VictorJuiz/thesis huggingface dataset:
Investigation of Escherichia coli Tat (twin arginine translocase) transport in vitro
Keywords: twin arginine translocase system
PhoX
alkaline phosphatase

The Twin arginine translocase (Tat) system catalyzes movement of folded proteins across the cytoplasmic membrane of bacteria and the thylakoid membrane of plant chloroplasts. This transport process requires energy in the form of the transmembrane proton motive force (PMF). The Tat system can be studied in vitro using inner membrane vesicles (IMVs) from E. coli overproducing the Tat components, TatA, TatB and TatC. However, the transport efficiencies of current in vitro Tat transport assays are low.
In this work, current in vitro Tat transport assays were compared and parameters that affect transport efficiencies were identified. Mild French press treatment of IMVs resulted in larger IMVs with higher transport efficiencies. Chloride ions were shown to inhibit Tat transport in vitro. Generation of a PMF by the activity of ATP synthase gave higher transport efficiencies than generating a PMF by NADH respiration. This understanding was applied to develop an optimized in vitro Tat transport assay that showed a higher transport efficiency than currently published methods. Fluorescently labelled Tat substrates were developed to allow quantitative analysis of Tat transport.
The transport of the purified native Tat substrate, CueO into IMVs was characterized using the optimized in vitro Tat transport assay. It was shown that the proton concentration (ΔpH) component of the PMF was sufficient to support Tat transport in vitro. It was observed that transport of CueO ceased in a time-dependent manner in the in vitro Tat transport assays. This loss of transport efficiency could be due, at least in part, to the presence of a PMF since transport efficiency was reduced when IMVs were pre-energized.
Substrates for future in vitro single molecule fluorescence microscopy studies of the Tat transport were developed in this work. One of the substrates is fluorescently labelled CueO. The second substrate is the native Tat substrate alkaline phosphatase PhoX from Vibrio fischeri which was able to cleave the fluorogenic compound AttoPhos® and can thus be used as an enzymatic reporter of Tat transport.
The structure of a native Tat substrate from Pseudomonas fluorescens, PhoX, was solved by X-ray crystallography at a resolution of 1.4Å. PhoX is a monomeric six blade β propeller with two α-helical bundle subdomains. PhoX was shown to have optimum activity at pH8.0. PhoX has a novel catalytic site which requires two Fe3+ (including a Cys-coordinated Fe3+) and three Ca2+ as cofactors. Mutagenesis studies showed that all the metal ions are required for the integrity of the active site. Co-crystallization of PhoX with vanadate, an inhibitor of PhoX which mimics the transition state, showed that hydrolysis of phosphomonoesters does not involve formation of a covalent phosphoenzyme intermediate. Instead, dephosphorylation of substrates is proposed to occur via a SN2 reaction with OH- as the attacking nucleophile.
Numerical solutions to a class of stochastic partial differential equations arising in finance
Keywords: Monte Carlo simulations
Stochastic PDEs
Credit basket derivatives

We propose two alternative approaches to evaluate numerically credit basket derivatives in a N-name structural model where the number of entities, N, is large, and where the names are independent and identically distributed random variables conditional on common random factors.
In the ﬁrst framework, we treat a N-name model as a set of N Bernoulli random variables indicating a default or a survival. We show that certain expected functionals of the proportion LN of variables in a given state converge at rate 1/N as N [right arrow - infinity]. Based on these results, we propose a multi-level simulation algorithm using a family of sequences with increasing length, to obtain estimators for these expected functionals with a mean-square error of epsilon 2 and computational complexity of order epsilon−2, independent of N. In particular, this optimal complexity order also holds for the inﬁnite-dimensional limit. Numerical examples are presented for tranche spreads of basket credit derivatives.
In the second framework, we extend the approximation of Bush et al. [13] to a structural jump-diﬀusion model with discretely monitored defaults. Under this approach, a N-name model is represented as a system of particles with an absorbing boundary that is active in a discrete time set, and the loss of a portfolio is given as the function of empirical measure of the system. We show that, for the inﬁnite system, the empirical measure has a density with respect to the Lebesgue measure that satisﬁes a stochastic partial differential equation. Then, we develop an algorithm to efficiently estimate CDO index and tranche spreads consistent with underlying credit default swaps, using a ﬁnite diﬀerence simulation for the resulting SPDE. We verify the validity of this approximation numerically by comparison with results obtained by direct Monte Carlo simulation of the basket constituents.
A calibration exercise assesses the ﬂexibility of the model and its extensions to match CDO spreads from precrisis and crisis periods.
The nonparametric approach to demand analysis: essays in revealed preference theory
Keywords: Revealed preference
consumer demand

