītālas within a cultural appropriation context. Non-Western music provided a safe space for him to explore the familiar, and served as validation for previously held creative interests, prompting the expansion and development of rhythmic techniques from the unfamiliar.
Chapter 1 examines the different forms of artistic cultural appropriation, drawing on the ideas of James O. Young and Conrad G. Brunk (2012) and Bruce H. Ziff and Pratima V. Rao (1997). I consider the impact of power dynamic inequality between ‘insider’ and ‘outsider’ cultures. I evaluate the relation between aesthetic errors and authenticity. Chapter 2 considers the internal and external factors and that prompted Messiaen to draw on non-Western rhythm. I examine Messiaen’s appropriation of Indian rhythm in relation to Bloomian poetic misreading, and whether his appropriation of Indian rhythm reveals an authentic intention. Chapter 3 analyses Messiaen’s interpretation of Śārṅgadeva’s 120 deśītālas and its underlying Hindu symbolism. Chapter 4 contextualises Messiaen’s Japanese poem Sept haïkaï (1962) in relation to other European Orientalist artworks of the late-nineteenth and early-twentieth centuries, and also in relation to Michael Sullivan’s (1987: 209) three-tiered definitions of japonism.
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Finite element limit analysis of offshore foundations on clay
Keywords: geotechnics
finite element analysis
finite element limit analysis
caisson
cohesive soil
limit analysis
adaptive mesh refinement
capacity analysis
mudmat
undrained clay
offshore foundations
plastic capacity

Capacity analysis is a common preliminary step in the design of offshore foundations. Inaccuracies in traditional capacity analysis methods, and the advancement of numerical modelling capabilities, have increasingly led designers to optimise foundations using more complex methods. In this thesis, the ultimate limit state capacity of a range of foundation types is investigated using finite element limit analysis.
Novel three-dimensional finite element limit analysis software is benchmarked against analytical solutions and conventional displacement finite element analysis. It is then used to find lower and upper bounds of foundation capacity, with adaptive mesh refinement used to reduce the bound gap over successive iterations of the solution. Rigid foundations subjected to short term loading on clay soil are analysed. The undrained soil is modelled as a rigid--plastic von Mises material, and attention is given to modelling any normal and/or shear stress limits at the foundation/soil interface.
Shallow foundations, suction anchor foundations, and hybrid mudmat/pile foundations are considered. Realistic six degree-of-freedom load combinations are applied and results are reported in the form of normalised design charts, and tables, that are suitable for use in preliminary design. Relationships between loading combinations and failure mechanisms are also explored. A number of case studies based on authentic foundation designs are analysed. The results suggest that finite element limit analysis could provide an attractive alternative to displacement finite element analysis for preliminary foundation design calculations.
Aspects of frustrated magnetism
Keywords: frustrated magnetism

Models of magnetism show complex collective behaviour which arises from simple interactions among microscopic degrees of freedom. Upon cooling from high temperatures conventional magnets typically undergo a phase transition to a magnetically ordered phase due to microscopic interactions which favour an ordered state. In frustrated magnets however, competing microscopic interactions place non-trivial constraints on the allowed configurations at low temperature, without selecting a unique ordered state.
In this thesis, we investigate the collective behaviour of a paradigmatic frustrated magnet, the classical Heisenberg model on the pyrochlore lattice with antiferromagnetic nearest neighbour interactions. Within a self consistent Gaussian approximation, we derive analytic expressions for correlation functions which match Monte Carlo simulations extremely well at all temperatures. We study the precessional dynamics of the model and provide a comprehensive description of the dynamics by constructing an analytically tractable stochastic model by extending the self-consistent Gaussian approximation to include dynamics. We relate these results to other highly constrained models.
Real experimental systems often have features that go beyond the phenomenology afforded by the simplest models; we investigate the effects of further neighbour interactions on paramagnetic spin correlations, and propose further neighbour interactions as the mechanism underlying experimentally observed patterns of scattering in frustrated spinel compounds.
In the dynamics linearized around a ground-state, the macroscopic degeneracy of the classical model leads to modes with zero frequency. Small perturbations stabilize ordered states and lift such zero modes to finite frequency. The ordered state has two widely separated energy scales both of which affect the dynamics, the leading scale of nearest neighbour exchange coupling, and the much smaller scale of the perturbation which relieves the frustration. We investigate the interplay between these widely different energy scales in setting the mode frequencies in states ordered by weak interactions.
On the mesoscale plasticity of nickel-base superalloy single crystals
Keywords: Laue diffraction
Dislocation Dynamics
Single crystal
Superalloy
X-ray Crystallography

