VictorJuiz/thesis huggingface dataset:
Mathematical modelling of lithium intercalation dynamics in battery electrodes

This thesis discusses mathematical models for phase separation pattern in electrode materials for lithium ion batteries.
The material is assumed to be composed of discrete "compartments", which might model individual particles in nanoparticle Lithium Iron Phosphate cathode material, for example, or individual layers in graphite anode material.
We first present deterministic ODE models to describe quasi-equilibrium and out-of-equilibrium lithiation/delithiation of such systems. In sequence, we examine a single compartment under voltage-control, a multicompartment system under current-control, and a multicompartment system under voltage-control. We show that the dynamics of a single compartment can be reduced to rapid switching between an "empty" state and a "full" state, and we identify the critical voltage at which the switch occurs under both static and dynamic conditions. We also identify the critical voltages for the multicompartment system to change stage. We find that the multicompartment system supports a large number of stable states in quasiequilibrium, and we further reveal that its dynamics may be extremely sensitive to initial conditions and control parameters.
We also explore how the dynamics are affected by discreteness and thermal noise by investigating the probability distribution of the lithium concentration. We first study a single-compartment and two-compartment systems, and then extend the analysis to more interacting compartments. We start with the discrete chemical master equations, and then derive a discrete-to-continuum model to explore the probability distribution during dynamic lithiation/delithiation. We identify distinct asymptotic regimes in which either discreteness and thermal noise are important or the dynamics is well captured by the deterministic model. We then compare the different phase-separation patterns predicted by the deterministic model and by the stochastic model, for quasi-equilibrium and out-of-equilibrium evolutions.
Finally, we explore how different interaction laws could impact the observed phase-separation pattern.

Advisor: Howell, P
Hall, C
Designing higher education curricula in innovation & entrepreneurship

Teaching the principles and practice of innovation and entrepreneurship (I&E) constitutes a growing focus in many universities, but this is a relatively new field in management studies, and so the means by which courses and curricula are designed are not well established. This thesis is composed of a portfolio of studies submitted as part of the Post-Graduate Diploma in Learning and Teaching in Higher Education (DipLATHE) at the University of Oxford. I cover the aspects of curricula and course design within I&E that may be particularly important given the applied nature of this topic and the relative youth of the discipline. The objectives of this work are to: 1. Provide a research-led assessment of the key components expected in an I&E curriculum; 2. Summarize experiments in teaching I&E material; 3. Investigate lessons from I&E courses and curricula from several other universities; and 4. Provide a specific framework for thinking about effective I&E curricula design. This framework, which I call “The Three Dimensions of I&E Learning,” provides a three-level approach to curricula design in I&E encompassing specific tools, abstract concepts, and experiential engagement.

Keywords: Experiential learning
Curriculum development
An analysis of negative liberty

Too many people analyse the concept of negative liberty in a way that obscures its place and significance in our lives. Here I seek to redress the balance by shining light on its structure and value. With respect to the essential structure of negative liberty and unfreedom, I push for a more intuitive, dynamic, and subjectivist agent-centred approach in place of the more mechanistic Hobbesian and austere Hayekian conceptions that have tended to predominate. Emphasising the importance of self-direction, authenticity and self-development to liberty delivers both a more coherent negative concept internally, and a notion that is more compellingly distinguished from its positive counterpart. Regarding liberty's relationship with coercion and manipulation, my explanation is that rational and emotional compulsion constrains negative liberty because it interferes with options and restricts freedom of choice. With respect to the significance of negative freedom and why we care about it, I consider its general, content-independent value to lie in its contributions to autonomy as well as to values more often associated with positive freedom such as individuality and self-realisation. Harnessing Mill's thesis, I highlight the importance of self-understanding and self-knowledge in the process of self-development, and explain from a non-utilitarian angle the nature of the negative opposition to paternalism and control.

Advisor: Green, L
Shifting foundations: understanding the relationship between John Cassian and Evagrius Ponticus

