VictorJuiz/thesis huggingface dataset:
Deep integration of power electronics in battery systems

This thesis explores the concept of Power Electronics Enhanced Battery Packs (PEEBPs) where each cell (or small groups of cells) is connected to an individual converter and can be bypassed without interrupting operation of the system. The control flexibility provided can enhance system reliability by enabling failed cells to be bypassed online and improve balancing performance by controlling the duty cycle of each cell according to their respective capacity. However, the increased amount of power electronics compared to conventional system designs can potentially increase cost and power losses, while introducing additional control challenges especially for large-scale systems including thousands of cells.
This thesis introduces a linear programming framework for evaluating the balancing performance of PEEBPs that perform duty cycle balancing, compared to energy redistribution active balancing circuits. The numerical results demonstrate the superior balancing performance of PEEBPs, especially when using cells with extreme capacity variations. In order to compare battery energy storage system (BESS) designs with different levels of integration of power electronics in the battery pack, a design methodology is proposed that takes into account power losses, reliability and cost. This methodology is used to compare three competing system designs for a 1 MW/ 1 MWh BESS connected at 11 kV. The results of this case study indicate more than an order of magnitude improvement in reliability when using a PEEBP (when the failure rate of the cells is similar to that of the power electronic switches), with a relatively small increase in power losses (~2% lower efficiency for the deeply modular PEEBP considered in this study).
Regarding the implementation of a PEEBP, the Cascaded H-Bridge multilevel converter (CHB) is identified as an attractive candidate due to its modular design and the ability to perform direct DC-to-AC conversion. This work presents a theoretical analysis of the operation of the CHB in a BESS application and proposes a method to achieve relative state-of-charge (RSoC) estimation by making pseudo open-circuit voltage (POCV) measurements. In order to address control complexity of large scale systems a hierarchical balancing control algorithm is proposed. In this case the system is organised in conceptual hierarchical layers and each layer is equipped with a local controller. The developed algorithm can achieve global cell balancing by balancing the objects of the intermediate layers of the system with limited information exchange between the local controllers. This hierarchical balancing algorithm is experimentally validated using a CHB-BESS comprising 144 lithium titanate cells.

Advisor: Rogers, D
Modelling the breakup of droplets in a turbulent jet

In this thesis, we model the breakup of oil droplets in a turbulent jet and the effect of surfactants in enhancing this process. The problem is motivated by deep-sea oil spills where, hundreds of metres below the sea surface, a pipe transporting oil ruptures and a turbulent oil jet is released into the sea. The jet’s turbulent mixing breaks up the oil into smaller droplets. These droplets are then eaten by microbes in the sea. To encourage this natural clean-up process, surfactants are added to the oil jet to reduce the oil-water surface tension and encourage droplet breakup. Our aim is to understand how to best apply the surfactant to maximise droplet breakup. To do so, we first examine and unify the large scale jet and small scale droplets without the presence of surfactants. We then incorporate the effect of surfactant addition to these models.
We begin by modelling an axisymmetric turbulent oil jet. Our key approach is to take advantage of the self-similarity of a jet to find similarity solutions for its velocity field and energy. Scaling laws are then used to understand the breakup of droplets due to turbulent mixing. We combine these large-scale jet models and small-scale drop models, using droplet population models to predict the droplet size distributions at different locations in the jet. We first do so numerically. We then find similarity solutions for the drop size distribution, by taking advantage of the self-similarity of the jet.
Finally we include the effect of surfactants. We use numerical and asymptotic methods to model their effect on the drop size distribution. This allows us to address two important questions: how much surfactant should be used and where should it be injected.

Keywords: Droplet breakup
Droplet population models
Turbulent jet
Surfactants
Deep-sea oil spill
Advisor: Hewitt, I
Howell, P
A systematic revision of the Afrotropical members of the dung beetle genus Catharsius Hope, 1837 (Coleoptera: Scarabaeidae)

