VictorJuiz/thesis huggingface dataset:
First-principles calculations of NMR parameters for materials applications

Nuclear magnetic resonance (NMR) is a powerful experimental technique for probing the local environment of nuclei in materials. However, it can be difficult to separate the large number of interactions that are recorded in the resulting spectra. First-principles calculations based on quantum mechanics therefore provide much-needed support for interpreting experimental spectra. In this way, the underlying mechanisms recorded in experimental spectra can be investigated on an atomic level, and trends can be noted with which to guide the direction of future experiments. This thesis presents two cases in which first-principles calculations do just that. The first is an investigation of the perovskite structures of NaNbO3, KNbO3, LiNbO3 and the related solid solutions of NaxK1-xNbO3, KxNa1-xNbO3 and LixNa1-xNbO3 in order to study how structural disorder affects their NMR parameters. The second investigation involves the calculation of the Knight shift in platinum, palladium and rhodium---in their elemental bulk forms and in a set of surface structures. The Knight shift is a systematic shift in the NMR frequencies of metallic systems. It arises from the hyperfine interaction between the nuclear spins and the spins of the unpaired conduction electrons. When calculating the Knight shift, it is found that the Brillouin zone must be very finely sampled. A discussion of core polarisation is also presented. This is the polarisation of core electrons as a result of their interaction with valence electrons. In the case of Curie paramagnets, core polarisation can have a significant effect on the calculation of hyperfine parameters.

Keywords: Knight shift
hyperfine
nuclear magnetic resonance
density functional theory
perovskite
Advisor: Yates, J
Toric chiral algebras

In this thesis, we investigate lattice chiral algebras as defined by Beilinson and Drinfeld. Given a factorisation monoid satisfying specific conditions and a super extension of this, Beilinson and Drinfeld show that one can push forward this line bundle (super extension) to give a factorisation algebra. Specifically, they describe this in the case of the factorisation monoid formed by taking &Gcy;-valued divisors set-theoretically supported over each divisor, for &Gcy; a lattice, as a method of constructing these lattice chiral algebras. In this work, we show that their definitions of such divisors, and of line bundles with factorisation on these, generalise to a wider class of objects given by taking coefficients in any cone, C, in a lattice. We show that, in this more general case, the functors of C-valued divisors with settheoretic pullback contained in S are ind-schemes, and, from this, that they form a factorisation monoid. Further, we show that super line bundles with factorisation exist on this factorisation monoid, and that if we have a super line bundle with factorisation on the factorisation monoid of C-valued divisors, we can push forward such a line bundle to get a chiral (factorisation) algebra as for lattices. Hence, we obtain a new class of chiral algebras via this procedure, which we call toric chiral algebras.

Advisor: Kremnitzer, K
Mixed-integer optimal control of fast dynamical systems

Many applications in engineering, computer science and economics involve mixed-integer optimal control problems. Solving these problems in real-time is a challenging task because of the explosion of integer combinations to evaluate. This thesis focuses on the development of new algorithms for mixed-integer programming with an emphasis on optimal control problems of fast dynamical systems with discrete controls.
The first part proposes two reformulations to reduce the computational complexity. The first reformulation avoids integer variables altogether. By considering a sequence of switched dynamics, we analyze the switching time optimization problem. Even though it is a continuous smooth problem, it is non-convex and the cost function and derivatives are hard to compute. We develop a new efficient method to compute the cost function and its derivatives. Our technique brings up to two orders of magnitude speedups with respect to state-of-the-art tools. The second approach reduces the number of integer decisions. In hybrid model predictive control (MPC) the computational complexity grows exponentially with the horizon length. Using approximate dynamic programming (ADP) we reduce the horizon length while maintaining good control performance by approximating the tail cost offline. This approach allows, for the first time, the application of such control techniques to fast dynamical systems with sampling times of only a few microseconds.
The second part investigates embedded branch-and-bound algorithms for mixed-integer quadratic programs (MIQPs). A core component of these methods is the solution of continuous quadratic programs (QPs). We develop OSQP, a new robust and efficient general-purpose QP solver based on the alternating direction method of multipliers (ADMM) and able, for the first time, to detect infeasible problems. We include OSQP into a custom branch-and-bound algorithm suitable for embedded systems. Our extension requires only a single matrix factorization and exploits warm-starting, thereby greatly reducing the number of ADMM iterations required. Numerical examples show that our algorithm solves small to medium scale MIQPs more quickly than commercial solvers.

