VictorJuiz/thesis huggingface dataset:
New developments in open quantum system dynamics

The dynamics of many chemical systems can be influenced significantly by interactions with their environment (bath). An exact treatment of this is often infeasible due to the exponential scaling of Hilbert space with the number of degrees of freedom. In this thesis, dynamical methods, which overcome this difficulty, are considered for spin systems coupled to spin baths as well as systems coupled to harmonic oscillator baths.
The thesis begins by considering recombination reactions of radical pairs, in which two electron spins interact with baths of nuclear spins. Motivated by inaccuracies observed in semiclassical treatments of the dynamics of a series of cryptochrome-based radical pairs, a new approach capable of treating the quantum dynamics of spin systems coupled to large baths of spins is presented. This method is validated for a series of central spin models, and is found to correctly describe the quantum dynamics of spin systems containing up to 1000 spins.
Following this, the validity of the conventional treatment of radical pair recombination reactions is explored by considering the coupled electronic, nuclear and spin dynamics of a model radical ion pair. The dynamics of this model is treated using the hierarchical equations of motion (HEOM) formalism, and the results obtained are used to validate a recently proposed series of master equations. The HEOM formalism exactly captures the quantum dynamics of systems that are coupled to harmonic baths. However, due to the scaling of its computational cost with the strength of the coupling, it often becomes impractical. To overcome this difficulty, an efficient tree tensor network-based approach is presented and valided by treating a series of simple models. Following this, it is applied to the calculation of electron transfer rates for a series of models spanning a wide range of physical regimes in order to validate a recently proposed interpolation formula for the calculation of electron transfer rates.

Advisor: Manolopoulos, D
Exploring the role of the RNA-binding protein SRSF3 in the developing heart

Understanding the molecular processes that govern cardiovascular development has the potential to inform regenerative strategies for disease states. Due to their versatile roles, epicardial cells are an attractive therapeutic target. However, using epicardial cells for therapy is hindered by our limited understanding of epicardial biology.
The embryonic epicardium is one of the main regulators of cardiovascular development, functioning to secrete essential growth factors and produce epicardium-derived cells (EPDCs) that contribute most coronary vascular smooth muscle cells and cardiac fibroblasts. Due to its complex biology, the molecular mechanisms that control epicardial formation and differentiation have not been fully elucidated.
SRSF3 is an RNA-binding protein that has essential roles in RNA processing, and it is highly expressed in the proepicardium and later in the epicardial layer during heart development. Deletion of Srsf3 from the murine proepicardium using the Tg(Gata5-Cre) or embryonic day (E) 8.5 induction of Wt1CreERT2 led to proliferative arrest and impaired epithelial-to-mesenchymal transition (EMT), which prevented proper formation and function of the epicardial layer. The epicardial requirement for SRSF3 was further assessed in a mouse epicardial cell line using RNA interference, which revealed that SRSF3 is required for production of Cyclin D1 and for EMT in response to TGFβ.
Induction of Srsf3 deletion with the Wt1CreERT2 after the proepicardial stage resulted in disrupted sprouting from the sinus venosus and elevated hypoxia at E13.5. Single-cell RNA-sequencing showed SRSF3-depleted epicardial cells were removed by E15.5. The remaining non-targeted cells became hyperproliferative and compensated for the loss, with normal epicardial contribution being detected at E17.5.
Due to the compensation mechanism, the existence of epicardial subpopulations was explored through assessment of published heterogeneous marker genes: Sema3d, Scx, Tcf21, Tbx18 and Wt1, using RNAscope, PrimeFlow and Single-cell RNA-Sequencing, in both wild-type and SRSF3 mutants. Complete overlap of the markers was detected, with no evidence of epicardial subpopulations, raising questions regarding the specificity of previously reported Cre lines.
This research supports a role for SRSF3 as a master regulator of RNA metabolism in epicardial cells, however, further studies are required to dissect the exact molecular mechanisms involved.