The Afrotropical members of the dung beetle genus Catharsius Hope, 1837 (Coleoptera: Scarabaeidae) are investigated and systematically revised. Morphological phylogenetic analyses of 138 taxa and molecular phylogenetic analyses of a subset of 15 taxa are conducted. The results indicate the paraphyly of the genus with regard the monotypic genus Copridaspidus Boucomont, 1920 and Catharsius is split into five species-groups. Biogeographical ancestral state reconstruction indicates that the woodlands to the south of the Congo Basin are the location of origin of the genus, with several independent colonisations of Asia. Dispersal-vicariance analysis shows that many dispersal events rather than vicariance events are responsible for the current geographical distribution of this genus. A new tribe, Catharsiini, is erected to include the genera Catharsius and Metacatharsius. Two genera, Copridaspidus and Catharsiocopris Balthasar, 1967, are synonymised with Catharsius. In total, 128 African species are recognised, of which 39 species are new to science. Name-bearing type specimens of 98 of 106 described taxa were studied with four neotypes and 48 lectotypes designated. Six taxa are raised from synonymy, eleven new synonymies are established and one species is placed as incertae sedis. The C. molossus species group of 29 species is fully revised with the re-description of 25 species and description of four new species. For each species of the C. molossus species group, images of both sexes and of the male genitalia are figured, along with distribution maps. A key to the five species-groups as well as a key to species of the C. molossus group are provided and a gazetteer of all African localities of Catharsius is compiled.

Advisor: Lewis, O
Daley, A
Wilkinson, M
Formal methods for evolutionary inference using ancient DNA

Ancient DNA has revolutionised our ability to study past evolutionary processes by enabling direct observation of genetic variation in past populations. However, current formal methods for evolutionary inference are challenged by the sparse and heterogeneous distribution of data in space and in time, typical of ancient DNA datasets, as well as sample age uncertainty. In this thesis, I introduce analytical approaches that explicitly address these problems and show how inference from ancient DNA can greatly benefit from analysis that formally compares different evolutionary and demographic scenarios. I apply these approaches to three different cases that represent a range of demographic histories and evolutionary questions spanning different time- scales, species and types of data. The first approach combines space and time into a single matrix that can be used to estimate levels of past within population mobility. I apply this method to human ancient DNA data spanning the last 35 thousand years to recover changes in mobility over this time period. The second approach combines spatially and temporally explicit simulations with ancient mitochondrial genome data, spanning the Northern hemisphere and the last 50 thousand years to reconstruct large- scale population dynamics in Grey wolves over this time period. The third approach uses likelihood-based analysis to reconstruct episodes of past selection from time series of ancient DNA data. I apply this method to genotype data spanning two thousand years from two loci in domestic chicken to estimate a number of selection parameters including the starting time of the selection. These case studies all illustrate how formal hypothesis testing in spatially and temporally explicit frameworks make it possible to directly link evolutionary histories to the climatic and archaeological records as well as historical sources and show how identifying potential drivers of evolution allow building a more detailed and complete picture of the past.

Keywords: time-series data
Methods
Bayesian analyses
Mobility
Chickens
Ancient DNA
Demographic history
Genetic selection
Wolves
Advisor: Larson, G
Studies of novel antibacterial agents and antibiotic resistance breakers towards combating multidrug resistant bacteria

β-Lactam containing compounds are the most important antibacterials. Following the discovery of the penicillins, successive generations of β-lactams (penicillins, cephalosporins, monobactams, carbapenems) have saved countless lives. Their use is threatened by growing resistance, of which the most important mechanism involves their hydrolysis by β-lactamases. There are two types of β-lactamases: the serine-β-lactamases (SBLs) and the metallo-β- lactamases (MBLs). Whereas SBL inhibitors are available, there are no clinically useful MBL inhibitors. This work covered the development of new types of MBL and SBL inhibitors.
One aspect of this work involved the development of new types of MBL inhibitors, in part inspired by structural and high-throughput screening approaches. Extensive chemical synthesis and screening of heteroaryl-carboxylate compounds were performed. Some of these exhibited potent inhibition against a panel of clinically relevant MBLs, including VIM-2. Lactivicin is the only naturally occurring small molecule that acts similarly to β-lactams which does not contain a β-lactam ring. However, very little structural-activity relationship studies have been performed on lactivicin. In my work, the synthesis of a novel lactivicin analogue with a modified lactone ring was achieved.
The Class D OXA SBLs are arguably the most worrying of all β-lactamases mediated resistance processes. Studies on OXA SBLs were performed with an array of inhibitors; the results inform on the mechanism of OXA inhibition, including the role of protein carbamylation in catalysis and inhibition.
Overall, the results suggest new possibilities for β-lactamase inhibition and should contribute to the effort to combat β-lactamase mediated resistance.

