VictorJuiz/thesis huggingface dataset:
Energy harvesting by using ferroelectric switching

The aim of the current work is to develop a novel energy harvesting method by using ferroelectric/ferroelastic switching and to establish a practical prototype device with stability and robustness. The results are expected to provide a deep mechanistic understanding of the polarization state in ferroelectrics and assist in the improvement of transducers’ performance in practical applications.
Ferroelectric/ferroelastic switching, which can generate greater energies and charge flows than those of piezoelectrics has attracted increased interest to improve transducers’ performance in recent years. However, the challenges of nonlinearity, fatigue degradation and the difficulty of driving an electrical cycle by stress have limited ferroelectrics’ use in energy harvesting applications. In the current work, by using a simple model of switching, a working cycle that could generate electrical energy from a harmonically varying source of stress is explored. The cycle uses depolarization by stress, followed by repolarization with combined electromechanical loading. A harvesting electric field and bias electric field are imposed to ensure a stable repeatable working cycle during the depolarization process and repolarization process, respectively. The bias electric field, which is much less than the coercive field, provides a preferred direction of repolarization. The conversion efficiency of this cycle is estimated and improvements to the cycle are explored by adjusting the electrical and mechanical field amplitudes.
The current work then explores a novel and robust ferroelectric energy harvester based on partial ferroelectric switching. The device is of simple construction and achieves a per-cycle energy density of about 1mJ/cm3, orders of magnitude greater than that of typical piezoelectrics. Instead of using an external electrical bias field, the internal residual electric fields, generated during a partial depoling of an electroceramic, are adopted to provide ‘memory’ of a preferred direction for repolarizing it. A crucial feature is the control of residual stress by poling the active material in stages, first in a mechanically unconstrained state, then adhered to a substrate before completing the poling process. Then the method works by partially depolarizing a poled ferroelectric using a single application of tensile stress, and then using cycles of compression to vary the polarization state. It is shown that only periodic compressive stress is needed to induce the energy harvesting cycles, yielding unique and promising mechanical attributes that limit fatigue or fracture during cyclic loading. The results show this prototype device operating stably over 0.5×106 cycles at low frequency. The explorations of various polarization states and resistive electrical loads are also carried out to improve the performance for further practical applications.

Keywords: electroceramic
energy harvesting
transducer
piezoelectric
ferroelectric/ferroelastic switching
Advisor: Huber, J
Site-selective strategies for the biological investigation of glycoproteins

Protein glycosylation is a post-translational modification that modulates numerous intracellular pathways and extracellular events. However, the study of glycosylated proteins is challenging since these are naturally produced as heterogeneous mixtures of different glycoforms. Moreover, isolation and characterisation of single glycoforms is not always feasible, and the chemical synthesis of such complex biomolecules is often impossible. Although several glycan-protein ligation methods have emerged in recent years, there is still significant progress to be made for the generation of true, homogeneous glycoform-mimics. This doctoral thesis aims at expanding the current toolbox used for the site-selective glycosylation of proteins with strategies that generate ‘near-native’ glycosidic linkages.
The ‘tag-and-modify’ approach has been widely recognized as a powerful method for the site-selective chemical modification of proteins. Herein, the application of this methodology for the synthesis of proteoglycan (PG)-mimics is described. A natural PG was homogeneously ‘tagged’ via enzymatic trimming of its glycosaminoglycan (GAG) chain, and a biocompatible radical ligation was developed to install a priming sugar. The minimally ‘modified’ PG was subjected to enzymatic GAG-polymerization and this allowed the unprecedented access to remodeled PG-analogues. Optimised conditions for the on-protein GAG-extension revealed interesting aspects pertaining to the activity of the employed GAG-synthase. Future work should reveal the utility of such methodology towards understanding the extent to which variously engineered GAGs affect the biological activity of their corresponding PG glycoforms.
In our work we also explored a cysteine (Cys)-based ‘tag-and-modify’ strategy for the generation of a homogeneous N-glycoprotein-mimic. We found that the presumed disulfide reshuffling of the native Cys-residues had impeded the site-specific chemical glycosylation at the inserted Cys-tag. Lastly, our focus turned towards further investigating the protein that uses the high energy glucose (Glc)-donor UDP-Glc to initiate, via autoglucosylation, the biosynthesis of glycogen. Close inspection of both its self-extended glycoforms and the more complex glucosylation states generated by the downstream enzymatic partners raised exciting new questions about the basic mechanisms of glycogenesis and glycogenolysis.

