VictorJuiz/thesis huggingface dataset:
Modelling the mechanisms of microsilica particle formation and growth

Microsilica particles arise as a byproduct of silicon furnace operation, created inside high temperature flames due to the combustion reaction of silicon monoxide with oxygen. These nanoparticles, which grow as silicon dioxide vapour condenses on the surface of existing particles, are used in a variety of composite materials. The size and quality of the particles affect the performance of the material used for such applications, and hence control of these quantities is of importance to manufacturers.
Motivated by this, we derive a mathematical model that connects local fluid flow, thermal and chemical conditions of the furnace to the formation and growth of microsilica particles. Since the regions where microsilica particles form are local to a very thin reaction zone, we focus on the dynamics within the flame front. We first study two distinct reductions of the model: the case of initially well-mixed or spatially homogeneous chemical species, and the case of initially separated chemical species. In the latter case, the one-dimensional domain is given by a cross section of the reaction zone and diffusion plays a dominant role in providing material to a combustion front. In order to incorporate fluid flow, we extend the previous work to 2-D by considering a mixing layer approach, that is, by assuming two parallel flows entering the domain with distinct velocities, temperatures, and concentrations. We study how the mixing layer evolves as both streams interact, and how mixing affects the formation and growth of particles. In all cases, we provide asymptotic approximations under various limits and neglecting the effect of the particles on the chemicals and temperature, and numerical solutions of the full model. Our results suggest that oxygen availability and a sufficiently high temperature are essential for the combustion reactions to occur, strongly influencing the width of the reaction zone and the particle size distribution. Furthermore, when the flow is almost uniform, fewer particles form and more of the total mass corresponds to large particles, in contrast with the non-uniform case.

Keywords: combustion
particle nucleation
asymptotic analysis
reaction-diffusion system
mathematical modelling
silicon furnace
particle growth
silica fume
microsilica
moment equations
mixing layer
Advisor: Oliver, J
Van Gorder, R
Muench, A
British commerce and Spanish government in New Granada in the early 18th century, from the asiento to the War of Jenkins' Ear

This dissertation presents a case study of the economic confrontation that eventually led to the War of Jenkins’ Ear between England and Spain in the early 18th century. It discussed the commercial competition taking place in New Granada in the years leading to the conflict, as exemplified by the experience of the South Sea Company factory in the port city of Cartagena, its efforts to penetrate the colonial market, and Spain’s response to this challenge.
While several studies have examined the issue before from a purely English, or purely Spanish perspective, this dissertation presented the two efforts as experienced by the colonial society of New Granada. The dissertation relied on both Spanish and English archival sources, allowing for a more comprehensive view of the complex economic, political and social exchanges taking place in New Granada at the time between the two powers. It also adds to the knowledge about a not very thoroughly-studied period of the economic history of New Granada, by documenting in detail the operations of the South Sea Company factory, the first organised English commercial settlement in the country.
The experiences of the South Sea Company in New Granada from 1713 to 1739 and its interaction with Spanish authorities and merchants there, showed both the limitations of English power against what was still strong Spanish administrative and military control over the South American mainland, as well as the English commercial vitality that was rightfully seen by Spain as a threat to the continuity of its empire there. While the focus of the study is to show how this rivalry was carried out in the local sphere of New Granada’s colonial society, it also provides elements for a wider view on the divergent imperial experiences of England and Spain.

Keywords: new granada
south sea company
war of jenkins' ear
spanish colonial history
contraband
Advisor: Deas, M
Atlas of the hole/house of dementia: the escutcheon, the hearth and the floor-cloth as motifs for dwelling and storytelling

