VictorJuiz/thesis huggingface dataset:
Simulation of, and with, first generation quantum computers

The year is 2022. Scientists and engineers inch ever closer to building a practical quantum computer. The excitement in the research community, that we might soon fulfil Feynman’s dream to leverage quantum mechanics in machines capable of exponentially quicker computation, is steadily growing. With promised revolutions in chemistry, condensed matter physics and machine learning, and an expected market of 1.8 billion USD by 2026, quantum computing fights for the spotlight amid international pandemics and climate catastrophe. But the journey ahead is not an easy one. Quantum computers, requiring precise control of extraordinarily delicate quantum systems, are unsurprisingly challenging to engineer and equally difficult to design. A demonstration of quantum advantage through the quantum solving of a practical problem faster than available classical means, remains a research ambition.
At the forefront of this research are classical computers: the machines which crunch the numbers in our calculations, which interface with our quantum experiments, and which render this very document. Without them, quantum computation would have remained a fanciful whim on Feynman’s chalkboard. Behind the rapidly growing repertoire of quantum algorithms lies an equally impressive and expanding corpus of classical simulation strategies.
This thesis is about utilising first generation quantum computers and predicting their behaviour using classical computers. It develops novel quantum algorithms to perform variational minimisation, Hamiltonian diagonalisation, and approximate circuit recompilation, all intendedly compatible with near-future machines. It also devises classical algorithms for efficiently simulating quantum variational algorithms, emulating quantum computers using high-performance supercomputing facilities, and showcases the author’s efforts in scientific software development. Incidentally, this thesis makes no direct use of current day quantum hardware facilities. We hope to convince the disappointed reader that such an endeavour is presently pointless.

Keywords: quantum computing
scientific simulation
high-performance computing
software design
algorithms
Advisor: Benjamin, S
Design of a modular soft robotic arm with proprioceptive capabilities

Proprioception is a trending topic in the field of soft robotics. It endows soft robots with the capability to retrieve their spatial configurations without external feedback for closed-loop control. This is usually achieved by embedding soft and stretchable sensors in the soft bodies of the robot to directly measure their deformations. In addition, taking advantage of their infinite DoFs and inherent compliance, multisegment soft robotic arms are designed to execute highly dexterous tasks in the cluttered environment. However, the integration of the proprioceptive sensors in the body of the soft arm is an ongoing challenge. Firstly, the embedded sensors need to accommodate for the compliance of the soft robotic arm. Secondly, where to place such sensors is a non-trivial problem. Lastly, the integration of these stretchable sensors involves complex fabrication steps. In this thesis, we aimed to address these challenges of proprioceptive soft robotic arm with our highly integrated solution - a multisegment soft robotic arm that is capable of proprioceptive sensing while minimising the number of sensors on-board. The proprioceptive sensors do not interfere with the motion of our soft robotic arm and they can be easily integrated and removed. The major contribution of our work is an novel sensing method for modular soft robotic arms. We also advanced this field by contributing: 1) an omnidirectional actuator design for multi-material 3D printing, 2) a modular approach for fast arm assembling and maintenance. By placing sensing arrays within the rigid joints, the variations of stress distribution over the top of segments were measured. Together with the shape information captured by the motion capture system, we obtained a dataset to train a mapping from the tactile sensor responses to the posture of the soft robotic arm using k-nearest neighbors regression. The experimental results demonstrated that the proposed approach was able to reconstruct the whole 3D shape of a three-segment soft robotic arm under piecewise constant curvature assumption.

Advisor: Maiolino, P
Hellenism and productivity in the early Schelling

This thesis explores F.W.J. Schelling’s conception of philosophical productivity during his early period in the context of Griechentum or German Hellenism. Schelling is a German Hellene and grows under the influence of Johann J. Winckelmann, considered the father of Griechentum. That Schelling understands philosophy as productive, means that he conceives of philosophy as a matter of producing intellectual intuitions and Hen kai Pan; in fact, these two are inseparable. For the production of intellectual intuition is according to the ambit of Hen kai Pan. That he does so as a German Hellene means two things: first, he formulates this conception of philosophy out of a direct engagement with Ancient Greek philosophical texts, primarily Plato’s; this is apparent especially in his early notes on Plato. In his engagement with the philosophical and religious doctrine of Hen kai Pan, Schelling inscribes himself in a tradition of philosophy that mostly consists of Ancient Greek philosophers; this doctrine informs his understanding of Wissenschaft and potencies. Second, this understanding of Ancient Greek philosophy is as philosophical as it is religious. Indeed, Hellenism undergirding Schelling’s conception of philosophical productivity entails a serious engagement with Greek religion, specifically Greek Mystery religions. A historiographical revision of Deutscher Idealismus and Jenaer Romantik, two contexts in which scholars generally place him, arises, and reveals the portrait of Schelling as a philologist, or, at least, a philosopher heavily informed by philology.

