VictorJuiz/thesis huggingface dataset:
Magmatism and glacial cycles: coupled oscillations?
Keywords: Pleistocene
Earth System Model
MOR
Mantle Dynamics
Volcanism
Paleoclimate
Radiative Forcing
Geophysics
Climate Modelling
Glacial cycles
Greenhouse
Climate Modeling

The Earth's climate system is driven by varying insolation from the Sun. The dominant variations in insolation are at 23 and 40 thousand year periods, yet for the past million years the Earth’s climate has glacial cycles at approximately 100 kyr periodicity.
These cycles are a coupled variation in temperature, ice volume, and atmospheric CO2. Somehow the Earth system’s collective response to 23 and 40 kyr insolation forcing produces 100 kyr glacial–interglacial cycles.
Generally it has been assumed that the causative mechanisms are a combination of ice dynamics (high ice reflectivity controlling temperature) and ocean circulation (changing carbon partitioning between the deep ocean and the atmosphere, and heat transport to the poles). However, these proposed mechanisms have not yet resulted in a compelling theory for all three variations, particularly CO2.
This thesis explores the role of volcanic CO2 emissions in glacial cycles. I calculate that glacial-driven sea level change alters the pressure on mid-ocean ridges (MORs), changing their CO2 emissions by approximately 10%. This occurs because pressure affects the thermodynamics of melt generation.
The delay between sea level change and the consequent change in MOR CO2 emissions is several tens-of-thousands-of-years, conceptually consistent with a coupled non-linear oscillation that could disrupt glacial cycles from a 40 kyr mode to a multiple of that period.
I develop an Earth system model to investigate this possibility, running for approximately one million years and explicitly calculating global temperatures, ice sheet configuration, and CO2 concentration in the atmosphere. The model is driven by insolation, with all other components varying in response (and according to their own interactions).
This model calculates that volcanism is capable of causing a transition to ˜100 kyr glacial cycles, however the required average volcanic CO2 emissions are barely within the 95% confidence interval. Therefore it is possible for volcanic systems and glacial cycles to form a 100 kyr coupled oscillation.
Mercenaries, missionaries and misfits: Competition in the ‘aid marketplace’ in Afghanistan.
Keywords: Refugees
Aid Marketplace
Afghanistan
Reintegration
Humanitarian Aid
UNHCR
International Development
Returnees

Both practitioners and academics have recently begun referring to humanitarian agencies operating within an active ‘aid marketplace’ in which limited funding pits actors against each other in pursuance of their own projects and wider aims. This thesis seeks to explore how the pressures of a competitive environment impact on the motivations and actions of aid actors at an individual and organizational level. Based on the common saying that aid workers are ‘mercenaries, missionaries and misfits’, I construct a typology of pressures (interest-based, altruistic, and bureaucratic), which, it is argued, can be used to explain and understand much of this competitive and collaborative behaviour. A particular focus of the thesis is the impact of these various influences on the process and politics of information transfer and discourse creation regarding the process of needs assessment, monitoring and evaluation. I explore all of these issues through the medium of a case study of UNHCR’s interventions in Afghanistan between 2001 and 2015, and seek to provide a detailed history of the agency’s activities, politics and challenges during this period. In particular I am interested in the motivations driving the agency’s actions; the strategies it has employed to achieve its aims; the calculated narratives that it has crafted to justify its interventions and attract greater support; and the very different ways in which it has approached the needs of different categories of displaced people.
Self-assembly in mechanical systems
Keywords: Membrane remodelling
Nonlinear continua
Self-assembly