Keywords: protein modifications
glycogenesis
site-selective
proteoglycans
glycoproteins
tag-and-modify
glycosaminoglycans
Advisor: Davis, B
Yue, W
Cortical regulation of sleep

Sleep is vital but the regulation of sleep is poorly understood. Over the past decades, several subcortical regions in the mammalian brain have been identified, which promote wakefulness or sleep and constitute a ‘sleep switch’. The neurophysiology of the circadian clock, with the suprachiasmatic nucleus of the hypothalamus at its centre, has also been elucidated. However, it is still unclear how the brain tracks the accumulating sleep debt during wakefulness and adjusts the duration and intensity of sleep accordingly. This core process of sleep regulation, termed ‘sleep homeostasis’, remains enigmatic. The cortex engages in characteristic oscillations during sleep that serve as electroencephalographic (EEG) markers of rapid eye movement (REM) and non-rapid eye movement (NREM) sleep. Slow waves, the hallmark of NREM sleep, indicate the depth of sleep and are used to determine the level of the homeostatic process. The aim of my DPhil project was to probe in mice whether cortex, and in particular neocortical layer 5 pyramidal neurons, contribute to the regulation of slow waves and sleep.
This project was divided into three subprojects. First, I present laminar recordings of neocortical activity during sleep in wild type mice, which suggest that layer 5 actively drives slow waves. Next, I describe the validation of a chemogenetic tool, which I initially planned to use for the manipulation of layer 5 pyramidal neurons. These experiments revealed unexpected effects of the chemogenetic actuators clozapine-N-oxide (CNO) and Compound 21 (Cmpd21) on sleep in wild type mice, which do not express designer receptors exclusively activated by designer drugs (DREADDs). Finally, I present extensive work on ‘cortical SNAP25-ablated’ (Rbp4-Cre;Ai14;Snap25fl/fl) mice, which served as a model for chronic silencing of neocortical layer 5 pyramidal and archicortical dentate gyrus granule cells. These mice displayed changes in neocortical dynamics during NREM sleep, a strong increase in wakefulness, and a reduced homeostatic response to sleep deprivation, while circadian measures were unaltered.
Together, my work suggests that the cortex may play an essential role in the regulation of sleep oscillations, architecture, and homeostasis. Further investigation into the cortical regulation of sleep could reveal neural circuits and molecular mechanisms underlying sleep homeostasis and identify novel targets for the manipulation of sleep in the clinic.

Keywords: cerebral cortex
sleep
layer 5 pyramidal neurons
mouse
sleep homeostasis
DREADDs
Advisor: Vyazovskiy, V
Molnar, Z
Akerman, CJ
Strongly-coupled QFTs from string theory

Strongly-coupled regimes of quantum field theory (QFT) are notoriously challenging to explore. In this thesis, which is divided into two parts, I address the question from a string theoretic perspective. I will focus on methods to map out the RG-flow, symmetries and phase structure, first taking a holographic point of view, then within the context of geometric engineering and brane-webs.
Holography constitutes a profound and potent way to describe strongly-coupled QFTs, especially when combined with sophisticated geometric techniques, and modern tools from QFT such as generalized global symmetries and their 't Hooft anomalies. In chapter 3 I will present our work on the gravitational dual of I/c-extremization for a 1d/2d N=(0,2) theory in the presence of a holomorphically varying axio-dilaton. This generalization makes the analysis suitable for F-theory supergravity solutions, and establishes a correspondence of the two extremization principles furnished by M/F-theory duality. In chapter 4 we develop new holographic methods to compute anomalies of discrete higher-form symmetries, and derive the topological field theory (TFT), which matches these anomalies in the infra-red (IR). This interplay of holography and generalized global symmetries shines new light on the topological sector of supergravity theories and its physical implications. We illustrate the approach in a rich non-conformal holographic setting, which flows to confining N=1 SU(N) Super-Yang Mills (SYM) in the IR, focusing on the 1-form symmetry and its mixed 0-/1-form symmetry anomaly, which is closely related to chiral symmetry breaking in gapped confining vacua.
Geometric engineering and brane-webs enable us to realize a vast array of superconformal field theories (SCFTs) whose salient features would otherwise be out of reach. In my research, I have focused on 5d N=1 SCFTs, which are intrinsically non-perturbative. In chapters 6 and 7 we establish a comprehensive description of 5d SCFTs in terms of Generalized Toric Polygons (GTPs) and map out their moduli space. Using the duality with brane-webs and insights from toric geometry we parametrize the extended Coulomb branch (CB) and determine an algorithm to compute the magnetic quiver (MQ) describing the Higgs branch (HB). We then apply these methods to all 5d SCFTs that flow to single gauge node theories in the IR with anti-symmetric and fundamental matter. Finally, in chapter 8 we identify a correspondence between 5d extended CB deformations and 3d Fayet-Iliopoulos (FI) deformations in the MQ, which elucidates how changes in the geometry of the HB are implemented as we move along the extended CB.