Keywords: F.W.J. Schelling
Greek religion
German philosophy
German Hellenism
Advisor: Rasmussen, J
The role of natural killer T cells in atherosclerosis

Atherosclerosis is a multifactorial, chronic inflammatory disease of the arterial wall starting in childhood. It is characterised by the gradual formation of lipid-, connective tissue- and immune cell containing plaques. The interplay between lipids and the immune system has proven key in its development. Natural Killer T (NKT) cells are at the interface between lipid metabolism and immunity, due to their restriction to lipid antigen-mediated activation by antigen presenting cells (APC). Although considered pro-atherogenic in mouse, the mechanisms involved in NKT cell activation in humans remain elusive and their role in human cardiovascular disease requires further study.
In this thesis, I identify lipoproteins very-low-density- (VLDL) and low-density (LDL) as vehicles for lipid antigen delivery and subsequent activation of invariant NKT cells. In the circulation, model lipid antigens bind to VLDL and LDL. Subsequent uptake by APCs is LDL-receptor (LDLR)-mediated, demonstrated in vitro and in vivo in mouse models. As a consequence, LDLR-mutant APCs of patients with familial hypercholesterolemia are impaired in their ability to activate invariant NKT cells, validating this mechanism in a human context. Moreover, the relation of NKT cell plaque-abundance with clinical outcome, patient- and plaque characteristics was studied in a human cohort. NKT cell abundance in plaques is inversely associated with plaque vulnerability, suggesting a protective role for NKT cells in stabilisation of the human plaque. Evidence of APC-NKT cell interaction in human atherosclerosis is currently lacking. To this end, I applied Hyperion Imaging Mass Cytometry (IMC) to human atherosclerotic plaques to study the NKT cell niche, revealing spatial evidence in situ of close cellular interactions of macrophages and NKT cells.
In conclusion, this thesis defines the mechanism of lipid antigen delivery to APCs by circulating lipoproteins, and its fundamental role in invariant NKT cell activation. It proposes innovative imaging modalities to study the APC-iNKT axis in the human plaque, and associates NKT plaque-abundance with clinical parameters for the first time. These novel insights further our understanding of the interplay of lipids and the immune system, underlying atherosclerosis.

Keywords: natural killer T cells
immunometabolism
immunology
imaging mass cytometry
Advisor: Monaco, C
Buckley, C
Schipper, H
The 1915 anti-Moor pogrom and ethno-religious violence in Ceylon, 1853-1915

The 1915 anti-Moor pogrom was the first major episode of popular ethno-religious violence in Ceylon. Between 29 May and 6 June 1915, Sinhalese-led violence targeted Moors (the largest Muslim ethnic group in Ceylon), and included murders, rapes, assaults, attacks on mosques and homes, and the destruction of over 4,000 shops. The spectre of ‘1915’ has in the last decade received renewed attention in the context of escalating anti-Muslim violence in Sri Lanka (Ceylon was renamed in 1972). Why did this violence take place between Sinhalese and Moors?
In my thesis, I re-open this neglected chapter in Ceylon’s history, critically re-examine the deeper roots of ethno-religious violence between Sinhalese and Moors, and present a historical narrative of cycles of intolerance and victimisation. I explore the role of colonial policies and discourse in bringing ethno-religious groups into conflict with each other, and reassess certain positions taken in the existing historiography on the pogrom, as well as popular narratives on the outbreak, spread and aftermath of the pogrom. I then examine the colonial state’s failure to pre-empt this violence in 1915 and its harsh belated suppression of the violence.
My research uncovers a longer-term history of ethno-religious violence and investigates the ethnic and religious sensibilities and identities that crystalised from the mid-nineteenth century onwards. To do so, I repeatedly shift lenses from the microscopic, to the local, to the global, in analysing Sinhalese-Moor contestation in the religious, economic, and social spheres, and the clash between indigenous practices and colonial legislation. In my treatment of the 1915 pogrom, I locate the violence within the global context (the Islamic revival, and later, the First World War for example), and shed light on broader historiographical questions pertaining to the history of British colonialism in Ceylon.