Inspired by biological membrane shaping in the cell through means of curvature-inducing proteins, we investigate the interplay between membrane curvature and the distribution and movement of shape-inducing objects which are free to move as a consequence of the underlying shape. We initially study the self-assembly of a filament, taken as a proxy for the cross-section of a biomembrane, which is primarily driven by the chemical kinetics of attaching proteins and find that, under certain mechanical stiffness regimes of the attaching proteins, pattern formation occurs. Regions of high and low protein concentration form before spatially uniform filament shapes are obtained by means of protein adhesion and movement governed by diffusion and local curvature-seeking. However, noting that the curvature-mediated protein movement on membranes has been biologically observed to be long-range, we next study the self-assembly of embedded inclusions on a membrane as a result of the underlying geometry. We first derive an interaction law for the shape-mediated interaction of inclusions which break symmetry and find that there is a finite equilibrium distance to which the inclusions will aggregate. We derive corresponding equations of motion which describe this curvature-mediated aggregation mechanism and, using this framework, we investigate some of the properties of these self-assembled configurations, including their energy, stability, and their collective elastic behavior. Lastly, we consider the interaction energies of embedded inclusions on a periodic domain and determine that this mechanism may explain computational results of how proteins form rings to promote tubulation on cylindrical membranes.
Synthesis and post-polymerisation modification of degradable polymers based on polycarbonates/polyesters prepared using ring-opening copolymerisation
Keywords: post-polymerisation modification

This thesis describes the synthesis of degradable materials based on functional aliphatic polycarbonates/polyesters synthesised via ring-opening copolymerisation (ROCOP) and post-polymerisation modifications.
Chapter 3 details the synthesis of cationic poly(ester-b-carbonate-b-ester) via ringopening copolymerisation of CO2 and vinyl-cyclohexene oxide (v-CHO), ringopening polymerisation (ROP) of rac-lactide, and subsequent post-polymerisation modifications of this material through a radical thiol-ene reaction and a quaternisation reaction. These cationic polymers show high surface zeta-potential (> 40 mV) and display effective antibacterial properties with killing efficiencies of > 99.9% against Gram-negative bacteria Escherichia coli.
Chapter 4 describes the synthesis of amphiphilic block poly(phosphoester-b-carbonate-b-phosphoester)s using ROCOP of CO2 and v-CHO and ROP of ethyl ethylene phosphate (EP). These amphiphilic block polymers self-assemble into either micelles or vesicles, depending on the hydrophobic/hydrophilic block ratio. The potential use of the vesicles in drug delivery is also described, and initial results detailing the enzymatic degradation of these vesicles are presented. In addition, the hydroboration-oxidation is investigated as a new post-polymerisation modification method to functionalise an alkene-containing polycarbonate, poly(vinylcyclohexene carbonate) (VPC). The hydroxyl functionalised polycarbonate shows improved hydrophilicity and cell adhesion, compared to the unfunctionalised precursor. The side chain hydroxyl groups are then tested for making graft poly(carbonate-g-phosphoester).
Chapter 5 further investigates the use of the hydroboration-oxidation reaction in functionalising poly(cyclohexadiene carbonate) (CPC) and poly(vinylcyclohexenemaleate) (V,MPE). A selective post-polymerisation modification is also demonstrated on a blend of CPC and VPC or V,MPE featuring both terminal and internal alkene groups using the hydroboration-oxidation method, where the terminal alkene groups are functionalised exclusively. Lastly, an orthogonal post-polymerisation approach is carried out on the unreacted internal alkene groups of hydroxyl-containing V,MPE via thiol-ene reactions to install other functional groups such as carboxyl, amine and methoxy-poly(ethylene glycol).
The arithmetic geometry of mirror symmetry and the conifold transition
Keywords: L-function
Mirror symmetry
limit mixed Hodge structure
large complex structure limit
Calabi-Yau threefold
mixed motives
conifold

The central theme of this thesis is the application of mirror symmetry to the study of the arithmetic geometry of Calabi-Yau threefolds. It formulates a conjecture about the properties of the limit mixed Hodge structure at the large complex structure limit of an arbitrary mirror threefold, which is supported by a two-parameter example of a self-mirror Calabi-Yau threefold. It further studies the connections between this conjecture with Voevodsky's mixed motives. This thesis also studies the connections between the conifold transition and Beilinson's conjecture on the values of the L-functions at integral points. It carefully studies the arithmetic geometry of the conifold in the mirror family of the quintic Calabi-Yau threefold and its L-function, which is shown to provide a very interesting example to Beilinson's conjecture.
Policing human rights: law, politics and practice in Northern Ireland
Keywords: Transitional Justice
Northern Ireland
Policing
Human Rights

