VictorJuiz/thesis huggingface dataset:
Heavy ion irradiation as a proxy to neutron irradiation in impure Fe and Fe-Cr alloys

The realisation of nuclear fusion energy will require materials that can withstand high doses of neutron irradiation, and one class of candidate materials for structural applications is reduced-activation ferritic-martensitic (RAFM) steels containing around 9% Cr. The present lack of a fusion neutron source has meant that much of the research into radiation damage has been conducted using specimens irradiated in fission test reactors, or by using heavy ion irradiation as a simulation method. This work explores details of the use of this emulation technique, alongside the effect of composition and impurities on radiation damage in these materials.
Beam rastering is often employed during heavy ion irradiation in order to deliver a more uniform dose across the target area in comparison to continuous irradiation with a defocused beam, but this practice has been reported to alter the radiation-induced microstructural changes. This work investigated this in Fe and Fe-Cr alloys, using nanoindentation. No difference in post-irradiation hardness was observed between samples irradiated with a rastered or defocussed beam.
A direct comparison of the microstructure and mechanical properties of heavy ion and neutron irradiated Fe-9Cr samples was made, and it was found that the segregation to dislocation loops and clustering of impurity elements Si and P reported in the neutron irradiated specimen was also present in the ion irradiated specimen. The α' precipitation reported after neutron irradiation did not occur after ion irradiation. The post-irradiation increase in hardness and yield stress of both samples were found to be the same, measured by nanoindentation and microcantilever testing. An increase in hardness of 0:88 ± 0:21 and 0:81 ± 0:26 GPa was found in the ion and neutron irradiated specimens respectively.
The increase in hardness for the neutron irradiated specimen was found to be less then the 1:5 ± 0:28 GPa reported for an identically irradiated Fe-6Cr sample.
The impact of carbon concentration on irradiation hardening in Fe was investigated by ion irradiating a high purity Fe sample containing regions of varying carbon concentration. Two samples were irradiated at two different dose rates, but no dose rate effect was observed. The increase in hardness however was found to increase with increasing carbon concentration, with a maximum increase of around 3 times that observed in pure Fe.
This work has identified some limitations of and future challenges for the use of heavy ion irradiation as a surrogate to neutron irradiation in the absence of a dedicated fusion materials testing facility.

Advisor: Roberts, S
Hardie, C
Redistributive authoritarianism: land reform and regime durability in the Middle East

A growing literature on land reform under autocracy shows that leaders often use the expropriation and redistribution to disempower incumbent elites and to signal a credible commitment to potential coalition members. Although these strategies have been found to extend leader tenure in Latin America (Albertus and Menaldo, 2012), these patterns have yet to be systematically tested in other parts of the world. Counter to the expectations generated by the Latin American experience, I find that leaders who pursue land reform in the Middle East and North Africa (MENA) have shorter tenures than non-reformers. This finding motivates my central research question: why are redistributive autocrats less likely to endure than their non-redistributive counterparts?
I address this puzzle in two stages. First, I argue that the legacies of European colonialism impacted the inclusivity of elite coalitions. In countries with legacies of exclusive coalitions, autocrats inherited more intense demands for redistribution than in countries with legacies of inclusive coalitions. Strong demands from previously excluded elites drove leaders to pursue radical land reforms. I use a medium-N quantitative analysis to uncover patterns regarding the implementation of land reform and the survival prospects of redistributive autocrats.
Second, radical reformers must also decide how to attract a loyal support coalition after redistribution is underway. Radical reformers who simultaneously extend cooptive state capacity through investment in and provision of “soft” institutions (e.g., agricultural cooperatives, health, education) are more likely to send a credible signal to potential members of an expanded supporting coalition. Alternatively, autocrats that pursue radical reform and rely on the expansion of repressive institutions (e.g., the military) are less likely to attract new supporters and are consequently more vulnerable to ouster. I turn to the case studies of Jordan, Iraq, and Egypt to disentangle the patterns suggested by the cross-national findings.

