VictorJuiz/thesis huggingface dataset:
Calabi-Yau threefolds and heterotic string compactification
Keywords: String theory
Calabi-Yau manifolds

This thesis is concerned with Calabi-Yau threefolds and vector bundles upon them, which are the basic mathematical objects at the centre of smooth supersymmetric compactifications of heterotic string theory. We begin by explaining how these objects arise in physics, and give a brief review of the techniques of algebraic geometry which are used to construct and study them. We then turn to studying multiply-connected Calabi-Yau threefolds, which are of particular importance for realistic string compactifications. We construct a large number of new examples via free group actions on complete intersection Calabi-Yau manifolds (CICY's). For special values of the parameters, these group actions develop fixed points, and we show that, on the quotient spaces, this leads to a particular class of singularities, which are quotients of the conifold. We demonstrate that, in many cases at least, such a singularity can be resolved to yield another smooth Calabi-Yau threefold, with different Hodge numbers and fundamental group. This is a new example of the interconnectedness of the moduli spaces of distinct Calabi-Yau threefolds. In the second part of the thesis we turn to a study of two new `three-generation' manifolds, constructed as quotients of a particular CICY, which can also be represented as a hypersurface in dP6 x dP6, where dP6 is the del Pezzo surface of degree six. After describing the geometry of this manifold, and especially its non-Abelian quotient, in detail, we show how to construct on the quotient manifolds vector bundles which lead to four-dimensional heterotic models with the standard model gauge group and three generations of particles. The example described in detail has the spectrum of the minimal supersymmetric standard model plus a single vector-like pair of colour triplets.
Growth of Galton-Watson trees with lifetimes, immigrations and mutations
Keywords: Galton-Watson process
continuous-state branching process
geometric infinite divisibility
neutral mutation
age-dependent branching
immigration
random tree
backbone decomposition

In this work, we are interested in Growth of Galton-Watson trees under two different models: (1) Galton-Watson (GW) forests with lifetimes and/or immigrants, and (2) Galton-Watson forests with mutation, which we call Galton-Watson-Clone-Mutant forests, or GWCMforests. Under each model, we study certain consistent families (Fλ)λ≥0 of GW/GWCM forests and associated decompositions that include backbone decomposition as studied by many authors. Specifically, consistency here refers to the property that for each μ ≤ λ, the forest Fμ has the same distribution as the subforest of Fλ spanned by the blue leaves in a Bernoulli leaf colouring, where each leaf of Fλ is coloured in blue independently with probability μ/λ.
In the first model, the case of exponentially distributed lifetimes and no immigration was studied by Duquesne and Winkel and related to the genealogy of Markovian continuous-state branching processes (CSBP). We characterise here such families in the framework of arbitrary lifetime distributions and immigration according to a renewal process, and show convergence to Sagitov’s (non-Markovian) generalisation of continuous-state branching renewal processes, and related processes with immigration.
In the second model, we characterise such families in terms of certain bivariate CSBP with branching mechanisms studied previously by Watanabe and show associated convergence results. This is related to, but more general than Bertoin’s study of GWCM trees, and also ties in with work by Abraham and Delmas, who study directly some of the limiting processes.
Eastern Han (AD 25-220) tombs in Sichuan
Keywords: burial
art
archaeology
Sichuan
tomb
Han China

This thesis concerns the factors underlying the popularity of the cliff tomb, a local burial form in the Sichuan Basin in China in the Eastern Han dynasty (AD 25-220). The development of the cliff tomb was held in a complex set of connections to the development of the burial forms, and existed through links to many other contemporary burial forms, the brick chamber tomb, the stone chamber tomb, and the princely rock-cut tomb. These connections and links formed to a large extent through the incorporation of the Sichuan area into the empire which began in the fourth century BC. It was in this context, a series of factors contributed to the formation and popularity of the cliff tombs in Sichuan. The hilly topography and the soft sandstone, easy to cut, provided the natural condition for the development of the cliff tombs. The decision to make use of this natural condition was affected by many factors rooted in the social background. The inherent nature of the cliff tomb structure was fully explored, which was then followed by a series of corresponding innovations on the pictorial carvings and the burial objects. The meaning of a continuous family embedded in the cliff tomb structure was explored, as the construction of the tomb was the result of the continuous endeavours from many generations of the family, and the physical form of the cliff tomb was a metaphor for a prosperous family. Following this intention of the tomb occupants underlying the design of the cliff tomb structure, the pictorial carvings and the burial objects in the cliff tomb made adaptations to make the cliff tomb an embodiment of relations between different family members and different generations.
On secularisation - structural, institutional and cultural determinants shaping individual secularisation
Keywords: inequality
secularization
international comparison
sociology of religion
modernization