This thesis presents a set of reflections in object and textual form on some questions of dwelling, memory and the experience of movement within architectural space. The research builds upon an older tradition of investigation into the phenomena of remembering and forgetting in the pre-enlightenment world. The exhibition is structured around the three figures of the escutcheon, the floor-cloth, and the hearth. Each of these figures opens up particular ways of moving between and around elements of a dwelling.
The methods and structures developed in this thesis respond to memory and the idea of the childhood home. These configure into mnemonic devices which are comparable to those rooted within the texts of the architect and theorist Juhani Pallasmaa and certain images that appear in Italo Calvino and Jorge Luis Borges. The research proposes that the human brain learns faster through analogy, that human cognition is wrapped within narrative and motion such as are inscribed on the mind and can easily be revisited. The objects, diagrams, paintings and installations contain a rich iconography of shapes and structures that prompt partial memory of real dwelling spaces. The textual component of some 15000 words follows the practice of the objects themselves in providing fragmented journeys through incomplete and misremembered spaces.
At the end of each chapter appear images of an ongoing architectural project for a sunglasses distributor in Spain that I have been undertaking during the period of this research, with all the pragmatic compromises and contradictions that this involves. The invitation offered to the viewer/reader is that those stresses that appear within the structures described in the thesis should be embraced in favour of the proposals it implicitly rejects.

Keywords: Cultural Dementia
Dementia
Exhibition making
Vernacular Architecture
Storytelling
Installation Art
Imagination
Mnemonics
Advisor: Kiaer, I
Taylor, B
Investigating the regulation of ACC1 activity in pancreatic beta cells

Aims:
Acetyl-coA Carboxylase 1 (ACC1) is an enzyme that couples glucose metabolism with de novo lipid synthesis in lipogenic tissues, by converting acetyl-CoA to malonyl-CoA. In beta cells, ACC1 plays a critical role in beta cell growth and insulin secretion . However, very little is known about how ACC1 activity is regulated in beta cells. The aims of the current project were to 1) assess the role of the AMP-activated protein kinase phospho-site serine 79 (ACC1S79) in beta cell function and whole body glucose homeostasis; and 2) screen for novel phospho-sites that may regulate ACC1 activity in beta cells.
Methods:
(i) To investigate the functional role of the ACC1S79 phospho-site in beta cell function, we studied a mouse model with ACC1S79 mutated to alanine (ACC1S79A), which were obtained by crossing ACC1 double knock-in mice 2 with wild type mice to isolate the ACC1S79A point mutation. We assessed glucose homeostasis in vivo and insulin secretion from primary islets.
(ii) We purified the ACC1 protein from transformed INS1 beta cells following culture with different glucose concentrations, and performed quantitative unbiased phosphoproteomics to characterise ACC1 phospho-sites. Mass spectrometry (LC-MS/MS) was performed using a Q- Exactive MS, mascot searches run against the Uniprot data base, and data analysed using MaxQuant and Perseus. We generated phospho-specific antibodies against key phospho-sites identified that exhibited a dynamic response to glucose stimulation, and used western blotting to investigate these sites further.
Results:
(i) Female ACC1S79A mice exhibited normal glucose homeostasis, whilst males showed lower fasting blood glucose, and a modest reduction in blood glucose during glucose and insulin tolerance tests compared to wild type littermate controls. No significant differences in fasted or glucose-stimulated serum insulin levels were found between the genotypes in vivo. Likewise, there was no significant change in insulin secretion from isolated ACC1S79A islets at baseline (2 mmol/l glucose) or in response to glucose-stimulation (7.5 and 20 mmol/l glucose).
(ii) Using quantitative phosphoproteomics, we identified twenty phospho-sites on the ACC1 protein in beta cells. ACC1S1215 was highly-phosphorylated at 2 mmol/l glucose, and showed a marked and highly significant reduction in phosphorylation in response to 15 mmol/l glucose, in contrast to the more modest changes in phosphorylation of ACC1S79. In contrast, phosphorylation of ACC1S25 and ACC1S49 was lower at basal glucose and increased upon glucose stimulation. Validation by western blotting confirmed that ACC1S1215 phosphorylation was highly-regulated by glucose, with ACC1S79 phosphorylation more subtle.
Conclusions:
Our data demonstrate that phosphorylation of ACC1S79 does not play a major role in insulin secretion in vivo or ex vivo. However, other phospho-sites identified by our phosphoproteomic screen may play a role in regulating ACC1 activity in beta cell and other ACC1-expressing tissues.