Keywords: leader tenure
land reform
Advisor: Rueda, D
Malik, A
Hybrid quantum-classical algorithms and error mitigation

These days, research groups such as Google, Microsoft, and Rigetti are working towards fabricating quantum devices which have hundreds to thousands of qubits. In recently proposed quantum algorithms, i.e. hybrid quantum-classical algorithms, such quantum devices are used as subroutines for calculation of classically intractable tasks. However, the applicability of hybrid algorithms was quite limited, for example, the search of the ground state, and simulation of the dynamics of quan- tum systems. In addition, near-term quantum devices are expected to be quite noisy, impairing the precision of computation seriously and removing any potential advantages with quantum computers. Therefore, it is necessary to extend the applicability of hybrid algorithms and mitigate errors on quantum computers.
In this thesis, we describe the generalisation of hybrid algorithms so that they can be applied to variety of problems, such as search of the spectrum of quantum systems, simulation of open quantum systems and even general mathematical tasks. The algorithm for finding spectra is useful for applications such as new drug discovery, design of batteries. Generally speaking, quantum systems of interest to physicists, chemists, and materials scientists inevitably interact with their environments, and quantum states are decohered. Therefore, to investigate quantum phenomena, new algorithms simulating open quantum systems are described in this thesis. Algorithms for general mathematical tasks such as matrix multiplication to a vector and solving linear equations, useful for a large number of problems, such as machine learning, are also presented.
Furthermore, in order to make hybrid algorithms useful, we also invented a practical error mitigation method for suppressing physical errors, which may make hybrid algorithms useful. We showed that errors can be suppressed for a quantum system with over 50 qubits for the current achievable error rate, which is believed to be hard to simulate with classical computers. Also, we generalised the error mitigation technique to be applied to mitigate algorithmic errors, which may enhance the accuracy of Hamiltonian simulation.

Keywords: Near term quantum computing
Feeding the city: a comparative study of agricultural production in Bronze Age systems of Western Asia

The development of large urban societies in Western Asia during the Bronze Age has often been viewed as a pivotal transition in human history. As part of this narrative, however, agriculture and the nature of food production have frequently been relegated to the rural hinterland and divorced from daily life in the city. This research aims to explore the relationship between established early cities and the specific systems of agricultural production needed to sustain them, by assessing the nature of farming practice at two key Bronze Age sites. These two sites, Hattusha in Central Anatolia and Tell Brak in north-eastern Syria, were both major urban centres with large socially stratified populations and control of widespread hinterlands. Additionally, they provide data from two climatic and environmental zones, as well as two different cultural settings, providing the opportunity to investigate the nature of agriculture under a range of variable conditions.
The archaeobotanical analysis of stored charred macro-remains assemblages from both sites has provided the opportunity to explore the relationship between crop choice, farming regime and urban society. Compositional, spatial and crop processing analysis has provided information regarding the origins of the material, as well as allowing the assessment of activities and depositional processes that may have formed the assemblages. Furthermore, the analysis of crop stable carbon and nitrogen isotopes combined with the functional ecology of arable weeds has allowed the identification of multiple crop management systems designed by each society. These results have revealed that both cities were reliant on low-input, low variance farming systems, but that within these systems a high level of agricultural variation was present. At Hattusha, correspondence analysis and crop stable isotope analysis have indicated that stored cereals were grown under a range of crop husbandry regimes. This included low-intensity systems characterized by low inputs of water and medium-low inputs of manure, and higher-intensity systems characterized by medium inputs of water and high inputs of manure. The existence of stored cereals grown under multiple regimes may suggest that the inhabitants of Hattusha were pooling resources from different areas within the wider rural hinterland. By contrast, crop stable isotope analysis and functional ecology analysis from Tell Brak have suggested that different species of cultivar were likely to have been grown in different areas of the landscape to maximise the potential arable yield of marginal environmental conditions. Overall, farming within both of these societies appears to have been a dynamic system that was adapted to overcome specific environmental and social challenges whilst also performing a key role in sustaining and supporting the urban population.