Experimental micromechanics of materials is a branch of science that seeks to build tight connections between composition, structure, processing and performance of materials under specific operating conditions required for particular technology applications. The present project is focused on the development of techniques that use the combination of electron, ion and X-ray microscopies to study the deformation behaviour of a particularly important class of metallic alloys used in the manufacture of aeroengines, namely, the so-called Ni-base superalloys. The complex hierarchical structure of these materials means that their macroscopic response is controlled to a great extent by the phenomena that play out on very fine scales, from angstroms (lattice spacing dimension) to nanometres (precipitates, phase boundaries, dislocations, chemical inhomogeneities) to microns (grains and their boundaries, defects and their clusters, dislocation pileups) to millimetres (component scale). Understanding the fine structure and deformation behaviour requires the development of specially configured experimental setup that allow the observation and quantification of deformation to external loading.
In this study, FIB-SEM methods for sample characterization and fabrication were combined with synchrotron-based X-ray diffraction and imaging techniques, and backed up by theoretical analysis and numerical simulation, to elucidate the origins of the strength of these alloys. Micropillar compression tests using in-SEM nanoindentation were used to reveal the size dependence of the apparent strength, and connection was made with the dislocation-mediated crystal slip to provide an explanation of the observed Hall-Petch type dependence with a modified Hall-Petch equation considering both intrinsic and extrinsic characteristic lengths introduced. X-ray scattering was used in the polychromatic micro-Laue mode and using Bragg coherent diffractive imaging to reveal the crystal distortion arising due to plastic deformation. A Discrete dislocation dynamics in the 2.5D formulation was used to obtain a model description of the observed phenomena. The key outcome of the work presented in this thesis lies in the successful development of advanced observational tools and relevant theoretical or computational models for mesoscale plasticity problems for crystal with complex microstructure.
Understanding antibody binding sites
Keywords: Protein Structure
Sequences
Antibodies
Complementarity Determining Regions
Protein Binding

Antibodies are soluble proteins produced by the adaptive immune system to bind and counteract invading pathogens. The binding properties of a typical human antibody are determined by the structure of its variable domain, composed of two chains – heavy and light and by the conformation of six loops located on the surface of the variable domain, known as Complementarity Determining Regions (CDRs).
In the first chapter, we describe our analysis of the conformational space occupied by five out of six antibody CDRs (L1, L2, L3, H1 and H2) and the development of a novel, length-independent method for grouping these CDRs into structural clusters (canonical forms). We show that using our method we can increase coverage and precision of assigning CDR sequences into clusters.
In the next chapter, we describe a method for ranking structural decoys of the CDR-H3 loop. We show that by computationally perturbing CDR-H3 decoys we can improve the performance of existing ranking methods. In the same chapter, we discuss the development of a method for high-throughput assignment of heavy-light chain orientation. The power of the method was demonstrated by assigning orientation to billions of potential Fv sequences.
The third Chapter describes the analysis of a large dataset of CDR sequences with the aim of identifying sequence patterns responsible for the loops’ structure. Using a neural network methodology, we found several groups of CDR sequences which might be indicative of previously-unseen conformations.
In the final results Chapter, we describe how we used the structural knowledge developed throughout the rest of the thesis to create a novel pipeline for computational antibody design. We show that the binders developed using our methodology had similar features to available antibody therapeutics and low predicted propensity to cause an immunogenic response. These results demonstrate the potential for using computational methods for designing high affinity therapeutics with human properties.