John Cassian is an Eastern-educated monk writing in the early fifth century for the monks of Gaul and is crucial to the development of Western monasticism through the transmission of Greek ascetic ideas to the Latin West. He is heavily influenced by the teachings of Evagrius Ponticus, a prolific late fourth-century Egyptian monk crucial to the development of Christian mysticism; however, there has been no clear line drawn between the influence of Evagrius and Cassian's own originality. While Cassian uses Evagrian asceticism to the fullest, he nevertheless places it onto a divergent theological foundation which fundamentally alters that inherited asceticism. Evagrius' asceticism is shaped by his anthropology, cosmology, soteriology, and eschatology – all of which are based on his understanding of Creation and Christology. The monk working through Evagrius' asceticism sees the world and all the divisions in it—e.g. body/soul, human/angel/demon, vice/virtue—as a temporary construct which facilitates the eventual obliteration of all divisions through salvation – including divisions between good and evil. Cassian, however, writes twenty years after Evagrius’ death and in a changed theological atmosphere, in which Evagrius' basic premises have become more controversial. Cassian is able to work an ascetic program previously defined by Evagrian theology into a legitimate and coherent asceticism based on a different understanding of Creation. This resembles Evagrius' asceticism to such an extent, that he has been called "merely a Latin translator". However, through fleshing out and comparing Cassian's understanding of the practical, the eight principal vices, the spiritual battle, and the contemplative life, it becomes clear that Cassian has a fundamentally different understanding of Creation and Christology, and this changes the relationship between body and soul, created and Creator, and corruption and salvation – all fundamental areas in an effective and coherent asceticism. Therefore, although the frame of his asceticism is Evagrian, the theological underpinnings of that asceticism create a vastly different experience for the monk through a different definition of humanity and the relationship between created and Creator.

Advisor: Booth, P
Higher-Order Cycloisomerisations of Enynamides

This thesis describes the development of a novel transformation of ynamides, and addresses more general questions of asymmetric cycloisomerisation. The rhodiumcatalysed [5+2] cycloisomerisation of ynamide vinylcyclopropanes A1 to [5.3.0]- heterobicycles A2 is established (Scheme i). We design a versatile substrate synthesis, which allows the preparation of diversely substituted enynamide substrates. Under achiral rhodium catalysis, the extent of substrate diastereo- and regioselectivity is investigated.
The reaction is rendered asymmetric with the use of chiral phosphoramidite ligands; where a mechanistic hypothesis for stereoselectivity leads to the development of a powerful catalyst system for the preparation of enantioenriched A3. A theoretical reaction analysis elucidates the mechanistic pathway, and gives an energetic rationale for our model of ligand stereoinduction. Our asymmetric catalyst system is applied to the [5+2] cycloisomerisation of chiral substrates in double stereodifferentiating transformations, where it is possible to synthesise previously inaccessible diastereomers of product A4.

Keywords: Catalysis
Cycloisomerisation
Ynamide
Advisor: Anderson, E
Moisture generation and transport at ice stream margins

Alterations to glacial mass balance brought about by dynamic changes in ice ow play a key role in the global climate system via sea-level rise, diminishing albedo and alterations to atmospheric circulation. A detailed understanding of these dynamics is therefore a prerequisite to making accurate predictions of future global ice extent and quantifying its feedbacks on the changing climate. Temperate zones are predicted to exist deep within the Antarctic ice sheet due to intense shear heating at ice stream margins. These are the lateral boundaries of fast- owing regions known as ice streams: rivers of ice which may account for up to 90% of the ow into ice shelves and the surrounding oceans. Thus understanding how ice streams and their margins evolve under temperate ice-water dynamics is of great importance in the climate science community. However, current efforts to include meltwater in glaciological models do not fully couple the dynamic ows of ice and water necessary in describing the full physics in these temperate zones and hence the physics of ice stream margins.
We suggest using a two-phase uid dynamical model to describe the movement of water through viscously deforming polycrystalline ice. We investigate the application of this theory to a planned experiment, designed to mimic glacial conditions and reproduce ice deformation in order to infer its rheology. Introducing the mathematics of two-phase ows, originally intended for applications in magma-mantle dynamics, we explain how these equations may equally be applied to ice-water mixtures. More speciffically, we explain how they apply to an experimental setup, drawing inferences on the evolution of ice stream margins. Solutions are identified under constant stress boundary conditions, achieving a stable steady-state porosity φ of 2% assuming a viscosity constant λ much larger than that used from analogy with mantle rocks. That is, we predict that the viscosity of glacier ice is much more sensitive to changes in porosity than that of the mantle. Using this model, the total drainage from Dragon Margin of Whillans Ice Stream, in the Ross Ice Shelf, West Antarctica, due to englacial melting is 36 m3yr-1 per metre downstream. We also lay the groundwork for a two-phase 1D numerical model, and provide recommendations for further modelling and experimentation based on our results.