Keywords: Approximate dynamic programming
Integer programming
Optimal control
Hybrid systems
Advisor: Goulart, P
Roles of BRCA1 and BRCA2 in DNA replication and genome stability

Genomic instability is a hallmark of cancer. The tumour suppressors BRCA1 and BRCA2 play key roles in genome integrity by promoting homologous recombination DNA repair and replication fork stability. Deficiency in these functions has been described as the Achilles heel of BRCA-defective tumours. This provides an important rationale for further exploring the roles of BRCA1 and BRCA2 in DNA replication and genome stability.
G-quadruplexes, alternative DNA structures formed by guanine-rich single- stranded DNA, represent natural replication fork barriers. This study demonstrates that treatment with the G-quadruplex-stabilising compound pyridostatin selectively decreases viability of BRCA1- and BRCA2-deficient cells by inducing replication stress and DNA damage.
Furthermore, this work identifies a new role of the Fanconi anaemia protein FANCD2 in limiting replication fork progression and genomic instability in human cancer cells lacking BRCA2. This function of FANCD2 is vital for BRCA2-deficient cell survival and affects treatment responses.
Finally, the data presented here reveal a synthetic lethal interaction between MRE11 nuclease and BRCA2. Characterisation of a novel chemical MRE11 nuclease inhibitor with activity on 2D and 3D cell culture models for BRCA2 deficiency highlights the clinical relevance for the use of MRE11 inhibitors for targeting BRCA2-deficient tumours.
In summary, this report describes novel roles of BRCA1 and BRCA2 relevant for selective targeting of BRCA-deficient tumour cells.

Advisor: Tarsounas, M
Post-translational mutagenesis: radical methods for protein modification

The naturally occurring post-translational modification of proteins expands the chemical and structural diversity available for protein function. Enzymatic processes are known to modify proteins after translation, and in many cases these modifications have been demonstrated to be critical for biological function. However, the paucity of methods for introduction of site-specific modifications to proteins remains a key obstacle to their biochemical study. Access to these naturally modified proteins has long been complicated by their low abundance, difficulties in purifying homogeneous samples from cellular samples and the intractability of bacterial expression systems towards post-translational modification.
In this thesis, we report an important step towards circumventing these issues by using a novel 'tag and modify' chemical strategy, termed 'post-translational mutagenesis'. We describe the development and application of C(sp3)–C(sp3) bond-forming reactions on proteins under biocompatible conditions, exploiting unusual free-radical chemistry to form a wide diversity of protein side-chains. Natural, unnatural, posttranslationally-modified (methylated, glycosylated, phosphorylated, hydroxylated) and labeled (fluorinated, isotopically-labeled) side-chains have been installed on a number of proteins. Extensive characterisation of modification site, connectivity and modified protein structure and function confirm the benign nature of our protocols. The modified proteins thus produced have been used to investigate novel aspects of epigenetic regulation of histone proteins, in the context of free histones and in nucleosome particles, and as novel 'isotope PTMs' for protein characterisation by NMR.
We believe this approach, a form of 'protein editing', will have wide application in biochemistry and synthetic biology for accessing diverse modified proteins for research.