Keywords: diabetes
insulin
beta cells
metabloism
Advisor: Cantley, J
Christian, H
Structural and functional studies of perforin-like proteins implicated in zoonotic parasitic diseases

MACPF/CDCs are an ancient superfamily of pore forming proteins that have evolved a critical role in both cellular defence and attack. Many copies of MACPF/CDC proteins are released by a cell before binding to target membranes, oligomerising and undergoing a large structural rearrangement to punch a hole into the membrane, typically killing the target cell. In this thesis the steps of pore formation from membrane recognition through to oligomerisation and membrane insertion have been investigated for several recently discovered MACPF/CDC proteins using a combination of structural and computational biology techniques.
Perforin-like proteins (PLPs) belong to the MACPF/CDC superfamily and are unique to apicomplexan parasites including Plasmodium and Toxoplasma. PLPs have a role in facilitating parasite escape from host cells following replication, however their precise mechanism of action is unknown.
Here, molecular simulation approaches were used to investigate the stages of pore formation of the Toxoplasma gondii PLP1 (TgPLP1). The mode of membrane binding of TgPLP1 was determined, while investigation of oligomerisation states of the MACPF domain led to the generation of a model for the TgPLP1 transmembrane pore structure. Plasmodium have 5 PLPs (PPLPs1-5), which are expressed at different points in their lifecycles. The crystal structure of the Plasmodium PLP1 APC domain is presented here, and molecular dynamics (MD) was used to investigate PPLP1 and PPLP2 membrane binding, showing that these proteins have distinct mechanisms of membrane binding.
Another recently discovered MACPF/CDC protein is perforin-2, a close relative to perforin, which is produced by both immune and parenchymal cells in the body to defend against intracellular bacteria. The structures of the perforin-2 monomer and pre-pore were recently solved, and here we used MD to investigate the initial steps of membrane recognition and oligomerisation of perforin-2. A key finding was that perforin-2 binds to the membrane with its MACPF domain facing away from the bilayer, therefore identifying a unique mechanism of binding and activation amongst the MACPF/CDC family.

Advisor: Stansfeld, P
Gilbert, R
Up-down ordered Chinese Restaurant Processes: representations and asymptotics

We study composition-valued Markov chains that appear naturally in the frame-work of up-down Chinese Restaurant Processes (CRPs), introducing first discrete time models as in a similar way to those introduced by Petrov (2009), and also in continuous time via a Poissonisation technique similar to that used in Pal (2011).
As time evolves in the continuous time model, new customers arrive (up-step) and existing customers leave (down-step) at suitable rates derived from the ordered CRP of Pitman and Winkel (2009). We relate such up-down CRPs to the splitting trees of Lambert (2010) inducing spectrally positive Lévy processes. Conversely, we develop a theorem of Ray–Knight type to recover more general up-down CRPs from the heights of Lévy processes with jumps marked by integer-valued paths. We further establish limit theorems for the Lévy process and the integer-valued paths that connects to work by Forman et al. (2018+) on interval partition diffusions.
Fulman 2009 shows that the framework of commutation relations can be used to study the behaviour of discrete time down-up Markov chains, and he applies this to the unordered up-down (α,θ)-CRP from Pitman 2006. We demonstrate that these techniques still yield valid results when applied to the ordered down-up (α,θ)-CRP of Pitman and Winkel 2009, and generalise a theorem of Fulman 2009 on the explicitform and asymptotics of the maximal separation distance from the case θ= 1 to general the case θ > 0.

Keywords: scaling limit
branching diagram
Ray-Knight theorem
Chinese Restaurant Process
stable process
composition
mixing time
Kingman lattice
squared Bessel process
Advisor: Winkel, M
Seeing the utan from the orang:  A decolonial Indigenous approach to orang utan conservation in Sarawak. 