This thesis comprises three principal essays, each of which provides a contribution to the literature on the nonparametric approach to demand analysis. In each essay, I develop novel techniques that follow in the revealed preference tradition, and apply them to tackle a series of questions that concern the mechanisms underlying consumer spending decisions. Each technique developed is tightly linked to a particular nonparametric theory of choice behaviour and is explicitly designed for use with a finite set of observations. My work draws heavily upon results from finite mathematics, into which I integrate insights from information theory and integer programming. The output of this endeavor is a set of methodologies that are largely free of auxiliary assumptions over the form of the unobserved structural functions of interest.
Providing greater detail on the work to come, my first essay extends and clarifies the nonparametric approach to forecasting demand behaviour at new budget regimes. Using insights from information theory and integer programming, I construct an operational nonparametric definition of global rationality and develop a methodology that facilitates the recovery of globally rational individual demand predictions. This is the first attempt in the literature to develop a systematic methodology to impose global rationality on nonparametric demand predictions. The resulting forecasts allow for unrestricted preference heterogeneity in the population and I demonstrate how these predictions can be used for coherent welfare analysis. In my second and third essays, I prove new revealed preference testability axioms for models that extend the traditional neoclassical choice framework. Specifically, in my second essay, I address the intertemporal allocation of spending by collectives, whilst my final essay integrates taste variation into the utility maximisation framework. In both of these essays, I develop my testable results into practical algorithms that allow one to recover salient features of individual preferences. In my second essay, a methodology is developed to recover the minimal intrahousehold heterogeneity in theory-consistent discount rates, whilst my final essay develops a quadratic programming procedure that facilitates the recovery of the minimal interpersonal and intertemporal heterogeneity in tastes that is required to rationalise observed choice patterns. Applying these techniques to consumption micro-data yields new empirical insights that are of relevance to the applied literatures on time discounting, family economics and the public policy debate on tobacco control.
'Words for music perhaps': W.B. Yeats and musical sense
Keywords: song
Nietzsche
Shelley
Irish poetry
Ireland
music
Irish writing
Yeats
dance
Pater
Mallarme

‘Poetry’ insisted Ezra Pound, ‘is a composition of words set to music’: his Cantos remembered ‘Uncle Willie’ downstairs composing, singing poetry to himself. This study examines the nature and effects of W.B.Yeats’s idiosyncratic but profound sense of music. For his poems were compositions set to music. They were saturated with musical themes; syntactically he professed to write for the ear rather than the eye; and he flung himself repeatedly into the breach between music and words, composing ballads, songs, and plays with music, and performing poetry with musical instruments. My thesis is that nature of poetry, spoken, read or sung, obsessed Yeats, and I hold it self evident that such an acutely self-conscious poetry will articulate this obsession: to use his own imagery, will bear the scars of its own birth.
What follows is a study of meaning, obsession, and influence, beginning with what Yeats knew and how he came to poetry: his father’s and his own vocalizations of the musical preoccupations of Scott and Shelley, viewed through the annotations of ‘the first book [he] knew Shelley in’ and the solipsistic singers and instrumentalists of his early verse. The theme of chapter two is Ireland: the musical resonances of Anglo Irish ballads and Irish verse are viewed through Yeats’s aurally-oriented canon-formation, as we examine his instinctual recitations and deliberate approach to Irish folksong through the mediation of Douglas Hyde.
The aesthetics of Wagner, Pater, and the French symbolistes frame the third chapter, which describes how poetry might approach the condition of music in the motivic organization of The Wind Among the Reeds. In chapter four the impact of Nietzsche’s profoundly musical philosophy is correlated for the first time with the exact moments of Yeats’s discovery of his texts, as Yeats’s plays and poetry move from ‘Apollonian’ languor to ‘Dionysian’ energy, from dream to song and dance. My final chapter uncovers the long history of the practical experiments Yeats made to perform poetry with a ‘psaltery’, and their resonating afterlife in subsequent poetry and poets.
No musician himself, Yeats’s musical sense has until now been entirely dismissed: this study shows how central it is to his art and to an understanding of the dominant aesthetic of the age.
At the vanishing point of law?  : international law and the use of force by Britain and Canada in the Korean War and Afghanistan Conflict
Keywords: War
International law
Britain
Canada
Afghanistan Conflict
Korean War