Keywords: String Theory
Holography
Supersymmetric Quantum Field Theory
Strongly-coupled Quantum Field Theory
Generalized Global Symmetries
Brane-webs
Advisor: Schafer-Nameki, S
Latin loanwords in Greek documentary papyri (c. 30 BCE to c. 200 CE)

Ancient Greek hosted hundreds of Latin loanwords (e.g. κεντουρίων ‘centurion’) as a result of contact between Greeks and Romans. Because previous studies of Latin loanwords have mostly concentrated on chronology, morphology, and lexicon, there has been no systematic investigation of their introduction and spread in specific contexts and the motives behind their choice or avoidance. This thesis is the first work to address such questions. It uses a large corpus of Greek texts, the papyri of early Roman Egypt (c. 30 BCE to c. 200 CE), a place that did not have much prior exposure to Latin, as they are generally closer to everyday language than literature and present numerous first attestations of loans with a high density and frequency.
The dissertation includes an introduction laying the linguistic and methodological groundwork and four chapters. The first two focus on a military-influenced setting, the Eastern Desert of Egypt with forts (Didymoi and Krokodilo) and quarries (Mons Claudianus), and the other two on an urban setting in the Nile valley, the city of Oxyrhynchus. Being at the opposite ends of a scale of Romanness and military influence, the two settings might have presented diametrically opposed linguistic outcomes. In fact, most findings are valid for both. Only the players and a few tendencies differ: if in the Desert loanwords spread from within the community, from the higher ranks and the military administration, in Oxyrhynchus loanwords at first enter the community mainly from outside, reaching it from a larger centre, Alexandria. But general trends are observable in both settings. Documents show that military loanwords are usually the first large group of loans to enter military and civilian settings alike. Loanwords are by and large introduced by a select and generally bilingual minority and spread through society mainly through a top- down process. This process is faster in smaller societies and slower in larger ones. The introduction and choice of loanwords is not usually the consequence of a deliberate policy, and loans are deliberately chosen, preferred, or avoided in specific cases only. This analysis deepens our knowledge of Latin influence on Greek in a newly conquered, Greek-speaking region like Egypt and furthers our understanding of Latin-Greek language contact and its consequences.

Keywords: Eastern Desert
Latin loanwords in Greek
language contact
borrowing
papyri
Oxyrhynchus
Roman Egypt
Advisor: Benaissa, A
Dickey, E
The incorporation of Dalits into India’s business economy & its implications for social and economic policies

Even after six and a half decades since Indian Independence, Dalits (ex-untouchables and oppressed castes) continue to experience caste-based discrimination and social exclusion in social as well as economic life. This research examines the incorporation of Dalits into the business economy - how they enter the market as owners of businesses rather than as wage-workers. The research has three key objectives: first, to analyse the spatial and sectoral patterns and variation of Dalit’s incorporation; second, to explain factors and processes affecting their entry; and third, to analyse the implications of key social and economic policies on Dalits’ incorporation.
This doctoral research project uses mixed methods, moves between different scales and deploys a wide range of evidence. The research estimates ‘indices of participation’ and produces a series of maps to show patterns and trajectories. It uses spatial econometric techniques to model quantifiable factors affecting Dalits’ entry. It relies on qualitative methods for individual case studies to unravel other factors and processes. Using Schaffer’s policy analysis framework, the research examines the politics of affirmative policies for Dalit businesses in the agenda-setting, the establishing of procedures and rules, and resource mobilisation.
The study revealed that the trajectory of Dalits’ incorporation is uneven and the spatial patterns across several sectors and regions show persistent under-representation. Urbanisation is the most significant predictor of Dalits’ incorporation. Dalits’ entry into the business is conditioned by the interactions of opportunities and resources and by the barriers created by subtle forms of exclusionary and discriminatory practices inherent in social structures, market institutions and the state. The study also found that the politics of patronage, of bureaucratic inefficiency, underinvestment and procrastination, and of domination of the business interests of higher castes are mutually reinforcing. This research has clear policy significance from the perspectives of equity and inclusiveness in the business economy.

