VictorJuiz/thesis huggingface dataset:
Thermodynamic Anomalies in Network-Forming Materials

The density maximum observed in water at 4oC at ambient pressure is perhaps the most famous of the thermodynamic anomalies. However, anomalous behaviour in liquids is more widespread, spanning not only water, but systems such as silicon, germanium, silica and beryllium fluoride. A link between these systems is the dominance of local tetrahedral geometries. It is widely believed that the existence of a liquid-liquid critical point is the source of the anomalous behaviour in water. However, alternative scenarios of the anomalous behaviour exist but are either of little more than theoretical significance or are limiting cases of the so-called liquid-liquid critical point scenario. Recent studies have focused on establishing connections between liquid structure and the observed anomalous behaviour.
This work systematically explores the influence of the structure on the thermodynamic anomalies of systems modelled with both a Stillinger-Weber (SW) potential and a polarisable ion model (PIM). These are chosen as models conventionally associated with "covalent" and "ionic" interactions respectively. The liquid structure is changed continuously by varying specific structure-related parameters in either model; the magnitude of the three-body interactions in the SW potential and the anion polarisation in the PIM. The progression of the anomalous behaviour is observed as a function of these parameters and an explanation is given in terms of the evolution of the local environments. The bounds for the emergence of anomalous behaviour are also observed and have been correlated with the polymorphism of the crystalline phase diagram. The relationships between different anomalies are derived from thermodynamic relations and all the reported scenarios were successfully reproduced. Enhanced sampling methods were used to further study SW liquids and a new scenario describing the anomalous behaviour is detected. The progression of this scenario as a function of the model parameter and liquid structure is studied.

Keywords: Thermodynamic anomalies
Molecular dynamics
Density anomaly
Stillinger-Weber potential
Polarisable ion model
Advisor: Wilson, M
Finite element methods for Monge–Ampère type equations

This thesis focuses on the numerical analysis of partial differential equations (PDEs), the main goal being the development and analysis of finite element methods (FEMs) for fully nonlinear elliptic PDEs, particularly Monge-Ampère (MA) and Hamilton-Jacobi-Bellman (HJB) equations.
There are two clear distinctions in the approaches that are undertaken in this thesis: firstly, for the approximation of solutions to the MA problem, we implement and analyse a continuous Galerkin (CG) FEM; secondly, to numerically solve the HJB equation, we employ a discontinuous Galerkin (DG) FEM.
Though the chosen approaches (CG vs. DG) applied to the MA and HJB type equations are distinct, the equations themselves are related. A longstanding result, proven by N. Krylov in 1987, allows one to characterise the MA equation as a HJB equation.
Another important theme of this thesis, motivated by domain assumptions, necessary for the well-posedness of MA type problems, and oblique boundary-value problems is the implementation and analysis of FEMs on domains with curved boundaries. In the case of DG methods, where the consistency of the method plays a key role in obtaining a priori error estimates for the numerical solution, this quantitative consideration requires new techniques to extend the existing DG framework.
he main contributions of this thesis are new results concerning the existence and uniqueness of numerical solutions to CG and DG finite element methods on curved domains, for both fully nonlinear elliptic equations, and linear elliptic equations in nondivergence form, with Dirichlet and oblique derivative boundary conditions, as well as optimal a priori error estimates. Furthermore, we prove several key results from the theory of finite elements in the context of curved finite elements, that do not appear to be available in the literature.

Keywords: Partial differential equations
Finite element methods
Numerical analysis
Advisor: Suli, E
Frontiers in protein-lipid interactions studied by native mass spectrometry

Coordination between membrane proteins and their surrounding lipid environment dictates the function of biological membranes. While the study of membrane protein-lipid interactions is challenging for well-established techniques due to their transient and dynamic nature, recent developments in native mass spectrometry (MS) enables interrogation of membrane protein-lipid interactions in a label-free and high-resolution manner. This thesis presents two major developments in the study of membrane protein-lipid interactions via native MS: (1) the development of suitable MS methods for the transfer and characterization of nanodisc assemblies, promising membrane mimetics alternative to classical detergent micelles; and (2) the characterization of the lipid interactions with class A GPCRs.
Nanodiscs were transmitted into the gas-phase and collisionally activated to produce mass spectra, which were highly complex. To interpret these spectra, a dual Fourier transform method (Chapter 2) and a mass defect analysis (Chapter 3) were developed, allowing the determination of the lipid composition and the stoichiometries of the lipid/protein components of the nanodiscs. Analysis of the spectral results revealed that nanodisc-based MS provides novel insights into annular lipid interactions. In addition, the dissociation behavior of nanodiscs upon collisional activation was explored to understand how best to characterize nanodiscs in the gas-phase.
In the second part of this thesis, the lipid interactions of class A G protein-coupled receptors (GPCRs) were carefully characterized by native MS and coarse-grained molecular dynamics simulations. Class A GPCRs were shown to preferentially bind phosphatidylinositol bisphosphate (PIP2) over related lipids and potential PIP2-binding hotspots were identified. The effects of PIP2 on GPCR-G protein coupling were then investigated employing a Gα protein mimetic. Together, this information leads to a hypothesis that PIP2 binding modulates GPCR-G protein coupling and identifies a potential lipid-binding motif. Overall, therefore this thesis develops two novel methodologies, the native MS of nanodiscs and G protein coupling, both of which facilitate studies of protein-lipid interactions in challenging systems.