This thesis takes an Indigenous decolonial turn for a rich, empirical analysis of the seemingly paradoxes of human-environment or human-animal relationships within the multi-scalar forces of conservation. Indigenous relations is more-than-human relations and further, necessitates fresh inquiry into specific politics and strategies of concealment that rural Indigenous communities may employ in response to conservation actions. This thesis seeks to understand the multiple Indigenous strategies to maintain relations with lands and orang utans through an interdisciplinary approach of decolonial and political ecology frameworks, including decolonizing ethnographic methods. In considering human-orang utan relations in ecological time and subtle Indigenous responses to conservation forces and action in Sarawak, Malaysian Borneo, I build on lndigenous decolonial and political ecology frameworks, including Vizenor’s (2008, 1999) Indigenous survivance and Simpson’s (2007, 2014) politics of refusal. I demonstrate the multiple ways human-orang utan relations are realized within the power relations of conservation work. These findings provide a theoretical and decolonial grounding of understanding the different ways of Indigenous Iban presencing, and provide a way forward in developing a decolonial political ecology of orang utan conservation.

Keywords: Sarawak
indigenous
Borneo
decolonial
orangutan
conservation
Advisor: Malhi, Y
Learning models in quantum computation and quantum control

We investigate learning models for implementing arbitrary unitary operations and perform quantum machine learning tasks. First, we discuss efficient constructions for building unitary transformations in U(d), thus providing upper bounds on the minimum time required to implement them. Second, we study the hardness of learning unitary operations in U(d) via gradient descent on the time parameters of an alternating operator sequence, and numerically find that, despite the nonconvexity of the loss landscape, gradient descent always converges to the target unitary when the sequence contains d2 or more parameters. Third, we introduce the first quantum boosting algorithm for converting a weak quantum learner into a strong accurate quantum learner for a Boolean concept class C; thereby achieving a quadratic quantum improvement over classical AdaBoost in terms of VC(C).

Keywords: Quantum machine learning
Quantum mechanics
Quantum computation
Advisor: Vedral, V
Lloyd, S
Towards a structural understanding of the iRhom/ADAM17 complex

The rhomboid-like superfamily consists of the active rhomboid proteases and the inactive rhomboid pseudoproteases. The latter group includes the iRhoms, a family of polytopic transmembrane proteins composed of a long N-terminal cytoplasmic domain followed by seven transmembrane helices (TMH), with a highly conserved loop between TMH1 and TMH2 called the iRhom Homology Domain (IRHD). There are two mammalian iRhoms; iRhom1, which is broadly expressed, and iRhom2, which is predominantly expressed in immune cells and skin. A key function of iRhoms is regulating A disintegrin and metalloproteinase 17 (ADAM17), a metalloprotease responsible for the cleavage of tethered ligands on the plasma membrane, including the primary inflammatory cytokine tumour necrosis factor α. iRhoms are responsible for the trafficking of the catalytically inactive and immature form of ADAM17 from the endoplasmic reticulum (ER) to the Golgi apparatus where the inhibitory pro-domain of ADAM17 is cleaved and removed. The iRhom/ADAM17 complex traffics to the cell surface where ADAM17 is now mature. Mature ADAM17 is activated by the phosphorylation of iRhom and therefore able to cleave its substrates. iRhoms have an indirect but important role in ADAM17-dependent cleavage of substrates and are increasingly viewed as regulatory subunits of ADAM17. The complex is stabilised at the cell surface as a result of the prevention of its degradation by FRMD8.
Before this thesis, little to no structural studies have been performed on the iRhom/ADAM17 complex. Understanding the complex at a structural level will enable further insight to the mechanisms by which these two proteins interact. Therefore, the aim of this project was to express and purify iRhoms alone and in complex with ADAM17 for structure determination.
The project initially started by characterising the IRHD, of human iRhom1 (IRHD1), with the aim of crystallisation because it is the only major ER luminal domain of iRhom that may interact with the extracellular domain of ADAM17. However, after insect cell expression and bacterial refolding of IRHD1 it became apparent that the IRHD may be more stable as part of the full length protein. Human cell lines were generated to stably overexpress mammalian and non-mammalian iRhoms with their corresponding ADAM17 and a chimeric form of human iRhom2 fused to FRMD8 (HsFRMD8iRhom2). Expression and sub-cellular localisation of the generated cell lines was verified and optimal solubilising conditions were determined for maximal protein extraction out of the membrane and for minimal complex dissociation. HsFRMD8iRhom2 chimera was successfully purified and preliminary cryo electron microscopy data was generated. Therefore, the results reported in this thesis provide a foundation towards solving the structure of iRhom and iRhom/ADAM17 complex.