Keywords: coronary vessel
proepicardium
epicardium
Advisor: Smart, N
Quantum chemical simulations of radical cation chemistry

The Diels-Alder (DA) reaction is among the most important and versatile methods in creating ring molecules, and factors governing stereoselectivity and rate have been widely studied. However, the chemoselectivity in products are often restricted, as electronic natures of the reactants (typically electron-rich diene and electron-poor dienophile) have to be matched.
On the other hand, in radical chemistry, the removal of a free election helps promote an entirely different chemical environment within the reactants. This has been experimentally shown to be imperative in forming a different set of products not predicted in neutral DA reactions using photochemistry or redox chemistry. Chapter 1 will encompass an overview of such reactions and also the different computational techniques applied in understanding this chemistry.
Using an emerging technique known as quasi-classical dynamics (QCD), coupled with Density Functional Theory (DFT), this thesis investigated the radical cation DA reaction of a small sample system (Chapter 2) to provide quantitative understanding to this observed phenomena, and discovered the existence of reactive intermediates that could not be predicted with Transition State Theory (TST). As these intermediates have exceptionally long lifetimes, they also describe the dynamical nature of forming different products via the same transition state, which provides a strong contrast against concerted reactions (Figure A.1). This has never been applied to the study of radical cycloadditions before. In Chapter 3, the same techniques were applied to a larger DA system to predict product stereoselectivity, and kinetics rate theory provided evidence of reversibility from the neutral products.
The different chemical environment promoted from the removal of a single electron is revisited in Chapter 4 in the field of atropisomerism. In the radical cation systems chosen, we observed an unprecedented lowering of the energy barriers towards racemization. This effect also created a two-step mechanism, which was subsequently explained using Frontier Molecular Orbital (FMO) theory, and could allow better methods in isolating atropisomers.
Once again, and lastly in Chapter 5, the aforementioned computational techniques (DFT and QCD) are utilized in understanding different reaction pathways in non-heme enzymes, this time with the addition of hybrid quantum mechanics/molecular mechanics (QM:MM). The selectivity between the radical rebound (RR) pathway and the desaturation pathway was revealed and these different pathways were observed under different timescales, which would facilitate better catalytic design that enables controlled selectivity.

Advisor: Paton, R
McGrady, J
The Antichrist tradition in Second Temple Judaism and early Christianity

My thesis, entitled “The Antichrist Tradition in Second Temple Judaism and Early Christianity”, answers the following research question: in ancient Jewish and early Christian thought, what is the function of antimessianism in relation to messianism? Bearing in mind the achievements as well as the shortcomings of the scholarship on the topic, I propose a new framework for the understanding of this phenomenon. Three core claims are advanced throughout the work. Firstly, the references to the Antimessiah/Antichrist should be understood to constitute a tradition within which certain texts and concepts were transmitted and re-engaged by successive reading communities. Secondly, there are non-Christian Second Temple Jewish sources which speak about antimessianic eschatological actors. Thirdly, antimessianic conflict is structured around two central motifs, namely violent conflict and mimetic rivalry.
The thesis consists of eight chapters. CHAPTER I offers a history of scholarship on the Antichrist and positions my research within it. CHAPTER II deploys reception historical tools to the study of certain passages of the Hebrew Bible which were taken by later Jewish and Christian interpreters as referring to the Antichrist. Subsequent chapters trace the antimessianic/Antichristological expectation in different ancient corpora: the Dead Sea Scrolls (CHAPTER III), the New Testament (CHAPTER IV), the extracanonical Biblical literature (CHAPTER V), the Patristic writings (CHAPTER VI). The conclusions of the thesis are presented in CHAPTER VII.
The major contribution of my work is to provide a viable methodology for the study of the Antichrist tradition along with its definition which allows to incorporate a wealth of previously disregarded sources. My study shows the presence of antimessianic speculation in Second Temple Jewish writings and the paramount importance of Biblical exegesis to its development.