Advisor: Bogaard, A
Charles, M
Hunting for water with MCS

Mars Climate Sounder (MCS) is an infrared radiometer aboard NASA’s Mars Reconnaissance Orbiter (MRO) launched in August 2005 and designed to characterize the temporal and spatial variation of temperature, dust and water profiles. MCS has nine spectral channels in the range 0.3–50 μm. An original goal of the mission was retrieval of vertical water profiles. This was to be done using two spectrally co-located channels (centred at 42 μm)—a narrow channel (B3), which was mainly sensitive to dust, and a broader overlapping channel (B2) sensitive to both dust and water. This has been severely compromised by the fact that the B2 and B3 filters did not meet their specification, with a much wider than expected spectral response.
This thesis is split into three parts attempting to assess the current ability of MCS to retrieve water vapour. In the first part, work was done assessing the ramifications on the water vapour sensitivity of the B3-B2 pair and the B2 channel alone through extensive simulation work. The B3-B2 pair were found to have a drastically reduced sensitivity to water vapour that was further reduced by the presence of dust and low temperatures. Radiance residuals of B2 from MCS observations showed that a water vapour signal is present in the channel. Simulations of MCS radiances and retrieval of synthetic observations revealed that the accuracy of water vapour retrievals is sensitive to the choice of aerosol particle size and that in the presence of moderate aerosol opacity (dust and water ice), aerosol radiance contribution in B2 is falsely misinterpreted as water vapour.
In the second part, work was done measuring the spectral response of the B3 filter in order to understand the process behind the spectral broadening in the B-channels. It was thought that random forward scattering of out-of-bandpass radiation by the mesh filter may be the cause of the widening. Using a custom-made jig and FTIR spectrometer, measurements were taken at several filter-detector separation distances. No change in the B3 response FWHM was observed as the distance was varied. In the final part, a two-stage retrieval method was applied to MCS observations for MY28 northern hemisphere summer (Ls=111–173°). Nightside vertical profiles of water vapour were retrieved for the first time showing interaction with the aphelion cloud belt directly. Possible interaction between dust and water cycles was seen. Retrieval results compared favourably with observations by others for both column abundances and vertical profiles. Of particular note was good agreement with results from Clancy et al. (2017) using vertical water profiles derived from CRISM retrievals of 1.27 μm O2 (1∆g) dayglow. A number of spurious retrievals were seen and these are attributed to the aerosol model choice problem seen in the simulations.

Keywords: Mars Climate Sounder
Infrared radiation
MCS
Mars
Advisor: Irwin, P
Vibrational effects in quantum transport through single-molecule junctions

This thesis is concerned with vibrational effects in resonant charge transport through molecular junctions. The first research chapter examines the role of non-equilibrium vibrational dynamics in charge transport through a molecular double quantum dot. We demonstrate that non-equilibrium vibrational effects in such a system can result in current suppression and negative differential conductance. The second research chapter describes how vibrational dynamics can be incorporated into the theoretical description of molecular junctions based on a Pariser-Parr-Pople Hamiltonian. As a case study, we consider a prototypical spiro-conjugated molecular junction. We demonstrate that the transport properties of this system are governed by an interplay between destructive quantum interference and Jahn-Teller distortion (an effect of vibronic origin). In the next chapter, we examine the role of collective vibrational coupling in charge transport through a two-site molecular system akin to the one considered in the first research chapter. We demonstrate that such interactions can significantly enhance the efficiency of transport through such a system, and also take this opportunity to analyse various theoretical descriptions of electron-vibrational interactions commonly used in the transport setting. In the fourth research chapter, we consider a single-site molecular system coupled to a collection of thermalised vibrational modes. We formulate a relatively simple yet powerful theoretical framework describing charge transport through such a system. We recover the Marcus and Landauer-Buttiker theories of transport in the limit of high-temperature and vanishing electron-vibrational coupling, respectively. We further show how lifetime broadening can be consistently incorporated into Marcus theory, and we derive a low-temperature correction to the semi-classical Marcus hopping rates. In the last research chapter, elements of this framework are applied to experimental measurements of charge transport through zinc-porphyrin molecular junctions. This joint experimental-theoretical study provides, for the first time, a full understanding of the resonant transport regime of graphene-based molecular junctions.

Advisor: Gauger, EM
Mol, JA
Briggs, GAD
Integrations and introgressions: a viral and genetic history of the human genome