Advisor: Schofield, C
The data market: policies for decentralised visual localisation

This thesis presents a Data Market for the dissemination of expertise in the form of locally accurate topometric maps which are agnostic to sensor modality and estimation strategies amongst arbitrarily large teams of autonomous vehicles with a common goal of localising well in a dynamic world.
Cooperation is at first centralised and allows for rapid construction of considerable maps by the conjoining of work uploaded by asynchronous processes before sharing expertise amongst the fleet by a selective downloading of mission-specific map contents. Embedding the centralised case within formalisations supporting distributed version control systems imposes obligatory commutation properties which ensure consistent integrity and eventual convergence in the state of each agent’s map, allowing us to consider how any number of decentralised agents operate in concert via data sharing policies that are germane to the shared task of lifelong localisation. Vendors in the market intermittently initiate exchanges based on either mission parameters or a demand for localisation capability and choose trading partners with discrimination based on an internally evolving set of beliefs in each other’s value as providers over a catalogue of distinct places of interest – which are treated as products for appraisal and purchase.
The system is implemented in more than 50 000 lines of C++ code and evaluated over hundreds of kilometres of monocular and stereo imagery from a comprehensive collection of warehouse, urban, and planetary analogue environments featuring diverse deviation in appearance due to textural, atmospheric, lighting, and structural dynamics and analysed over an exhaustive combination of the sensory records of the Oxford RobotCar Dataset.

Advisor: Newman, P
Simulating brain resting-state activity: what matters?

In the field of computational neuroscience, large-scale biophysical modelling is a bottom-up approach to study the interaction between brain structure and function. In this thesis, we propose two models of varying biophysical plausibility as a mechanistic explanations for spontaneous brain activity, as measured with magnetoencephalography (MEG).
Mathematically, these models take the form of large systems of non-linear coupled delay-differential equations, and we implement software to numerically solve such systems efficiently. After analysing the empirical data and extracting key features of interest (relating to the temporal dynamics of measured signals), we use Bayesian optimisation to fit our models with two different parameterisation of increasing complexity: first assuming a spatially uniform brain in which the pattern of connections between cortical regions is the only source of temporal structure in the simulations; and second allowing smooth variations of intrinsic parameters across the cortical surface. Our results outperform those published in the scientific literature to date.
We contribute an original derivation of a conductance-based model, and an in-depth analysis of the effects of intrinsic model parameters; software to build and simulate large models of delay-networks efficiently; a new approach to the exploration of high-dimensional spaces in the context of Bayesian optimisation (using space-partitioning); an original parameterisation allowing smooth spatial variations of intrinsic parameters across the cortical surface (using spherical harmonics); a novel analysis of structural brain data (from tractography), and several original methods to analyse MEG data (e.g. exploiting the Hilbert phase and extending Riemannian metrics).

Keywords: Delay-differential
Differential equations
Bayesian optimisation
Gaussian-Process surrogate
Neuronal mass
Neural network
Mean-field model
Resting-state
Biophysical model
Magnetoencephalography
Advisor: Woolrich, M
Jbabdi, S
Sotiropoulos, S
Modulating reward learning in healthy adults with transcranial direct current stimulation: Towards a novel treatment for depression

It has recently been proposed that deficits in reinforcement learning are a core feature of depressive disorders. This thesis aimed to investigate whether transcranial direct current stimulation (tDCS) could be applied to alter these learning processes in healthy adults and individuals with symptoms of depression. A first study assessed the psychometric properties of a computerised reinforcement learning task, which was the main paradigm used in the tDCS studies. Next, a neurostimulation study was designed to examine the effects of tDCS of the dorsolateral prefrontal cortex (DLPFC) on reinforcement learning parameters in healthy adults. It was found that prefrontal stimulation was associated with faster learning from positive but not negative outcomes when applied during task performance. The subsequent study investigated whether this effect of neurostimulation could be harnessed to augment a cognitive training paradigm aimed to enhance learning from either positive or negative events. No evidence was found that tDCS could boost effects of cognitive training on either reinforcement learning or affective biases in information processing in healthy adults. Finally, a pilot study examined whether tDCS of the DLPFC could affect reward learning in a sample of individuals with subclinical depression. While interpretations of the findings were limited by the study’s small sample size, there were indications that active tDCS might enhance learning rates for both positive and negative outcomes during stimulation in this population. Altogether, this work presents preliminary evidence that non-invasive brain stimulation can transiently alter reinforcement learning processes in healthy adults and subclinical depression. Additional research is needed to examine the potential of this technique as a clinical intervention for depression and related psychiatric disorders.