Advisor: Bockmuehl, M
Chronology, dialect and style: studies in the distribution of linguistic archaisms in early Greek hexameter poetry

The chronology of early Greek hexameter poetry is obscure. Some scholars have attempted to make arguments about the relative chronology of the texts based on their differing use of certain linguistic forms. In the introductory chapter the history of the question is surveyed, and statistical arguments are used to establish which of the previously studied linguistic forms are most worthy of further study. The next three chapters are each concerned with one linguistic form – thematic genitives in -οιο and -ου; the observance and neglect of digamma; and the use of different kinds of tmesis, ‘initial’ and ‘non-initial’. In each chapter, possibly underlying factors are analysed.
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I argue that for each feature the factor of formularity or repetition needs to be taken into account, since repeated phrases distort the statistics. For the thematic genitives, it was found that the ending chosen is highly determined by the metrical structure of the words in question, and that each metrical structure differs in its use of the ending. I also argue that the -οιο ending is stylistically marked as appropriate for heroic hexameter texts. For the digamma, it is argued that issues of dialect play a particularly important role, and a parallel with the similar phenomenon of resonant lengthening is drawn out. It is also shown that different words treat digamma differently. Lastly, it is found that the distribution of different types of tmesis is dependent on whether they are found in speech and narrative. In each case, it is argued that chronology is relatively unlikely to be a factor in the distribution.
In the last chapter, it is argued that there might be a significant stylistic element in the distribution of all three factors, where the more archaic linguistic forms became stylistically marked through their association with certain registers or kinds of poetries. A model for this process is sketched out, according to which, the more likely a kind of hexameter performance was to remain conservative as across generations, the more likely it was to have the archaic forms associated with it, thus producing stylistic marking.

Advisor: Willi, A
Figured funerary stelai from Roman-period Anatolia, 100 BC-AD 400: regional considerations of cultural, social, and economic expressions in funerary contexts

This thesis presents a multi-faceted, case-study based examination of regionalism and use of figured funerary stelai from fifteen sites in Roman-period Asia Minor and Galatia, focusing on local patterns of iconography and epigraphy as well as broader regional comparison of these trends. These non-door stelai, a sample of 302 monuments, are flat-face stones decorated with relief figures from a narrow selection of iconographic-types. This study offers a synthesis of all aspects of figured-stele use in the case-study sites, encompassing constituent elements of the monuments and consideration of stele-use between city and countryside, taking into account local geo-political histories, and approaching stelai as simultaneously private and public monuments of self-display. Section I focuses on stelai in the sepulchral landscape of Roman-period Anatolia, the technical details of the stelai themselves, and situating stelai in the economics of commemoration. There follows in Section II a detailed assessment of the iconography and epigraphy of the case-study figured stelai. Questions of represented socio-economic levels, stele-use vis-à-vis settlement patterns, and regional customs of commemoration are the subject of Section III, exploring relationships between patrons, deceased, and stele components. Iconography and epigraphy on these monuments highlight the ‘standardization’ of motifs in the Roman period and local shifts in image emphases and patron priorities, including the development of more individualized iconography with the expanded socio-economic spectrum employing this monument to include not only some ‘elite’ but also gladiators and farmers among other occupations. Similar expansion appears in the geographic distribution of figured stelai, incorporating regions with limited pre-Roman traditions for the monument. The simultaneous broadening of both the socio-economic levels of patrons and the geographic regions of use represent distinguishing characteristics of Roman-period figured-stele patterns.

Keywords: Funerary archaeology
Roman Anatolia
Roman archaeology
Advisor: Smith, R
An investigation of the highly conserved long non-coding RNA CEROX1