Human rights are a defining feature of how the Police Service of Northern Ireland (PSNI) has been 'imagined and made' in its post-conflict society. This thesis marks the first attempt to make sense of how human rights are articulated, interpreted and applied by those intimately involved in Northern Irish policing. Based on extensive access to the PSNI, I marshal qualitative data collected from interviews with over one hundred police officers from various departments. I tour four sites of local policing to expose and examine the vernaculars and practices of human rights that lurk within each. The story I tell over the course of eight chapters is one of a police service trying to sustain human rights as a central narrative to explain its daily work and build its organisational identity in a divided society, to varying degrees of success. I argue that human rights are, in fact, a malleable, contested and conditional concept to 'imagine and make' a police service and regulate the decision-making of its officers; perhaps much more so than police reformers in Northern Ireland had realised or the PSNI wish to acknowledge.
In the first half of the thesis, I identify and deconstruct how the PSNI's chief officers and local political parties seek to express and mobilise competing visions, values and agendas through human rights narratives. I then pay close attention to how human rights are interpreted and translated by junior officers performing two forms of routine policing in N.Ireland: the 'dirty work' of the Tactical Support Group and the 'community work' of Neighbourhood Policing Teams. I ask to what extent officers have internalised human rights as way of making sense of their daily work. In the second half of the thesis, I explore police officers as an important, but poorly understood, class of human rights practitioner. To better grasp how officers interpret and apply human rights standards, I closely analyse two sites of policing where distinct schemes of human rights-based regulation exist: public order policing and police custody. This thesis contributes to understandings of the concept of human rights, its interactions with law and politics and the condition of policing in contemporary Northern Ireland.
The making and breaking of SAS-6: structural insights and inhibitor search for n-terminal domain dimerisation
Keywords: Centriole
SAS-6
Inhibitor Screening
STIL
Protein Dimerisation

SAS-6 is the structural core of the forming centriole - a cylindrical protein complex, which is an essential component of the centrosome. Oligomerisation of SAS-6 is crucial for successful centriole duplication and is achieved through two dimerisation domains in the SAS-6 protein; a long C-terminal coiled-coil domain and a globular N-terminal dimerisation domain. As core components of the centrosome, centrioles help facilitate various cellular functions. They are involved in the anchoring of flagella and cilia to the membrane and in coordinating the spindle apparatus during chromosome segregation. A deeper insight into the molecular mechanisms at play in the centriole duplication process would have implications on our understanding of fundamental cell division processes and a number of related diseases.
Here the involvement of an unstudied loop region in the C. elegans SAS-6 N-terminal domain dimerisation is described. Combining structural biology, biophysical and computational techniques, the molecular interactions of this loop were explored, contributing to the oligomerisation of SAS-6 at the N-terminal dimer interface. Furthermore, the screening and testing of small molecule inhibitors of the SAS-6 N-terminal domain dimerisation is described, targeting a hydrophobic pocket in the domain. Two candidate compounds are presented as a result of the screens and next steps towards structure based compound design are suggested, based on computational analysis. The search for inhibitory compounds includes a set-up of an in-house virtual screening pipeline, as well as in vitro screening efforts and a new crystallographic structure of the H. sapiens SAS-6 N-terminal domain. By investigating the making and breaking of the SAS-6 N-terminal domain dimerisation, light is shed on so far neglected details of this essential protein-protein interaction and advancements towards a SAS-6 oligomerisation inhibitor described, which could ultimately be used for new approaches in cell cycle research and might open up new avenues for medical research by binding a disease relevant target.
Exploration of DNA systems under internal and external forcing using coarse-grained modelling
Keywords: DNA nanotechnology
single molecule force spectroscopy
non-equilibrium physics
molecular dynamics
DNA
force-extension curve
oxDNA