Advisor: Lea, S
Freeman, M
A Franc appraisal: the political economy of macroeconomic policy in the CFA zones

This thesis analyses how economic policies and outcomes in 14 countries in Western and Central Africa are shaped by the CFA franc monetary arrangement with France. This is a complex institution that reflects tensions between macroeconomic policy considerations, ambitions on regional integration and the reality of post-colonial international relations. In light of increasing scrutiny, and reforms announced in 2019, the three main chapters examine leading contemporary issues and contribute to the current debate concerning the future of this Franco-African arrangement.
The first chapter analyses how a fixed exchange rate may restrict the ability of low-income, resource-rich economies to reap long-term benefits from natural resource endowments. Through the lens of the so-called resource curse, CFA members are shown to have a less favourable experience than neighbouring non-CFA countries.
The second chapter considers how the CFA arrangement may influence fiscal policy decisions in unintended and undesirable ways. The empirical findings show fiscal policy to be on an unsustainable path in the zones. They also show that countries’ fiscal stances are affected by the policies of fellow member countries, and that this effect is much stronger than in non-CFA Sub-Saharan African countries. Lastly, it argues that conventional fiscal frameworks are inadequate to address such an unconventional arrangement.
Chapter Three argues that a number of the economic and political factors that have supported the continuation of the CFA arrangement have receded markedly over the six decades since its members gained independence. In addition, policy restrictions imposed by the arrangement remain as relevant as ever, as the prior two chapters highlight.
Brought together, these chapters paint the CFA arrangement as increasingly difficult to justify in its current form from an economic and political perspective. However, the thesis conclusion describes why a growing case against the CFA franc may not be enough to precipitate sweeping changes.

Keywords: Francophone Africa
Macroeconomics
CFA franc
Post-colonial
Africa
Monetary unions
Macroeconomic policy
Currency unions
Advisor: Adam, C
The HMGB1-CXCL12 heterocomplex and its interaction with CXCR4 as a target for tissue repair

Reduced High Mobility Group Box 1 (HMGB1) protein binds to CXC Ligand 12 (CXCL12), signals through CXC Receptor 4 (CXCR4) to promote tissue regeneration and accelerates repair by transitioning stem and progenitor cells to GAlert. Therefore, administration of fully reduced HMGB1 (FR-HMGB1) could prove beneficial in clinical practice. However, local conversion of FR-HMGB1 to the disulfide form (DS-HMGB1) may result in deleterious inflammation through signalling via Toll-Like Receptors 2 and 4, and the Receptor for Advanced Glycation End Products (RAGE).
Engineering HMGB1 to eliminate these potentially deleterious properties requires knowledge on the mechanism of its interaction with CXCL12, for which there is sparse literature. I identified the residues involved in formation of the heterocomplex using a combination of peptide arrays, biolayer interferometry and nuclear magnetic resonance. With these, and the published literature on the interaction of HMGB1 with its proinflammatory receptors, I designed a panel of HMGB1 derivatives aimed at removing the deleterious activities. I identified a construct comprising two HMG B Boxes in tandem (DbB-HMGB1) which is unable to signal through either TLR-2 or TLR- 4 and has greatly decreased RAGE binding but retains regenerative activity equivalent to FR-HMGB1 in vivo and in vitro.

Keywords: CXCL12
HMGB1
CXCR4
DAMPs
Advisor: Duerr, K
Burgess Brown, N
Nanchahal, J