Keywords: Social Exclusion
Business Economy
Discrimination
Entrepreneurship
Uttar Pradesh
India
Dalit
Spatial Analysis
Mixed Methods
Policy Studies
Advisor: Walker, R
Harriss-White, B
Societal selection and historical materialism

This DPhil thesis is an attempt to provide a detailed account of Marx’s theory of history which relies on a quasi-Darwinian mechanism. Building on the debate around G.A. Cohen’s Karl Marx’s Theory of History: A Defence, I argue that a selective mechanism between societies can underpin some of the key theses of historical materialism. In societal selection, the view I propose, greater development of the forces of production leads to a competitive advantage for those wielding these forces. Therefore, societies which adopt more developed forces of production ̶ or relations of production which foster the development of the forces of production -̶ will tend to be those that succeed, expand and impose their practices on others, at the expense of societies with less developed forces. This, in a manner similar to natural selection, creates a broad tendency for forces of production to develop and for relations which enable further development of these forces to emerge. This thesis will not just be and account of this process, which has already been presented in a more limited form by others; it will also attempt to detail the mechanisms underlying this process in order to tease out what a historical materialism that is based on societal selection would look like. How do forces of production translate into advantage in (generally military) competition? What is the role of imitation and human intention in the theory? How do the mechanisms of historical materialism play themselves out? What account does this theory have of class struggle and human agency? What kinds of predictions would this theory yield? Answering these questions will not only provide a more complete view of historical materialism but also address the critiques levied against this selectionist view. The goal of this thesis is to propose a detailed theory which can provide a compelling account of human history.

Keywords: Analytical Marxism
Marxism
Political Theory
Socialism
Historical Materialism
Advisor: Leopold, D
Identification of novel players implicated in replication-dependent and independent DNA interstrand crosslink (ICL) repair

The integrity of the genome is constantly under threat from within and without. Cells rely on the evolutionary conserved DNA damage response (DDR) mechanism to orchestrate the repair of DNA lesions and thus prevent the accumulation of mutations. One of the most deleterious types of DNA lesions, interstrand crosslink (ICL), occurs when a crosslinking agent forms covalent bonds with both strands of the double helix and tethers them together. The most well-studied among ICL repair pathways is the Fanconi Anaemia (FA) pathway, the disruption of which gives rise to a disorder of the same name. Both the FA pathway and the more recently-discovered NEIL3 pathway are replication-dependent. However, replication-independent pathways also exist and they are likely responsible for the repair of ICLs in non-dividing cells.
This thesis describes the optimisation of a purification scheme, which was designed to identify hitherto unknown players in ICL repair out of a pool of nuclear proteins. The scheme exploited the likely binding preference of such proteins for crosslinked over non-modified DNA probes. Two types of probes, linear and replication fork mimic, were designed to capture the proteins putatively associated with replication-independent and -dependent ICL repair pathways, respectively. The scheme was successfully used to identify UHRF1 and BOD1L1, two proteins with already known links to ICL repair, as well as THYN1, an EVE-domain-containing protein with no established roles in DDR. THYN1 is rapidly recruited to ICL sites in vivo and its absence confers hypersensitivity to psoralen-induced ICLs. THYN1 operates in the same pathway as FANCD2 in the repair of psoralen-derived lesions; however, unlike FANCD2, its activity is not cell cycle-dependent. Interestingly, THYN1 exerts a negative influence on MMC and cisplatin repair in FANCD2-deficient cells. Identification and analysis of putative THYN1 binding partners may help to explain this phenotype and to elucidate the molecular mechanisms which underpin THYN1-mediated repair.

Keywords: DNA damage repair
DNA interstrand crosslink (ICL) repair
Fanconi Anaemia (FA) pathway
THYN1
Advisor: Cohn, M
Alkyne probes and natural products

This thesis is split into two projects, both of which involve efforts to synthesise compounds containing alkynes. The first project is related to the synthesis of probes to label plant CYP450s, a key superfamily of enzymes involved in plant metabolism. The second project details efforts undertaken towards the synthesis of natural products isolated from the Laurencia genus of red algae.
Chapters 1 and 3 provide introductions to the respective projects. CYP450 enzymes and activity-based protein profiling (ABPP) are introduced in chapter 1. Chapter 3 provides some background to the Laurencia natural products; the biosynthetic postulates proposed for the formation of the diverse skeletons seen in the chemical structures are presented and a selection of interesting total syntheses carried out by numerous groups are also set forth.
Chapter 2 details the synthesis of CYP450 probes of a number of generations (termed G1 through G4) and outlines some of the challenges faced not only in the synthesis of these probes, but also with respect to observing labelling of the CYP450 enzymes in planta.
Chapters 4 and 5 concern the synthetic endeavours undertaken towards the total synthesis of ent-laurepinnacin, a natural product from the Laurencia genus, using a key silver(I)-mediated skeletal rearrangement involving complex oxonium ions as key intermediates. Chapter 6 concludes the thesis by detailing the development of an alternative protocol for the skeletal rearrangement, allowing access to alternative natural products ent-(E)-notoryne and laurendecumenyne B.

Keywords: organic chemistry
synthesis
Advisor: Burton, J
Van Der Hoorn, R