The profound simplicity and versatility of the molecule at the heart of all earth- bound life forms, DNA, continues to inspire new frontiers of scientific inquiry. Central to many of these, including the de novo design of novel DNA nanostructures and the use of DNA to probe the principles of biological self-assembly and the operation of cellular nanomachines, is the interaction of DNA with forces, both internal and external. This thesis comprises a survey of three key ways coarse- grained simulations using the oxDNA model can contribute to efforts to characterize these interactions. First, a non-equilibrium data analysis framework based on the Jarzynski equality from statistical physics is validated for use with oxDNA through the reconstruction of free energy landscapes for canonical DNA hairpin systems. We provide a framework for assessing errors in the method and apply it to study a system for which conventional equilibrium simulations would be impractical: DNA origami ‘handles’ proposed for use in force spectroscopy experiments. Next, we simulate the forcible unravelling of three DNA origami structures, the largest systems yet studied with simulated force spectroscopy. We combine these results with experimental AFM data to probe the mechanical response of origami in unprecedented detail, highlighting the effect of nanostructure design on unfolding behaviour. Lastly, we examine the validity of using widely-employed polymer elastic models to predict internal entropic forces in ssDNA. We develop a framework for measuring internal forces in the oxDNA coarse-grained model and apply it to analyze the pico-Newton range forces exerted by a recently proposed DNA origami force clamp, ultimately concluding that conventional means of estimating internal ssDNA forces are often inaccurate and should be supplemented with coarse-grained simulations. In addition to providing new insights about the DNA systems we present, our results highlight the significant fruits of complementing experimental studies with coarse-grained simulations.
Investigations of time-interpolated single-slope analog-to-digital converters for CMOS image sensors
Keywords: Pixel
CMOS Image Sensors
Column Parallel
Time to Digital Converter
Analog to Digital Converter

This thesis presents a study on solutions to high-speed analog-to-digital conversion in CMOS image sensors using time-interpolation methods. Data conversion is one of the few remaining speed bottlenecks in conventional 2D imagers. At the same time, as pixel dark current continues to improve, the resolution requirements on imaging data converters impose very high system-level design challenges. The focus of the presented investigations here is to shed light on methods in Time-to-Digital Converter interpolation of single-slope ADCs. By using high-factor time-interpolation, the resolution of single-slope converters can be increased without sacrificing conversion time or power.
This work emphasizes on solutions for improvement of multiphase clock interpolation schemes, following an all-digital design paradigm. Presented is a digital calibration scheme which allows a complete elimination of analog clock generation blocks, such as PLL or DLL in Flash TDC-interpolated single-slope converters. To match the multiphase clocks in time-interpolated single-slope ADCs, the latter are generated by a conventional open-loop delay line. In order to correct the process voltage and temperature drift of the delay line, a digital backend calibration has been developed. It is also executed online, in-column, and at the end of each sample conversion. The introduced concept has been tested in silicon, and has showed promising results for its introduction in practical mass-production scenarios.
Methods for reference voltage generation in single-slope ADCs have also been looked at. The origins of error and noise phenomenona, which occur during both the discrete and continuous-time conversion phases in a single-slope ADC have been mathematically formalized. A method for practical measurement of noise on the ramp reference voltage has also been presented.
Multiphase clock interpolation schemes are difficult for implementation when high interpolation factors are used, due to their quadratic clock phase growth with resolution. To allow high interpolation factors a time-domain binary search concept with error calibration has been introduced. Although the study being conceptual, it shows promising results for highly efficient implementations, if a solution to stable column-level unit delays can be found. The latter is listed as a matter of future investigations.
Detection of alpha-synuclein conformational variants from gastro-intestinal biopsy tissue as a potential biomarker for Parkinson's disease
Keywords: neuropathology
biomarker
proximity ligation assay
Parkinson's Disease
Alpha-synuclein