Amid growing catalogues of long non-coding RNAs (lncRNAs), experimentally characterised examples are few, especially for the recently identified subpopulation that are enriched in the cytoplasm. Amongst these are lncRNAs whose activity is proposed to be mediated by the competitive endogenous RNA (ceRNA) mechanism. De-repression of miRNA targets results in concerted gene expression changes following ceRNA modulation in numerous in vitro models, but evidence of in vivo physiological relevance is lacking.
In light of this, the novel human lncRNA CEROX1 was subjected to a multifaceted characterisation to investigate its potential as a physiologically important candidate ceRNA. In vitro molecular biology and in silico bioinformatic approaches were used to investigate the expression, conservation, activity, and regulation of CEROX1. It was found that CEROX1 is both extremely highly expressed and highly conserved, being expressed and enriched in the central nervous system of eutherian mammals. In particular, CEROX1 is highly enriched in cells of the oligodendrocyte lineage, and putatively associated with the process of oligodendrocyte differentiation.
Modulation of CEROX1 and its murine orthologue Cerox1 in vitro results in concerted regulation of complex I of the mitochondrial electron transport chain; these are therefore the first lncRNAs identified with such a role. In line with its putative activity in regulating energy metabolism in the developing CNS, CEROX1 was found to be upregulated in vitro in response to calcium signalling, which contributes substantially to cell signalling pathways between neurons and glia including oligodendrocytes.
In addition to the conserved mitochondria-regulating role of CEROX1, evidence of translation of a 234 residue open reading frame was uncovered in vitro and in vivo, suggesting recent evolution of the locus towards a protogene state.
This work highly supports CEROX1 as a promising in vivo ceRNA candidate, although future study is required to pursue its role in regulating energy metabolism in the CNS.

Advisor: Sirey, TM
Ponting, CP
Davies, KE
Oliver, PL
The 1860 Japanese embassy and the opening of American civilization

The 1860 Japanese Embassy to the United States sparked a whirlwind of national optimism and cultural fantasy that challenged America’s linked conceptions of race, “civilization,” and power. This dissertation argues that, over the brief course of the 1860 Japanese Embassy, the Japanese, and their interactions with those normally on the periphery of diplomatic narratives, opened various epistemic communities to new understandings of “civilization” and hierarchies of personhood as experienced through the lens of the role and future of Japan. At the same time, within the embassy itself, Sendai retainer Tamamushi Sadayū (1823–1869) rejected race and human exploitation as hierarchies of “civilization,” separated morality from “Westernization,” and perceived the intra-hierarchical compassion he believed he saw in America as the key to Japan’s future political stability. Tamamushi’s ideas and transnational experiences manifested themselves in his activity as a military commander for the Northern Alliance in the Boshin War (1868–1869). The new knowledge revealed by this study alters the historical understanding of the nineteenth-century Japanese influence on American intellectual discourse, as well as the dual narratives of kaikoku (Japan’s “opening”) and bunmei kaika (“civilization and enlightenment”), two of the defining periods in Japanese history. Analyzing the largely forgotten 1860 embassy reveals various local actors reimagining the place of Japan and themselves in the meaning and pursuit of a better world. This reshaping of various world visions inspired by encounters between the Japanese and transnational actors expands our understanding of the production of identity and solidarity, Japanese and American civil war history, the role of gender in interracial encounters, transnationalism, and Japan’s shift from the Tokugawa to the Meiji era.

Advisor: Konishi, S
Essays on information and incentives in financial markets

This thesis comprises three essays in financial economics. The common thread is the interaction between incentives and information in financial markets. Chapter 1 analyzes a model in which a credit rating agency's (CRA's) rating is followed by a market for credit risk that provides a public signal - the price. A more accurate rating decreases market informativeness, as it diminishes mispricing and, hence, incentives for investor information acquisition. On the other hand, more-informative trading increases CRA accuracy incentives by making rating inflation more transparent. We analyze implications for policy and the real economy. Chapter 2 develops a model of the interaction between executive compensation and stock market prices, and analyzes its implications for corporate short-termism. We show that inefficient short-termism can arise in equilibrium as a self-fulfilling prophecy, due to strategic complementarities between the firm's investment horizon and investors' decision to acquire information about short-term performance or long-term value. The model helps us assess evidence presented in the "myopia" debate and yields novel implications regarding ownership structure, executive compensation, and managerial horizon. Finally, Chapter 3 analyzes a model of competition between credit rating agencies (CRAs). In equilibrium, investors buy only assets that received high ratings from multiple CRAs. This has two contrasting effects on the quality of certification. On the one hand, the issuer needs to pass the screening of multiple CRAs; other things being equal, this improves certification. On the other hand, it has the perverse effect of incentivizing dishonest ratings, by introducing a team dimension that dilutes the CRAs' reputational concerns. When the perverse effect dominates, competition reduces the quality of certification. However, mandating disclosure of indicative ratings can restore the first-best outcome.