Advisor: Davis, B
Essays on the market for corporate bonds

This thesis contains three empirical studies on the US corporate bond market; each chapter is self-contained and can be read independently. Chapter 1 studies the impact of credit rating changes on corporate bond returns. This study uses a large dataset of corporate bond transactions from the TRACE database for the US corporate bond market, combined with credit rating changes from Fitch, Moody's and Standard and Poor's (S&P), to analyse over 22,000 bonds, coupled with approximately 28,400 rating events over nearly six years. The results show that the bond market responds to news on credit quality asymmetrically: credit rating downgrades, representing bad news for bond holders, produce the strongest response in returns, whilst upgrades do not generate a statistically significant increase in returns. Chapter 2 analyses how order flow (investor "buy" and "sell" trades), impacts corporate bond prices. Order flow plays an important informational role, acting as a conduit through which private information about fundamental value is aggregated into prices. Using intraday transaction data from the TRACE database, I analyse over 1,000 of the most liquid corporate bonds, a total of 9.5 million trades. Drawing on similar studies of other markets, the relationship between returns and order flow is modelled using a vector autoregression, and the information content of a trade is measured as the long-run price impact of a shock to order flow. Price impacts are particularly strong and significant for order flow from institutional investors and for bonds with higher default risk, higher volatility and lower liquidity. Chapter 3 provides novel evidence on the importance of high frequency measures of volatility and correlation for the corporate bond market. Realized measures of volatility have been shown to be important in modelling and forecasting equity, exchange rate, and Treasury bill return volatility. We merge the NYSE's TAQ database of high frequency equity prices with the TRACE database, and show that the information contained in high frequency data is valuable in modelling the dynamics of the firm-level covariance matrix of bond and stock returns, for over 100 individual U.S. firms.

Keywords: liquidity
price impact
correlation
credit ratings
corporate bonds
Advisor: Sheppard, K
Role of the actin cytoskeleton in regulating LYVE-1 lateral diffusion and function

The lymphatic endothelial receptor LYVE-1 investigated here is a weak binder to its ligand hyaluronan (HA) and uses receptor clustering to achieve the avidity required for stable interaction to HA. These clustering based interactions are highly dynamic and are often controlled by several molecular players that contribute to receptor functional changes. One such contributor is the cortical actin cytoskeleton. As the actin cytoskeleton lies immediately below the membrane surface, it creates compartments on the membrane that control the receptor organisation, dynamics and allows physical interaction of the receptors with actin, which either hinder or enhance their functions. In this study, I investigate the role of the actin cytoskeleton in regulating the dynamics and function of LYVE-1. At first, the native organisation of LYVE-1 and cross-linked clustered state of LYVE-1 (that are known to cause avidity induced increase in HA binding), on primary human dermal lymphatic endothelial cells (HDLECs), were identified by confocal and super-resolution STED microscopy. Following which the effects of actin disassembly on LYVE-1:HA binding function and cross-linked clustering of LYVE-1 were investigated using FACS and STED microscopy. The dynamics of LYVE-1 during actin steady state or disassembly was studied using diffusion measurements on primary and cytoplasmic tail truncated hLYVE-1 transfected HDLECs. The results from the diffusion experiments suggest that LYVE-1 mobility decreases after actin depletion and correlates with the increase in HA interaction as determined by FACS during actin disassembly, although there was no change in the surface organisation of LYVE-1. Further diffusion measurements using STED-FCS showed that LYVE-1 was 'trapped' or confined on the membrane surface of HDLECs in native conditions. This data along with biochemical assays show a hitherto unknown direct link of the actin cytoskeleton regulating LYVE-1:HA binding and dynamics, giving an indication of how LYVE-1 in vivo may modulate binding to HA.