Gastrointestinal (GI) alpha-synuclein (ASN) detection may represent a clinically useful biomarker of Parkinson’s disease (PD), but this has been challenged by conflicting results of recent studies employing different immunohistochemical (IHC) methods and reporting diverse morphological patterns with variable biological interpretation. To increase sensitivity and specificity, we applied three different techniques to detect different possible conformations of ASN in GI tissue derived from biopsies of the GI tract, which were obtained from a longitudinally followed, clinically well-characterized cohort of PD subjects and healthy controls (HC) (Oxford Discovery study). With IHC, we used antibodies reactive for total (T-ASN-Abs), phosphorylated (P-ASN-Abs) and oligomeric (O-ASN-Abs) ASN; with the ASN Proximity Ligation Assay (AS-PLA), we targeted oligomeric ASN species specifically; finally, with the Paraffin-Embedded Tissue Blot (PET-Blot) we aimed to detect fibrillary conformations of ASN specifically. Optimisation and validation of the PET-Blot and PLA techniques was carried out with studies on brain tissue from subjects with ASN pathology, and these experiments were used to gain insight into morphology and distribution of different conformational variants of ASN in the brain of subjects with Lewy pathology.
We specified all the detected morphological staining patterns with each technique interpreting them as pathologic or non-specific. Correlation to clinical symptoms was assessed to investigate the potential predictive or diagnostic value of specific staining patterns as biomarkers.
A total of 163 GI tissue blocks were collected from 51 PD patients (113 blocks) and 21 healthy controls (50 blocks). In 31 PD patients, GI biopsies had been taken before PD diagnosis (Prodromal PD group); while in 20 PD patients biopsies were obtained after PD diagnosis (Manifest PD group). The majority of these tissues blocks were from large intestine (62%), followed by small intestine (21%), stomach (10%) and oesophagus (7%). With IHC, four ASN staining patterns were detected in GI tissue (Neuritic, Ganglionic, Epithelial, and Cellular), while two distinct staining patterns were detected with AS-PLA (cellular and diffuse signal) and with AS-PET-Blot (ASN-localised and peri-crypt signal). The level of agreement between different techniques was generally low, and no single technique or staining pattern was able to reliably distinguish PD patients (Prodromal or Manifest) from HC.
Overall, our study suggests that even specific detection of ASN conformational variants currently considered pathologic was not adequate for the prediction of PD. Future studies with these or other novel techniques focusing on the upper part of the GI tract could overcome current limitations in sensitivity and specificity.
Diplomacy with memory: West German and Austrian relations with Israel
Keywords: past legacy
diplomacy
West Germany
foreign policy
Israel
Austria
collective memory

This thesis analyses international state behaviour by countries that share a historic legacy, and examines the delicate relations between West Germany, Austria and Israel in the wake of the Second World War as a case study. In it I propose a model – ‘diplomacy of memory’ - for this currently untheorized form of diplomatic conduct in order to explain how countries use official memories of their past on the international stage. Linking the interdisciplinary concept of collective memory with International Relations, my study characterizes the practice of 'diplomacy with memory' as a distinct policy undertaking that shapes and broadcasts historical narratives internationally for strategic foreign policy objectives.
To empirically test the diplomacy of memory model, this thesis investigates the two cases of West German-Israeli and Austrian-Israeli relations in the aftermath of World War II. Within these selected pairs, four core bilateral debates are analysed: first, reparation payments to Israel in 1951/52; second, the trial of Nazi war criminal Adolf Eichmann in Jerusalem in 1960/61; third, the Six-Day War in 1967 and fourth, the Yom Kippur War and oil crisis of 1973. While the first two cases explore how the memory of the Nazi past is leveraged as part of later diplomatic strategies, the latter two, which concern West Germany’s and Austria’s reaction to the Middle East conflict, reveal a more subtle connection between national memories and foreign policy choices around key international conflicts.
This study engages in historical inquiry, based on archival documents and other primary sources in all three countries, to demonstrate how a country’s collective memory is invented and deployed on the international stage. Combining the theoretical aim of specifying the link between national narratives and diplomacy with the qualitative analysis of two historic cases, this thesis rests at the intersection of International Relations and History.