Advisor: Meyer, M
Shapiro, J
Urban lives and urban legends: re-examining the slum in Dar es Salaam, Tanzania

This thesis brings together literature on slums in urban economics and institutions in political science with new empirical data. In doing so, it contributes knowledge to both bodies of research while also advancing the multidisciplinary discourse on cities in international development. It uses a mix of research methods to examine theories about the emergence and persistence of slum deprivation. It takes a case study approach, drawing on large-scale household survey data to measure patterns in characteristics of slum households and their housing as well as semi-structured interviews and focus groups to understand the processes that underpin these observations. This analysis reveals that most slum households in Dar es Salaam are not poor, and that there is no clear relationship between informality and housing quality. Institutions play a key role in explaining these results: strong informal land ownership and transfer arrangements eliminate differences in transaction risks across formal and informal owners, while weak land coordination institutions trap well-located middle-income housing at slum standards. The analysis shows that slum theories which rely on expectations about market behaviour will have limited explanatory power unless they can better account for the mediating influence of informal market institutions on this behaviour. Improved understanding of informal institutions is needed to refine these theories and to improve their predictive power. The thesis concludes by drawing insights from the analysis of informal institutions in Dar es Salaam into potential foundations of a more complete market theory of slum deprivation.

Keywords: Tanzania
Slums
Housing markets
Advisor: Sanchez-Ancochea, D
Gollin, D
Wetting of pulsed plasma fluoropolymers

The work presented in this thesis is an investigation of the surface properties of fluoropolymers synthesized via pulsed plasma polymerization. The focus is on perfluoroalkyl acrylate (PFAC-n, where n is the number of carbons in the perfluoroalkyl chain) polymers which are used in the manufacture of military protective clothing. The aim of the study is to understand how PFAC-n polymer surfaces interact with liquids, particularly chemical warfare agents (CWA’s). The properties of some other fluoropolymers are also briefly investigated; the acrylate group in PFAC-6 is exchanged for an alkene (PFO) and a perfluoroalkyl (PFH) group. Additionally, a co-polymer of PFAC-6 and 2-hydroxyethyl methacrylate (HEMA) was synthesized which shows good potential for use in oil/water separation.
The surfaces were characterized using 19F solid-state nuclear magnetic resonance (NMR) spectroscopy, X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM) and contact angle goniometry. It is shown that plasma conditions resulted in degradation of PFO and PFH, whilst PFAC-n polymerizes with retention of functionality. PFAC-4 and -6 exist in the liquid state at room temperatures, whilst PFAC-8 and -10 are disordered polycrystalline solids. All show increased side-chain ordering at the surface compared to the bulk, with preferential segregation of CF3 at the surface. The two liquids have increased ordering compared to the solids at room temperature and are therefore lower in surface energy.
The time- and temperature-dependence of contact angles of ethylene glycol (EG) and n-hexadecane (n-HD) is investigated, and these are shown to trigger surface reorganization of PFAC-n when the polymers are in the liquid state. The wetting behaviour of some CWA’s and CWA simulants is also examined, and it was found that the CWA’s display lower contact angles on PFAC-n than predicted by the wetting of conventional probe liquids, such as ethylene glycol and n-hexadecane, or by the wetting of CWA simulants.

Keywords: Nuclear Magnetic Resonance
T1
Surface Rearrangement
Acrylate
Wetting
X-ray Photoelectron Spectroscopy
Fluoropolymer
Chemical Warfare Agent
Atomic Force Microscopy
AFM
Plasma
Fluorocarbon
Spin Lattice
Fluoroalkyl
XPS
Methacrylate
Surface Reconstruction
NMR
Perfluoroalkyl
Plasma polymer
Contact Angle
Advisor: Perkin, S