Advisor: Hewitt, I
Katz, R
Electroanalysis of single nanoparticles via particle-electrode collision processes

This thesis begins with the investigation of size- and density-effects of AgNP arrays in voltammetry, including the study of size-dependent adsorption behavior by observing thallium underpotential deposition on AgNPs, and surface coverage eects of AgNP modified electrodes in voltammetry showing the transition from convergent to linear diffusion.
The main focus of this thesis is next presented: the electroanalysis of nanoparticles (NPs) studied via their impacts with an electrode via both indirect (i:e: electrocatalytic) and direct electrochemical measurements. The study first realises the direct detection and sizing of silver NPs (AgNPs) using anodic particle coulometry (APC). This theme is then extended to gold and nickel NPs, aggregation studies and the measurement of sticking coecients. Furthermore, the determination of nanoparticle concentration is realised by measurement of the flux to electrodes.
In contrast to APC, electrode-particle impacts using surface tagged NPs provide a non-destructive way of sizing the NPs from the charge associated with one monolayer of "tag". In addition to tagged NPs, underpotential deposition and bulk deposition of metal onto single AgNPs are also observed as part of the studies of indirect electrochemical measurement. Finally the charge transfer kinetics of the oxidation of silver and nickel nanoparticles is studied.

Advisor: Compton, R
Development of an end to end spectral image simulator for WEAVE

The WHT Extreme Aperture Velocity Explorer (WEAVE) is a form of ground-based wide-field spectrograph, planned to be installed at the prime focus of the 4.2m William Herschel Telescope (WHT). The instrument has a two degree field of view and full coverage of the visible wavelength from 366nm to 950nm. Using fibre-optic pick-offs at the focal plane, it can also observe up to 960 simultaneous spectra for each configuration. The fibre-fed spectrograph consists of a collimator mirror, dichroic and two correcting lenses before each of two volume phase holographic (VPH) gratings and two eight-lens cameras. The two cameras have been designed to have the same lens shapes and have almost the same glass blank and the design also reduces the ghost between the surfaces of the lenses. The unique part of the instrument is called the 'Positioner'; fibres on the positioner can be moved in the focal plane to pick the required target.
The WEAVE survey is expected to start observing by 2018. Here we report on the development of the details of an end-to-end image simulator for WEAVE which can be used to generate data to test the image processing and analysis pipelines. The WEAVE simulator is aimed to: 1) verify the whole data acquisition, reduction and calibration procedure throughout the WEAVE science processing and archiving (SPA), 2) generate high signal-noise reference images that can be used as fitting templates for the extraction of the real spectra, and Point Spread Function (PSF) mapping and 3) verify the feasibility of the scientific objectives, to allow the survey planning to be optimized before the instrument is commissioned.

Advisor: Dalton, G
Quantum technologies for enhanced sensing and light absorption

The counterintuitive properties of quantum mechanics have the potential to produce revolutionary new technology. The applications of these devices are both vital and diverse: the efficient generation of energy from light, sensing and measuring with exquisite precision, and information processing with unparalleled speed. In this thesis, I use the theory of open quantum systems to investigate quantum technologies for enhanced sensing and light absorption. In the first research chapter, we develop a new method for describing qubit dynamics in the Rabi model. We obtain a new expression for the ac Stark shift, which enables practical and precise qubit thermometry of an oscillator. In the second research chapter, we demonstrate that it is possible to invert the phenomenon of Dicke Superradiance using nanostructures and quantum control. This creates the possibility of a new class of quantum light absorption technologies with a super-linear scaling in the absorption rate. In the final research chapter, we investigate another means of enhancing light absorption. We show that phonon assisted transitions to ratchet states in rings allow absorbed excitions to be protected from reemission.

Advisor: Gauger, E
Lovett, B
Benjamin, S
Inference for partial orders from random linear extensions

The study of random orders and of rankings models has attracted much work in the combinatorics and statistics literature. However, there has been little focus on random partial order models for statistical modelling. A partial order on a set P corresponds to a transitively closed, directed acyclic graph h(P) with vertices in P. Such orders generalize orders defined by partitioning the elements of P and ranking the elements of the partition. Observed orders are modelled as random linear extensions of suborders of an unobserved partial order h(P) evolving according to a stochastic process, and inference on the partial order is of interest.
Chapter 1 reviews some static random partial order models. Of particular interest for modelling is a latent variables model based on the random k-dimensional orders and a parameter controlling the mean depth of a partial order. In Chapter 2, it is extended to a stochastic process on latent variables to describe a partial order evolving continuously in time. As a Hidden Markov model, the process is observed by taking random linear extensions from suborders of the partial order at a sequence of sampling times. The posterior distribution for the unobserved process is doubly-intractable. The basis for a numerical inference algorithm in Chapter 3 is Particle MCMC with an efficient particle filtering transition distribution on the latent variables. Sampling latent variables relates to the well studied problem of estimating multivariate normal orthant probabilities, for which Chapter 4 gives a new importance sampler. It is competitive with existing samplers under some conditions on the covariance. Inference on the partial order process is computational, and Chapter 5 gives some numerical algorithms to reduce the complexity of some common latent variables computations. Lastly, Chapter 6 applies Chapter 2 and 3 to dynamic ranking problems in the areas of historical research and sport tournaments.