Advisor: Jackson, D
Eggeling, C
Laser writing of coherent colour centres in diamond

Optical active point defects in crystals have gained widespread attention as photonic systems that could be applied in quantum information technologies[1, 2]. However, challenges remain in the placing of individual defects at desired locations, an essential element of device fabrication. Here we report the controlled generation of single negatively charged nitrogen-vacancy (NV-) centres in diamond using laser writing[3]. Aberration correction in the writing optics allows precise positioning of the vacancies within the diamond crystal and subsequent annealing produces single NV- centres with a probability of success of up to 45%, located within about 200nm of the desired position in the transverse plane. A simple model was established to understand the mechanism of vacancies generation and estimate the success probability of NV- centres generation. Selected NV- centres display stable, coherent optical transitions at cryogenic temperatures, a prerequisite for the creation of distributed quantum networks of solid-state qubits. Strain measurement results of selected NV- centres show that the broadening of NV- optical transitions is due to local strain. The results illustrate the potential of laser writing as a tool for defect engineering in quantum technologies and extend laser processing to the single-defect domain.

Advisor: Smith, J
Asymmetric Syntheses of Polycyclic Amines

This thesis centers on the asymmetric synthesis of polycyclic amines, focussing on three distinct classes of polycyclic alkaloid natural products. The work aims to use common methodology of lithium amide conjugate additions as the source of asymmetry in all cases, and for each product class a single strategy is used to synthesise a variety compounds.
Chapter 1 describes the importance of the synthesis of polycyclic alkaloids, highlighting three classes of compounds and documenting prior synthetic strategies. The classes discussed are: the Hancock alkaloids, hydroxymethyl-substituted azabicycles, and the tetraponerine alkaloids.
Chapter 2 describes two separate synthetic strategies towards the Hancock alkaloid (–)-cuspareine, one using a benzyne mediated cyclisation and one a Buchwald-Hartwig cyclisation. The Buchwald-Hartwig methodology was also applied in the synthesis of two more Hancock alkaloids (–)-galipinine and (–)-galipeine; the synthesis of (–)-galipeine led to a reassignment of the structure of the natural product.
Chapter 3 describes work in the synthesis of four [x.y.0]-azabicycles with differing in ring sizes (x, y = 3, 4). The strategy employs sequential SN2-like ring-closing reactions to form the bicyclic structures where pyrrolizidine, indolizidine and quinolizidine scaffolds can be accessed. Amongst the products are two natural alkaloids, (–)-lupinine and (+)-isoretronecanol.
Chapter 4 describes the synthesis of all eight tetraponerine alkaloids T1–8. Two sequential lithium amide conjugate addition reactions allow for the synthesis of the differing ring-sizes and diastereoisomers displayed by the eight alkaloids. Ring-closing metathesis and diamine condensation with 4-bromobutanal provide the ring-closing steps in the syntheses.
Chapter 5 contains full experimental procedures and characterisation data for all compounds synthesised in Chapters 2–4.

Advisor: Davies, S
The role of technology in Pakistani private schools: the principals' perspective

Investment in technology in the field of education has increased radically over the past 2 decades. The main reason for this is the notion that technology will restructure our schools and reform the system of education. Although this trend initially began in developed economies, it can now also be witnessed in various developing countries. Both policymakers and technology companies are supporting this trend, however, a number of researchers have repeatedly made calls for critically assessing the usefulness of integrating these technologies in schools.
The primary aim of our study is to explore the perceptions and experiences of private school principals in Pakistan regarding the implementation of digital technologies. In most developed countries, there was an evident push from the governments to integrate technology in schools. However, in the case of Pakistani private schools there is no government intervention for technology integration as the schools are owned and operated by individuals and private trusts. Many of these individual school owners also act as the principal at their schools as well. Based on the aforementioned information, the views of these school principals are invaluable to understand technology integration in Pakistani private schools.
The analysis from the interviews, which was the sole technique used to gather data, revealed that the majority of principals viewed technology integration positively. Abundance of information and enhancement of student learning were seen by them as the two key values of technology. The interviewees emphasized that overreliance on technology can have a negative impact. The school heads identified four major barriers to successful technology integration: teachers’ readiness; cost of technologies; school culture; and state infrastructure.