This thesis deals with the determinants and mechanisms of individual secularisation processes in a cross-national perspective. In this ‘collected volume’ of six stand-alone articles, I examine religious beliefs and behaviours as well as attitudes towards religion and politics, whereby the validity of the main theories of religious change (classical secularisation theory, existential security hypothesis, supply-side explanations, historical/cultural approaches and conflict theories) are put to an empirical test. The main conclusion is that the fundamental mechanisms suggested by secularisation theories are valid and that we can identify main determinants of religiosity worldwide. However, only a combination of existing approaches is capable of explaining a broad range of the phenomena observed.
Chapter 1 (co-authored with Nan Dirk de Graaf and Peter Schmidt) deals with the fundamental mechanisms that facilitate the socialisation of religious beliefs. Under conditions of high inequality, religion acts as a source of social capital that benefits the religious socialisation of individuals outside of the family context. If levels of inequality fall, this ‘social value of religion’ is diminished and religious socialisation depends more strongly on parental efforts, thereby gradually leading to intergenerational secularisation. In Chapter 2 (co-authored with Anja Neundorf) we show that the state in Eastern Europe played a crucial role in de-establishing as well as re-establishing religious plausibility structures, which explains lower levels of religious belief in Cold War cohorts as well as the religious revival after the end of the Cold War. Chapters 3 and 4 examine the topic of religion and politics and the mechanisms behind the support for the 9/11 attacks in the Muslim world. Levels of existential security and income inequality have a strong impact on the preferences for religious politicians in a cross-sectional as well as in a longitudinal perspective. Moreover, religiosity and altruistic behaviour run the risk of being converted into pro-terrorist support under conditions of high levels of inequality and low development levels. The final two chapters show that –in a world-wide comparison development levels, inequality and the Socialist history of countries explain 75% of the variation in religiosity between countries. Furthermore, future developments in religious change will also be subject to changes in fertility. The main drivers of secularisation processes can be identified, but for the majority of the world population these conditions are not met at present, nor will they be met in the near future.
Genetic engineering of the primary/secondary metabolic interface in tobacco BY-2 cells
Keywords: Nicotiana tabacum
Tobacco
Metabolomics
Plant Cell Culture
Metabolic Engineering
Tobacco BY-2 cells
Citrate Synthase
13C MFA
Suspension Cultures
TCA cycle
HMGR
Isoprenoid Biosynthesis
Metabolic Flux Analysis
13C-FLUX
Phytosterols
GC-MS
Secondary Metabolism

The supply of precursors from primary metabolism is often overlooked when engineering secondary metabolism for increased product yields. This is because precursor supply may be assumed to be non-limiting, and it is considered difficult to engineer primary metabolism, because control of carbon flow (flux) is generally distributed among most enzymes of the pathway.
The aim of this thesis was to increase the production of sterols, part of the isoprenoid class of secondary metabolites, in tobacco (Nicotiana tabacum) Bright Yellow 2 (BY-2) cell cultures. This was achieved by genetically engineering increased activity of mitochondrial citrate synthase, an enzyme of the tricarboxylic acid (TCA) cycle that is involved in the provision of cytosolic acetyl coenzyme A, the primary metabolite precursor to sterols. Metabolic flux analysis revealed that citrate synthase exerts significant control over cyclic TCA cycle flux in BY-2 cells and suggested that increasing the activity of downstream enzymes within secondary metabolism could lead to a further redirection of TCA-cycle-derived precursors into sterol biosynthesis. Attempts were made to achieve this by genetically engineering increased activity of 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR), a key enzyme of secondary metabolism involved in sterol biosynthesis. Consistent with previous research, transgenic lines had increased sterol levels. However, the high sterol phenotype was unstable, and attempts to co-express HMGR and citrate synthase genes were unsuccessful.
The thesis demonstrates that increasing the provision of precursors to secondary metabolites can result in increased yields of those secondary metabolites but suggests that in most cases the activity of enzymes within secondary metabolism has a greater effect on those yields. It also reveals that single enzymes can exert significant control of flux within primary metabolism, although the control exerted by specific enzymes probably changes with the demands placed on metabolism.
Radiation damage in protein crystallography: susceptibility study
Keywords: radiation damage
specific damage
preferential damage
atomic displacement parameters
atomic B factors