Keywords: Depression
reinforcement learning
transcranial direct current stimulation
computational
tDCS
Advisor: O'Shea, J
Browning, M
Development of an alginate based microcarrier for cell expansion

Mesenchymal stem cells (MSCs) are potential therapeutic candidates, owing to their differential ability. However, the gap between availability and demand of MSCs requires alternative expansion methods from 2D flasks such as microcarriers which provide a high surface area to volume ratio. However, current commercial microcarriers support low cell attachment and difficulty in cell detachment.
This study developed genipin crosslinked alginate-chitosan microcarriers to overcome the aforementioned issues with commercial microcarriers. Alginate beads produced by electrospraying were coated with chitosan and crosslinked in genipin. The degree of crosslinking was determined through fluorescence of genipin-chitosan conjugates. By implementing a high crosslinking temperature of 60°C compared to the traditional 37°C, the microcarrier production time was significantly decreased.
To ensure microcarrier stability under cell culture conditions, atomic force microscopy (AFM) based indentation assessing the local elastic reduced modulus (E*) was performed in parallel to measurement of bead swelling. Results generally show stability of E* and diameter of microcarriers. Additionally no significant differences in bead diameter between microcarriers crosslinked at 60°C compared to 37°C demonstrating the high crosslinking temperature did not affect the bead swelling behaviour.
MSCs cultured on these microcarriers had a higher cell attachment and twice the proliferation rate compared to the commercial microcarrier Cytodex 1. Unlike in Cytodex 1, cells easily detached under trypsin treatment and did not require extended incubation periods or intense agitation. Furthermore, the possibility of freeze drying the microcarriers was also investigated to reduce storage and transportation costs of the microcarriers.

Advisor: Ye, C
On the decidability of finite extensions of decidable fields

This paper is primarily concerned with the following question which first appeared in Koenigsmann’s On a Question of Abraham Robinson’s:
Is a finite field extension of a decidable field always decidable?
This offers a “twist” to a question that was originally posed by Abraham Robinson in 1973 which had asked whether every finitely generated extension of an undecidable field remains undecidable. The above-mentioned work of Koenigsmann from 2016 (and independently, a result of Cherlin, van den Dries, and Macintyre much earlier in the 1980s) showed that there are indeed undecidable fields which admit decidable finite extensions. This paper aims to show that one could, similarly, find examples of decidable fields which admit undecidable finite extensions, thereby answering the above-stated question negatively.
This result is achieved by identifying a sufficient condition which a decidable field must satisfy in order for it to have an undecidable finite extension. In an earlier iteration of this work, we had pointed out what we had believed to be one such condition. Unfortunately, this turned out not to be the case, which we illustrate using an explicit example. Through this demonstration, we were able to accentuate the weakness of the formerly mentioned criterion, which we strengthen in this thesis. We provide justification that the strengthened criterion is indeed sufficient – any decidable field satisfying this strengthened criterion would form a counterexample to the above-mentioned question.
We study one such class of decidable fields, known as the wonderful extensions of the rational numbers, first introduced by Ershov in the early 2000s, whose (sufficiently saturated) elementary extensions satisfy this strengthened criterion. This provides us with a concrete counterexample which shows that there are indeed decidable fields which admit undecidable finite extensions. We also point out various attempts at finding other counterexamples to the above-mentioned question, the difficulties faced in those instances, and some further questions in the flavour of the above-mentioned question that appear to be interesting in their own rights.

Advisor: Koenigsmann, J
Rural commercial capital: accumulation, class and power in Pakistani Punjab

The thesis examines the processes of capital accumulation, class formation and agrarian change taking place in small town ‘provincial’ Punjab, Pakistan. It does so through an analysis of the system of commodity markets in two distinct areas of the province. Based on extensive field research, it argues that agricultural markets are differentiated not only by function and technology but also by economic segmentation. At the top of the commercial hierarchy in both areas, it identifies a group that accumulates capital across the rural-urban, agro-commercial divide, that we term rural commercial capitalist (RCC). The thesis examines the strategies through which they establish control over commodity markets, raise finance and organize labour and how these strategies shape the institutional structure of the Agro-commercial markets themselves. Finally, it argues that in order to understand the evolution and current composition of the class, its diverse origins in distinct status groups need to be identified in order to understand the processes of class formation taking place in Pakistan more concretely.

Advisor: Harriss-White, B
Sud, N