This thesis examines important aspects of Canada and Britain’s participation in the Korean War of 1950-53 and the Afghanistan Conflict of 2001-present with a view to better understanding how international law influenced this participation, and whether key leaders and officials understood said law as a binding and distinct phenomenon. It draws on constructivist International Relations (IR) theory and “interactional” International Law (IL) theory, and employs a method of historical reconstruction and process tracing. I argue that, contrary to what realism might predict, international law helped define and shape each state’s possible course of action in the wars, and the justifications that could be made for their behaviour. More specifically, Canada and Britain’s involvement in the conflicts suggests that, when states use force, international law can play four broad roles: 1) it helps constitute the identities of the actors at issue; 2) it helps regulate the political and military practice of the actors at issue; 3) it permits and legitimates certain political and military practices that otherwise might not be permitted; and 4) it helps structure the process by which agents seek to develop and promote new legal rules and legitimate practice. However, I also contend that, contrary to what IL scholars might predict, the discourse and actions of Canadian and British leaders and officials during the Korean War and Afghanistan Conflict offer mixed support for the hypothesis that, when states use force, policy-makers understand international law as a binding and distinct set of legal rules, and the legal status of these rules impacts their decision-making. In sum, my findings suggest that international law can play important roles in world politics and the use of force by states, but it is unclear whether these effects are attributable to an obligatory quality in law.
Quantum structures in photovoltaic devices
Keywords: gallium arsenide
Solar Cells
Photovoltaics
electroreflectance
lead sulphide
Graphene Electrode
Optoelectronics
External quantum efficiency
Indium Arsenide
aluminium arsenide
Advanced characterisation
Fullerenes
quantum dots
zinc oxide
Squaraine
colloidal quantum dots

A study of three novel solar cells is presented, all of which incorporate a low-dimensional quantum confined component in a bid to enhance device performance.
Firstly, intermediate band solar cells (IBSCs) based on InAs quantum dots (QDs) in a GaAs p-i-n structure are studied. The aim is to isolate the InAs QDs from the GaAs conduction band by surrounding them with wider band gap aluminium arsenide. An increase in open circuit voltage (VOC) and decrease in short circuit current (Jsc) is observed, causing no overall change in power conversion efficiency. Dark current - voltage measurements show that the increase in VOC is due to reduced recombination. Electroreflectance and external quantum efficiency measurements attribute the decrease in Jsc primarily to a reduction in InGaAs states between the InAs QD and GaAs which act as an extraction pathway for charges in the control device.
A colloidal quantum dot (CQD) bulk heterojunction (BHJ) solar cell composed of a blend of PbS CQDs and ZnO nanoparticles is examined next. The aim of the BHJ is to increase charge separation by increasing the heterojunction interface. Different concentration ratios of each phase are tested and show no change in Jsc, due primarily to poor overall charge transport in the blend. VOC increases for a 30 wt% ZnO blend, and this is attributed largely to a reduction in shunt resistance in the BHJ devices.
Finally, graphene is compared to indium tin oxide (ITO) as an alternative transparent electrode in squaraine/ C70 solar cells. Due to graphene’s high transparency, graphene devices have enhanced Jsc, however, its poor sheet resistance increases the series resistance through the device, leading to a poorer fill factor. VOC is raised by using MoO3 as a hole blocking layer. Absorption in the squaraine layer is found to be more conducive to current extraction than in the C70 layer. This is due to better matching of exciton diffusion length and layer thickness in the squaraine and to the minority carrier blocking layer adjacent to the squaraine being more effective than the one adjacent to the C70.
A large displacement finite element analysis of a reinforced unpaved road
Keywords: unpaved roads
soil reinforcement

A series of finite element predictions of the behaviour of a reinforced unpaved road consisting of a layer of fill compacted on top of a clay subgrade with rough, thin reinforcement placed at the interface, is described in this thesis. These numerical solutions are obtained using a large strain finite element formulation that is based on the displacement method, and are restricted to the case of plane strain, monotonic loading. Separate elements are used to model the soil and reinforcement. In the finite element formulation, an Eulerian description of deformation is adopted and the Jaumann stress rate is used in the soil constitutive equations. Elastic perfectly-plastic soil models are used which are based on the von Mises yield function for cohesive soil and the Matsuoka criterion for frictional material. Emphasis is placed on obtaining new closed form solutions to parts of calculations that are performed numerically in many existing finite element formulations. The solution algorithm is based on a "Modified Euler Scheme". The computer implementation of the formulation is checked against an extensive series of test problems with known closed form solutions. These include the analysis of finite deformation of a single element of material and the calculation of small strain collapse loads. Finite cavity expansion is also studied. This numerical formulation is used to perform back analyses of a series of reinforced unpaved road model tests. The reinforcement tensions, and the stresses at the interface with the surrounding soil, are calculated using the numerical model and discussed with a view to identifying the mechanisms of reinforcement. Two existing analytical design models of the reinforced unpaved road are described and critically reviewed in the light of the finite element results.
Ensemble based quantum memory and adiabatic phase gates in electron spins
Keywords: spin dynamics
adiabatic passage
electron paramagnetic resonance
quantum memory