Protein structure models obtained from X-ray crystallography are subject to radiation damage. The resulting specific alterations to protein structures can be mistaken for biological features, or may obscure actual protein mechanisms, leading to misidentification or obscuration of biological insight. The radiation chemistry behind this site-specific damage is not well understood.
Radiation damage processes progress in proportion to the dose absorbed by the crystal in the diffraction experiment. Doses can be estimated using existing software, but these assume idealised experimental conditions.
To simulate complex diffraction experiments, including treatment of imperfect X-ray beam profiles and inhomogeneous dose distributions, a new program, RADDOSE-3D, was developed. RADDOSE-3D can be integrated into beamline software to provide convenient, more accurate, comparative, and publishable dose figures, also facilitating informed data collection decisions.
There is currently no method to automatically detect specific radiation damage in protein structure models in the absence of an 'undamaged' reference model. Radiation damage research therefore generally relies on detailed observation of a few model proteins.
A new metric, BDamage, is designed and used to identify and quantify specific radiation damage in the first large-scale statistical survey of 2,704 published protein models, which are examined for the effects of local environments on site-specific radiation damage susceptibility. A significant positive correlation between susceptibility and solvent accessibility is identified.
Current understanding of radiation damage progression is mostly based on a few consecutive structure model 'snapshots' at coarse dose intervals. The low sampling rate considerably limits the ability to identify varying site susceptibility and its causes.
Real space electron density data are obtained for crystals of different mutants of a RhoGDI protein with very high sequence identity, to determine sensitising and stabilising factors for radiation induced structural changes. Utilising a newly developed data collection and analysis protocol, these changes could be tracked with unprecedented time resolution.
Laser wakefield acceleration in tapered plasma channels — theory, simulation and experiment
Keywords: Physics
Dephasing
Laser Wakefield Acceleration
Plasma density ramps
Tapering plasma channels
Particle Acceleration

Laser-plasma accelerators are of great interest because of their ability to sustain extremely large acceleration gradients, enabling compact accelerating structures. Laser-plasma acceleration is realized by using a high-intensity short pulse laser to drive a large plasma wave or wakefield in an underdense plasma.
This thesis considers the effect of axial plasma density upramps on laser wakefield acceleration. Theoretical groundwork shows that tapered plasma channels can be used to mitigate one of the main limitations of laser plasma acceleration, that is, dephasing of an electron beam with respect to the plasma wave. It is shown that it is possible to maintain an electron bunch at constant phase in the longitudinal electric fields of the laser wake field. This leads to an increased energy gain of an electron trapped in the wakefield. The required shape of the density slope is difficult to implement in experiments. Therefore, a linear density ramp is also considered which is predicted to also increase the energy gain beyond that possible in a uniform density plasma.
Towards an experimental implementation it was studied how a suitable gas density profile can be established in a capillary. This was done employing simulations using the computational fluid dynamics tool kit OpenFoam and comparing these to measurements of the axial density profile based on Raman scattering. It was demonstrated that a linear density ramp could be established by applying different pressures on the capillary gas inlets. The dependence of the density profile on the capillary parameters, such as, capillary diameter and length and inlet diameter were also studied. The results of the simulations and the measurement showed excellent agreement and demonstrate that approximately linear density ramps can be generated by flowing gas along a capillary of constant cross-section
Laser wakefield acceleration in plasmas with longitudinally varying density was investigated in an experiment at the Astra Laser at Rutherford Laboratories. The experiment utilised ionisation injection in order to operate in the mildly non-linear regime of laser-wakefield acceleration. The measured electron energies agree well with the theoretical predictions. It was demonstrated that an increase in the energy gain can be obtained by driving the accelerator in a ramped plasma, the electron spectrum is more narrow and the injected charge increases significantly.
Measurements of the X-ray spectrum emitted by the betatron motion of the accelerated electron bunch allowed the transverse radius of the bunch to be deduced. These measurements showed that retrieved electron bunch radius is inversely proportional to the longitudinal density gradient, that is a plasma density upramp (downramp) has a decreased (increased) electron bunch radius.
A history of the Molemas, African notables in South Africa, 1880s to 1920s
Keywords: Indirect Rule
History of the British Empire in Bechuanaland
Family History
Silas Molema