Keywords: identity formation
First World War
Moors
religious revival
Sinhalese
Ceylon
Sri Lanka
ethno-religious violence
Advisor: Strathern, A
Bio-medical degeneration in Britain, 1850-1914: theory and evidence

During the second half of the nineteenth century leading to the First World War, a belief emerged that European populations were manifesting a process of physical and biological decline. This belief was inspired by social changes caused by industrialization and urbanization and by the apparent rationales of evolutionary biology, which appeared to place conflict and competition at the center of species development. Degeneration was not a positive or clearly defined theory. It drew upon existing theories of heredity and disease to express a sense of discomfort about progress and the competition between nations. The persistence of degeneration was a product of a bio-medical environment in which knowledge was provisional and rapidly changing. Because of this, ideas about hereditary disease and decline could not be definitively refuted even as an understanding of disease pathology, heredity and epidemiology consistently improved. In the British national context, degeneration would be notable in two particular arenas – the impact of urbanization and the study of recruiting statistics as a proxy for assessing the health of the population. These avenues demonstrated not only the tenacity of ideas about hereditary physical decline over a sixty-year period but also the equally tenacious responses from physicians and public health experts who disagreed with the fundamental assumptions of degeneration. This thesis will address the conflicts about the content of degeneration theory and will examine the existing knowledge about heredity and disease that made the refutation of degeneration so challenging. It will also examine official investigations at the turn of the 20th century, inspired by revelations gained from the poor health of army recruits, to look more carefully at how a concrete study of a social problem led to a rejection of pessimistic conclusions about public health.

Keywords: degeneration
heredity
Britain nineteenth century
medicine
Britain twentieth century
evolutionary biology
On a bounded runtime algorithm for the homeomorphism problem for hyperbolic manifolds

We give a bounded runtime solution to the homeomorphism problem for closed hyperbolic 3-manifolds. This is an algorithm which, given two triangulations of hyperbolic 3-manifolds by at most t tetrahedra, decides if they represent the same hyperbolic 3-manifold with runtime bounded by 2²tO(t).
Along the way we prove two supplementary results, both of which we also prove in higher dimensions. First, we prove that one can compare geometric triangulations of hyperbolic n-manifolds in time bounded by 2²tO(nt³), n≥ 4, 2²tO(t), n = 3.
Second, we show that the length R of a systole of a closed or finite hyperbolic n-manifold (n ≥ 3) admitting a triangulation by t n-simplices can be bounded below by a function of n and t, namely R ≥ 1/ 2(nt)o(n⁴t).

Advisor: Lackenby, M
Bridson, M
Investigating the role of ASPP2 in post-implantation mouse embryos

My research focuses on the role of ASPP2 (Apoptosis-stimulating of p53 protein 2, encoded by the TP53BP2 gene) during early post-implantation development. ASPP2 has multiple important biological functions, including roles in the control of cell polarity, tight junction formation, cell proliferation, differentiation and apoptosis.
To study the molecular basis of ASPP2 function in post-implantation development, I generated a mouse line in which exon 4 of ASPP2 is flanked by LoxP sites. Using genetic crossings, this allowed me to generate various mouse lines that were used to study the function of ASPP2 in the whole embryo and in specific tissues.
My results indicate that gastrulation is able to proceed in ASPP2-/- embryos – all 3 germ layers appear to form correctly. However, the embryo becomes progressively more disordered as development proceeds, resulting in embryonic lethality by E9.5. Somites are present at E8.5 and E9.5, showing that mesoderm-derived structures can form. The somites, however, are smaller than their wildtype counterparts. Additionally, instead of the normal structure of a single layer of somitic cells surrounding a central cavity, the somites have a disorganised structure with multiple cell layers and often lack a cavity.
Heart formation is also affected in these mutant embryos. By E9.5, there is no heart structure, with the absence of a beating heart. I crossed the ASPP2flox/flox mouse line to a line expressing CRE under the Mesp1 promoter, which controls early cardiac progenitor formation. These mice developed normal hearts at E8.5 and E9.5, implying that the perturbation in cardiac development is a secondary defect, likely caused by disturbances to the surrounding tissues meaning that the cardiac progenitors do not receive the signals they require to continue developing.
Thus, my research has indicated that ASPP2 is essential for post-implantation embryonic development. The mesoderm initially forms correctly but as the embryo continues to develop, the mesoderm-derived somites become disrupted, indicating a role for ASPP2 in regulating the epithelial architecture of the somites. Similarly, as seen in the heart, the disorganisation of structures leads to secondary defects later in development, ultimately resulting in embryonic lethality. These results demonstrate the importance of ASPP2 and shed light on some of the functions that it may play in development.

Advisor: Srinivas, S
Royer, C
Reducing agriculture's environmental impacts through diverse producers

The world food system is characterised by millions of diverse producers yet approaches to increase productivity and environmental sustainability that are effective in light of this remain underexplored. Here I present data revealing that the environmental impacts and productivity of different producers are highly variable. I then present evidence that an effective approach to improve outcomes given this heterogeneity would require environmental and productivity monitoring by each producer and communication of this information up supply chains and through to consumers. With colleagues, I develop an environmental science toolkit to enable producers to monitor their environmental impacts and a filetype to represent agri-environmental data which would support producers to communicate their impacts. I then explore how an environmental impact labelling scheme could trigger the creation of this measurement and communication system while also incentivising substantial behavioural change. Overall, this thesis develops, and then starts delivering on, a sustainability and productivity solution for agriculture.