The human genome combines archaic relics which have been obtained through two biological vehicles: viral infection and interbreeding. In this thesis I explore detection methods that search for the products of these biological processes, starting with some of the oldest fossils in our genome: viruses. I examine the most recently active endogenous retrovirus (ERV) family in humans: human endogenous retrovirus-K (HERV-K), human mouse mammary virus-like 2 (HML2), also known as HK2. I collaboratively developed and benchmarked the software STEAK for detecting mobile element and retroviral integrations in high-throughput sequencing data. Using STEAK on 70 whole genome sequences (WGS), I show that all polymorphic HK2 integrations found in Europeans are also present in African populations and estimate that HK2 activity stopped prior to the emergence of modern humans. The second half of this thesis investigates the outstanding question, did archaic and modern humans admix in Africa? Non-African populations today carry 1-5% of Neanderthal and/or Denisovan admixture. However, it remains unclear whether archaic introgression is present in African populations. I use WGS simulations to assess a current archaic reference-free method, S*, under different demographic models varying in divergence dates, admixture dates, and admixture proportion. I show that in the absence of an archaic reference and an obscure demographic history, S* results must be interpreted with caution given its sensitivity to demographic processes. Using S* and Sprime on African WGS, I find that putatively introgressed regions detected by both methods are notably long and old haplotypes. I show with D-statistics that African populations such as the San share excess derived alleles with Denisovans but not with Neanderthals. These analyses collectively support a model where interbreeding took place between an ancestral human population and other archaic hominins within Africa. Overall, this thesis elucidates the relationship between the human genome and the archaic sequences it hosts.

Keywords: archaic introgression
population genetics
human evolutionary genetics
HERV-K (HML-2)
Africa
human endogenous retroviruses
Advisor: Capelli, C
Focused ultrasound: a non-invasive brain stimulation modality

Non-invasive brain stimulation techniques allow for excitation or inhibition of neural activity via externally applied stimuli. Recently, ultrasound (US) has been shown to stimulate neurons with better spatial localisation than existing electrical stimulation modalities. We present a review of the literature in both the central and peripheral nervous systems demonstrating a range of effects from de novo action potential generation in isolated cell preparations to cognitive responses in humans. However, several questions remain before the technique can become widespread. These include: methods to accurately model, and deliver, transcranial US to specific brain targets; the safety of the approach from both a mechanical and thermal standpoint; elucidation of the fundamental mechanisms through which acoustic perturbations result in nervous system modulation; and the development of monitoring techniques to confirm US focusing in vivo as well as to detect the induced effects. In this thesis, we focus on the delivery and safety aspects. We present numerical simulations using k-Wave and experimental measurements demonstrating focusing to areas of the visual cortex using ex-vivo human skulls with single-element transducers. We show that targeting of many areas can be achieved without the use of lenses or arrays. Furthermore, we conduct an in-depth safety review detailing the parameter spaces over which studies have been conducted and highlighting any damage areas. In current human studies the technique appears to be safe with minimal, if any, side effects. Finally, we report findings from a human pilot study with the aim of modulating sites within the visual cortex. We present direct evidence of strong non-specific auditory activation following bursts of US confirming previous animal studies. These effects can confound US neuromodulation trials and demands further attention before US can realise its potential as both a scientific instrument to probe brain function and as a therapeutic modality to modulate brain activity.

Keywords: Ultrasound
Brain stimulation
Neuromodulation
Advisor: Cleveland, R
The involvement of hypoxia in APOBEC-mediated mutagenesis in multiple cancers

Mutational signatures have been studied to associate mutations to their originating causes. One such signature is that of the APOBEC family of proteins. APOBEC proteins are normally involved in innate immunity, playing a role in the defence against foreign genetic material by inducing mutations in single-stranded DNA and RNA. APOBECs have recently been associated to mutations in the genomes of multiple human cancers. The regulation of APOBEC genes is currently poorly understood, especially in the context of cancer. Recent evidence suggests that certain APOBEC genes can be upregulated in immune cells exposed to hypoxia. I explore this path further by studying the association between hypoxia and APOBEC expression and activity in cancer using RNA-Seq, mutation, and amplification data from 6723 patients in 13 cancer types. My results show evidence of correlation between hypoxia and APOBEC gene expression as well as mutagenic activity, specifically APOBEC3A and 3B. I also show that APOBEC3B is involved in pathways that overlap with those associated with hypoxia, contrary to the other APOBEC family members. Finally, I provide a comparison of the methods used to evaluate the APOBEC mutational signature. Overall, this study provides preliminary evidence for the association between APOBEC and hypoxia. It also raises many questions, but it provides solid grounds for future studies to be conducted in more depth about this topic.

Keywords: Computational Biology
Mutational Signatures
Genomics
Hypoxia
Cancer
Advisor: Buffa, F