Advisor: Nicholls, G
Synthesis and biological characterization of natural and designed sugars

Carbohydrates represent a keystone among biological molecules. Well known as a source of energy, sugars also form the backbone of various biopolymers, act as markers and receptors for cellular communication and modulate lipid and protein functions. As such a powerful class, carbohydrates represent a useful pool from which both nature and man have drawn structures to produce biologically active compounds with a variety of modes of action. Beyond their importance to biology, sugars have represented attractive synthetic targets to chemists given their densely functionalized scaffolds.
The work presented in this thesis aims to employ synthetic chemistry to provide both natural and designed carbohydrates in order to carry out biological studies to improve our understanding of these compounds' particular effects. In the first part, a synthesis is developed for the carboline disaccharide domain of the cytotoxic enediyne, shishijimicin A. The route employs a Reetz–Müller-Starke reaction to install the domain’s quaternary center, with addition of a carboline dianion to complete the target.
Iminosugars represent the focus of the second portion of the thesis. These polyhydroxylated alkaloids have long been investigated for their ability to mimic single sugars, inhibiting various glycosidases and glycosyltransferases. The endocyclic nitrogen atom of members of this class can act as a functional handle for alkylation, with increased chain length increasing both potency of enzyme inhibition and toxicity in cellula. Specific iminopyranose structures with D-gluco stereochemistry have broad-spectrum antiviral activity, while those with D-galacto stereochemistry are antiviral with respect to hepatitis C, but not other genetically related viruses. Reported herein are syntheses of classes of iminosugars to determine the influence of both N-alkylation chain length and iminopyranose stereochemistry on the spectrum of antiviral activity. Complementing antiviral activity with isolated enzyme inhibition assays, the work aims to identify new targets for next generation antivirals.
Finally, the prototypical iminosugar, D-deoxynojirimycin, is conjugated to a second natural product, D-α-tocopherol. By replacing the more common normal alkyl group with a lipid, the goal was to reduce cellular toxicity, while also taking advantage of the natural active transport for the lipid to increase uptake of the drug. Surprisingly, this change provided a marked shift in selectivity of enzyme inhibition and antiviral ability. In order to fully characterize the mechanism, the mentioned enzymatic and antiviral studies were supplemented with lipidomic, STED-microscopy and pharmacokinetic investigations.

Keywords: Antiviral
Glycosidase
Iminosugar
Enediyne
Synthesis
Advisor: Zitzmann, N
Nicolaou, K
Diverse firing patterns of neurons of the medial septum and their hippocampal targets

The medial septum has a profound influence on the activity of the hippocampus, through cholinergic and GABAergic innervation. During exploration and paradoxical sleep, the hippocampus produces a prominent voltage oscillation of theta frequency (4-12 Hz), which represents the synchronous activity of hippocampal neurons. This organisation includes the temporal redistribution of inhibition throughout the subcellular domains of pyramidal neurons, via the theta phase locked activity of diverse interneuron populations. GABAergic septo-hippocampal neurons fire rhythmic, phase locked action potentials during theta oscillatory epochs. Within the hippocampus they project exclusively to interneurons; stimulation of the septum disinhibits pyramidal neurons. If the septo-hippocampal projection is inactivated, theta oscillation no longer occurs and animals demonstrate behavioural deficits in episodic memory. This evidence led to the hypothesis that septal rhythmic inhibition of interneurons is a crucial step in the pacing of the hippocampal theta oscillation in vivo.
I used extracellular recording and the juxtacellular labelling method of neurons under anaesthesia in vivo to investigate how the electrophysiological activity of septal neurons correlated with the identity of the cell, its axonal arbour and synaptic targets in the hippocampus. I tested the hypothesis that septal neurons display a selective and non-uniform innervation of interneurons and the firing phase and/or spike timing of septal neurons is correlated with that predicted of the innervated hippocampal interneuron(s).
I found a diversity of medial septal neurons, which was partially predicted by the firing frequency change during sharp wave associated ripple oscillations. Septal neurons which display significantly different firing patterns and axonal arbours may share molecular markers detected by immunohistochemistry. The axonal arbours of septal neurons were limited to a relatively small area within the hippocampus. Within those regions I defined some of the synaptic targets of three neurons and suggest that septal GABAergic neurons selectively innervate hippocampal interneuron types. Furthermore, the preferred theta phase of septal neurons was out of phase with that predicted for their identified target cells, indicating that septal GABAergic neurons may suppress the firing of interneurons rhythmically during theta.

Advisor: Viney, T
Lapray, D
Somogyi, P