Keywords: sustainability
agriculture
environment
Advisor: Milner-Gulland, E
Malhi, Y
Greyner, R
Imaging biomarkers for cardiovascular risk prediction with CT techniques

Title: Imaging biomarkers for cardiovascular risk prediction with CT techniques
Background: Coronary plaque formation, progression and rupture are still the major cause for myocardial infarction. Although many ways for the identification of high-risk plaques have been developed and evaluated over the last decade, they are still not able to forecast the development and rupture of an individual plaque precisely. With the increase of new techniques such as radiomics and the fat attenuation index (FAI), new risk stratification techniques for coronary plaques could be established.
Methods: The first part developed an automated coronary plaque segmentation tool for calcified and non-calcified plaque components. The second part compared statistical versus radiomics-based automated plaque classification approaches. These two parts aimed to facilitate an automated coronary plaque analysis on future big cohorts. In the last part, FAI around plaques (pFAI) was analysed and differences between individual coronary plaque categories were compared.
Results: After showing excellent results on intra- and interobserver analysis for the manual segmented dataset, a model for calcified plaque components achieved very good results, even outperforming metrics from the interobserver analysis. The radiomics-based approach for non-calcified plaque detection proved the feasibility of this method by showing good initial results. While an automated plaque classification based on two first-order statistical values has already worked well, radiomics were able to even outperform this in terms of accuracy and diversification of plaque types. Measured pFAI revealed significant differences between individual plaque classes based on their degree of calcification.
Discussion: Although the size of the manual labeled and segmented datasets was limited, meaningful models for an automated coronary plaque segmentation and classification were developed. Further, it was shown that FAI around different plaque types provides additional information on their inflammatory status and, therefore, eventually on their individual risk, which has to be investigated on plaque-specific outcome data in the future.

Keywords: cardiac imaging
coronary plaques
HRP
FAI
Advisor: Antoniades, C
Neubauer, S
Tomlins, P
Discontinuous Galerkin discretisation in time of the second-order hyperbolic PDEs

A discontinuous Galerkin (DG) time-stepping method is presented for solving second-order hyperbolic partial differential equations (PDEs). The proposed numerical method combines the hp
-version discontinuous Galerkin finite element method (hp-DGFEM) in the time direction with an H1(Ω)-conforming finite element approximation for the spatial variables. We start with the construction and analysis of the discontinuous-in-time scheme to linear hyperbolic PDEs of second order in Chapter 2. Our analysis shows that this method is consistent and stable, with arbitrarily high-order convergence rates in the temporal domain for sufficiently smooth solutions. Error bounds in both energy and L2 norms are derived. These error estimates show that this method allows for a broad range of hp-refinement strategies with varying time step sizes and polynomial degrees, thus having the potential to give exponential rates of convergence. Numerical experiments on linear wave equations and elastodynamics systems show significant gains in accuracy over existing time integration schemes.
We then extend this DG time-stepping method to approximate solutions of second-order quasilinear hyperbolic systems in Chapter 3. In particular, we study the nonlinear elastodynamics problem. The resulting numerical scheme is stable and convergent, and we derive a priori error bounds at nodal points in the L2-norm for sufficiently regular solutions. Numerical experiments on a nonlinear elastodynamics problem with smooth solutions demonstrate the convergence rates.
Chapter 4 further applies this discontinuous-in-time scheme to a nonlinear damped equation, which is derived from Maxwell's equations by assuming a linearly polarised wave propagating on an infinite cylindrical domain. Again, we show a priori error estimates of the solutions at the nodal points in this chapter. Numerical experiments on nonlinear wave equations illustrate and confirm these theoretical findings.

Keywords: Discontinuous Galerkin method
Discontinuous time stepping
Numerical analysis
Finite element method
second-order hyperbolic PDEs
Nonlinear PDEs
Advisor: Suli, E
Exploring the ring-forming chemistry of yndiamides

Yndiamides are a uniquely capable class of doubly heteroatom-substituted alkynes which provide access to many diverse nitrogen-rich structures. This thesis describes the development of new ring-forming reactions of yndiamides. In the course of this work three project areas have been explored:
1. A cycloisomerisation transformation to form fused pyrroles, using either gold-catalysis or by heating in the absence of a catalyst (Chapter 2).
2. Two rhodium-catalysed [2+2+2] cyclotrimerisation reactions which form 1,2-diaminobenzene derivatives (Chapter 3). Mechanistic studies on this reaction were also carried out using computational methods (Chapter 4).
3. Catalytic methods to synthesise diaminopyridine and diaminopyridone derivatives from yndiamides. (Chapter 5).

Keywords: Yndiamide
Advisor: Anderson, EA