This thesis is a family history of Silas Molema and his three children from the late 1880s to the late 1920s. The Molemas were a family of devout Methodists and educated chiefs in Mafikeng north of British Bechuanaland (part of the Cape colony in 1895) but they held extensive landholdings across the border in the Bechuanaland Protectorate. The thesis explores education, landholding and political office as strategies through which the Molemas attempted to maintain their position of class, status and power. Chiefs perceived formal annexation by Britain in 1885 also as opportunity to pursue greater self-determination, preserve the institutions of chiefly rule, and sustain respectable livelihoods. These aspirations had come to be experienced and understood as sechuana, which was a fluid reconstruction of tradition that helped Molemas and other Bechuana notables straddle incongruous cultural spheres along a racially and ethnically diverse colonial frontier. The thesis argues that nationhood was a key identification through which Molemas and other educated Bechuana saw themselves, and considers why they imagined their nation within the British Empire. The thesis also points to the various historical transformations and private entanglements that enmeshed various conceptions of nationhood into the everyday experience of the family as an emotive and socialising institution. These sentiments of nationhood profoundly shaped this family’s self-understanding, and mediated the choices children made about work, marriage and other significant relationships. The challenge to transfer inherited privilege across generations shaped identities, intersected with the reconfiguration of the local political economy, and impinged upon structural transformations in southern Africa.
Cavity ringdown spectroscopy for broadband and microfluidics applications
Keywords: condensed phase
detection
cavity enhanced
pH
kinetics
spectroscopy
gas phase
microfluidics
broadband
supercontinuum
cavity ringdown

Cavity Ringdown Spectroscopy (CRDS) is a highly sensitive, absorption spectroscopy technique. From the measurement of the decay of light within an optical cavity, spectroscopic parameters of an absorbing sample can be determined. Thus far the technique has mostly been applied to gas-phase samples. The work described in this thesis attempts to extend the technique to the condensed phase. A supercontinuum source and streak camera detector were used to enable broadband measurements (~ 500 – 600 nm) of the absorption spectra of gaseous NO2 and I2 samples. The setup had a detection sensitivity of 20 ± 7 ppm, and was capable of making an accurate measurement of the wavelength-dependent reflectivity of the cavity mirrors. Microfluidic devices have been employed in a range of fields for purposes including small volume organic synthesis, environmental monitoring and medical diagnosis. They enabled us to make measurements on condensed phase samples by integrating a ‘test’ microfluidic chip into a single wavelength CRDS setup and flowing liquid through its channels. Using a series of rhodamine 6G solutions the detection sensitivity of our setup was determined to be (4.2 ± 0.3) x 10-6 M, with a sample volume of 12.3 nL. The technique was also used to measure the titration curve of phenolphthalein prepared in a series of buffer solutions with pHs ranging from 7.7 to 11.0, and was capable of determining the pH of nanolitre samples to an accuracy of ± 0.028. In the final set of measurements reported here, the technique was used to follow the kinetics of the iodine clock reaction. The results showed good agreement with bulk measurements made using a single-pass spectroscopic technique.
'Le parfait Ambassadeur'. The theory and practice of diplomacy in the century following the Peace of Westphalia
Keywords: diplomacy
diplomats
Peace of Westphalia
international relations
political science

This thesis examines the theory of diplomacy in the formative phase of the European states-system. From the viewpoint of the discourse on the 'ideal ambassador', it explores early modern diplomacy as cultural history encompassing ideas, discourses, perceptions and 'codes'. The scope of study is the century following the Peace of Westphalia (1648), and three states and regions (France, Britain, the Holy Roman Empire) serve as case studies for a comparative approach of diplomatic theory and practice. In five parts, the adaptation of the theory and practice of diplomacy to the new demands of international relations after 1648 are considered. The first section sets the stage by illustrating that the mid-seventeenth century was regarded as a turning point in the practice of diplomacy. Part II examines diplomatic theory as a particular 'language' in its intellectual and socio-professional contexts. While published treatises on the 'ideal ambassador' build the core of this study, related genres of international law theory, ceremonial theory and political and state science are also taken into account. From the viewpoint of this diplomatic theory, the following section examines the ways in which the instruments and practices of diplomacy were aligned to the new framework. These ranged from changes in the structural framework of diplomacy to the evolution of norms and procedures of negotiation, international law and ceremonial. Part IV reconsiders the issue of 'professionalism' in diplomatic theory with regard to the preparation and training of diplomats. Special attention is given to proposals for diplomatic 'academies', which are for the first time examined in comparison. Finally, section V recasts the findings of this thesis in a comparative perspective. It underlines that, with the emergence of a states-system, the techniques of diplomacy became formalised and uniform, constituting a common European diplomatic practice. Against the background of the different regional and structural conditions, the alleged model role of France in the evolution of diplomatic theory and practice is re-evaluated.