Keywords: Computer
Tech
Ed-Tech
Principals' perspective
Internet
Education
Role of technology
Private schools
Pakistani Schools
Pedagogy
Technology
Schools
Advisor: Winters, N
Applications of the gauge/gravity duality

This thesis investigates applications of the gauge/gravity duality to strongly coupled quantum field theories. After a review of the duality and of correlators and transport in quantum systems, we present our results on second-order non-conformal hydrodynamics. We derive new Kubo formulae for five second-order transport coefficients in non-conformal relativistic fluids. We then apply these Kubo formulae to a class of non-conformal holographic fluids at infinite coupling. We find strong evidence that the Haack-Yarom identity, known to relate second-order coefficients in conformal holographic fluids at infinite coupling, continues to hold in holographic fluids without conformal symmetry: Within our class of models, we prove that it still holds when leading non-conformal corrections are taken into account, and we show numerically that it is also obeyed beyond leading order. This provides further evidence that the identity may be a universal feature of strongly coupled fluids. Next, we present our results on magnetic spin impurities in strongly correlated systems. We build a holographic two-impurity Kondo model, identifying the inter-impurity interaction as double-trace deformation. Our numerical results for the phase diagram suggest a quantum phase transition between a trivial phase with uncorrelated spins and no Kondo screening, and a non-trivial phase with anti-ferromagnetic correlations and simultaneous Kondo screening. Computing the spectrum in the single-impurity case, we observe Fano resonances, which at low temperatures we identify with the Kondo resonance.

Keywords: Gauge Field Theory
Kondo model
Hydrodynamics
AdS/CFT Correspondence
Quantum Field Theory
General Relativity
Advisor: Starinets, A
Membrane filtration: fouling and cleaning in forward osmosis, reverse osmosis, and ultrafiltration membranes

A comparison of fouling in osmotically driven processes with that in pressure driven processes is the main focus of the thesis. Forward osmosis (FO) and reverse osmosis (RO) have received considerable attention for water treatment and seawater desalination. This research compared the nature of fouling in FO mode with that in RO starting with the same initial flux in connection with cleaning effects and then comparing to those in ultrafiltration membranes. In all cases, with cleaning as an integral part, the extent of fouling reversibility, and the question whether a critical flux could be determined were examined.
The work during the first phase (undertaken at Oxford) quantified the removal of reversible fouling through rinsing by cold and hot water for a range of concentrations using the foulants dextran and carboxymethyl cellulose. The flux-TMP relationship was conventionally compared to that of the clean water flux.
The later phase (at Singapore) compared the fouling in FO and RO by alginate in terms of multiple parameters using cellulose tri acetate (CTA) and thin film composite (TFC) membranes. Silica and alginate were selected as model foulants. Whilst experimental water flux profiles in the present study did not exhibit significant differences in trend between FO and RO fouling, foulant resistance for FO was found to be increasingly greater than for RO with the progression of the fouling tests. This was further corroborated by membrane autopsies post fouling tests; both foulant mass deposition density and specific foulant resistance for FO were greater than for RO. The analysis clearly revealed that FO is essentially more prone to fouling than RO which was presumably due to less flux decline in FO (or greater average flux) as compared to that in RO in result of ICP-self compensation effect which is opposite to the prevailing claim in the literature. Additionally, the present study did not find evidence that hydraulic pressure in RO has a role in foulant layer compaction.
FO membrane fouling by real waters was the focus of the final phase of the research at SMTC. Pilot scale FO experiments were conducted on spiral wound CTA membrane with treated waste water obtained from a NEWater factory (Singapore) as the feed. In the second stage, experiments were repeated at bench scale with membrane coupons taken from the spiral wound membranes used earlier. The key finding was that the mass transfer coefficients in the Spiral-Wound module were around 50% lower than the corresponding values in the flat sheet unit and this severely limited the fluxes. The reason could be attributed to strong internal concentration polarisation in the former, where tightly wound spacers act to increase the structural parameter.

Keywords: Fouling
Membrane Filtration
Ultrafiltration Membranes
Reverse Osmosis
Forward Osmosis
Advisor: Field, R