Quantum computing has been a new and challenging area of research since the concept was put forward in 1980s. A quantum computer is a computer that processes information encoded in systems that exhibit quantum properties and is proved in theory to be more powerful than classical computers. Various approaches to the implementation of the quantum computers have been studied over the decades, each of them having their own advantages and disadvantages in terms of the lifetime of the quantum information, processing time, and scalability of the implementation. Proposals for hybrid quantum processors are interesting because they benefit from the advantages of each comprising system, and thus providing a promising approach to a practical quantum computer.
In this thesis, I demonstrate experimentally the principle of utilizing electron spin ensembles as a quantum memory for hybrid quantum processors. I demonstrate the storage and on-demand retrieval of multiple bits of quantum information into and from a single electron spin ensemble by applying magnetic field gradient pulses. I then study the coupling between an electron spin ensemble and a three-dimensional microwave cavity, in the aim of discussing the condition for the coherent information transfer between the excitations in solid-state matter and photons. As an alternative to the high power pulses in electron paramagnetic resonance (EPR), I study the possibility of controlling the electron spin states via adiabatic processes. I demonstrate the implementation of adiabatic geometric phase gates in electron spins and compare their performances to other phase gates achieved with microwave pulses in both simulation and experiment, verifying the robustness of the adiabatic gates against certain type of noises. Finally I present the simulation method developed for simulating the pulsed EPR experiments in this thesis, using a model more general than some currently-existing simulation packages.
In the hall of mirrors: the Arab Nahda, nationalism, and the question of language
Keywords: liberalism
language and nationalism
Middle East studies
intellectual history
sectarianism
critical theory

The dissertation examines the foundations of modern Arab national thought in nineteenth-century works of Buṭrus al Busta̅ni̅ (1819-1883) and Aḥmad Fa̅ris al Shidya̅q (1804-1887) in which occurred an intersection of language-making practices and a national pedagogic project. It interrogates the centrality of language for Arab identity formation by deconstructing the metaphor "language is the mirror of the nation," an overarching slogan of the nineteenth century, as well as engaging with twentieth-century discussions of the Arab nation and its Nahḍa. The study seeks to challenge the conventional historiography of Arab thought by proposing a re-theorisation of the Arab Nahḍa as an Enlightenment-Modernity construct that constitutes the problematic of the Arab nation.
The study investigates through literature and literary tropes the makings and interstices of the historical Arab Nation: the topography of its making. It covers a series of primary understudied sources: Busta̅ni̅'s enunciative Nafi̅r Su̅riyya pamphlets that he wrote in the wake of the 1860 civil wars of Mount Lebanon and Damascus: his translation of Robinson Crusoe, dictionary, and encyclopaedia. As well as Shidya̅q’s fictional autobiography, linguistic essays and treatise, and travel writings on Europe. The dissertation engages with these works to show how the 'Nahḍa' is a constituted by inherently contradictory and supplementary projects. It forms a moment of fracture in history and temporality – as does the Enlightenment in Europe – from which emerges a seemingly coherent national narrative.
Protein-protein recognition in biological systems exhibiting highly-conserved tertiary structure: cytochrome P450
Keywords: magnetic resonance
cytochrome P450
kinetics
enzyme engineering
structural biology

Protein tertiary structure is more conserved than amino acid sequence, leading to a diverse range of functions observed in the same fold. Despite < 20 % overall sequence identity, cytochromes P450 all have the same fold. Bacterial Class I P450s receive electrons from a highly specific, often unidentified, ferredoxin, in which case the hemoprotein is termed “orphaned”.
CYP199A2, a Class I P450, accepts electrons from ferredoxins Pux and HaPux. Five orientation-dependent and one orientation-independent DEER measurements on paramagnetic HaPux and spin-labelled CYP199A2 yielded vector restraints, which were applied to building a model of the CYP199A2:HaPux complex in silico. A different binding mode was observed compared to P450cam:Pdx and P450scc:Adx, both recently elucidated by X-ray crystallography. This protocol was also applied to the CYP101D1:Arx complex. The first three measurements indicate that this heterodimer does not have a similar orientation to CYP199A2:HaPux, P450cam:Pdx, or P450scc:Adx.
P450cam was fused to putidatredoxin reductase (PdR) to explore the kinetic effects with a view to improving electron transfer to orphan P450s. Heme incorporation of this enzyme depends on linker length. In whole cells, the fusion was more active after longer incubations. In vitro kinetics of the fusion exhibited some co-operativity and enhanced kinetics over the unfused system under steady-state conditions.
The putative iron-sulfur biosynthesis ferredoxin PuxB had been engineered by rational mutagenesis to support catalysis by CYP199A2. It was confirmed this arose from improved protein-protein recognition. Engineering of E. coli ferredoxin based on these findings was carried out, resulting in electron-transfer to CYP199A4 from a novel engineered alien ferredoxin.