Keywords: GPCR
protein-lipid interactions
MS
nanodisc
Advisor: Robinson, C
Social evolution in natural microbial populations

To survive and thrive in their environment, bacteria engage in a multitude of cooperative and competitive behaviours. These behaviours often rely upon the secretion of extracellular public goods that are costly to produce but are essential for effective communication between cells, scavenging of iron and nutrients, protection from biotic and abiotic stresses and engaging in antagonistic competition. These cooperative and competitive behaviours have been studied extensively under controlled laboratory conditions but the extent to which social interactions can drive evolutionary change, shape population structure or promote and maintain diversity in natural bacterial populations remains unclear. In this thesis I explore the extent, form and consequences of social interactions in natural bacterial populations and also how a non-social bacterial trait, the production of functional amyloids, can shape cooperative and competitive dynamics.
Using natural soil populations of the bacterium Pseudomonas fluorescens, I explore (1) what drives bacteriocin-mediated competition in these populations by revealing the extent of bacteriocin production in the population and testing whether the strength of interaction is determined by spatial proximity, genetic relatedness or overlap in resource requirements. Using the same isolates I also reveal (2) the extent of potential public goods cheats in the population and demonstrate that potential cheats my be limited in their ability to proliferate by the presence of different forms of public good they cannot utilise. I then take an experimental approach to (3) investigate how a non-social bacterial trait, the production of functional amyloids, can shape cooperator-cheat dynamics in populations of Pseudomonas aeruginosa. I reveal that functional amyloids appear to bind public goods involved in iron acquisition and this may limit their availability to public goods cheats. Finally, I (4) assess the contribution of functional amyloids towards defence against conspecific bacteriocins, revealing that their presence appears to contribute towards individual defence against these toxins but not collective defence.

Advisor: West, S
Griffin, A
'Giving the worker his house': intervention, interaction, and inaction in three French cities, c. 1840-80

The history of working-class housing in nineteenth-century France is dominated by narratives of isolated successes, legislation at the end of the century, and the experience of housing in Paris above all other cities. Because of this, the significance and diversity of provincial French experiences have been overlooked. This obscures the very real and important role that different local elite strategies concerning the 'housing problem' played in provincial cities through the century, regardless of whether they impacted national housing policy. Just as important as direct interventions – which sought to improve legislation or build new houses – were strategies of interaction, which focused on working-class families impacted by poor housing without necessarily improving conditions, and self-conscious strategies of inaction, whereby provincial elites consciously chose not to intervene in the domain of workers housing because of what they judged more pressing economic, social, or political concerns.
By comparing the strategies employed by industrial and municipal elites in the three textile cities of Roubaix, Mulhouse, and Lyon between c. 1840-80, this thesis explores the multifaceted nature of the 'housing question' and responses to it. In this thesis, I reveal the diversity of elite strategies regarding housing, which were driven by a distinct combination of different local, regional, national, and international conditions. Through incorporating both failure and inaction alongside successful intervention and distinctive interactions, I not only overcome the dominant narratives in histories of housing, but I also offer a fresh interpretation of the social history of the heterogeneous, overlapping, and occasionally conflicting different elites that existed in nineteenth-century provincial France. The ways local industrial and municipal elites chose or chose not to tackle their specifically local housing situations reveal to us the different ways that interactions with workers and their domestic milieu shaped the construction of identities in nineteenth-century France.

Keywords: Lyon
Roubaix
Comparative
France
Second Empire
Logements insalubres
Housing
Mulhouse
Advisor: de Bellaigue, C
Whyte, W
Radiofrequency safety modelling of parallel transmit magnetic resonance imaging

Radio-frequency (RF) safety plays an important role in Magnetic Resonance Imaging (MRI) with the goal of assuring patient safety and preventing excessive RF heating. Historically, RF safety in MRI has been monitored using pre-calculated specific absorption rate (SAR) limits which indicate the amount of energy that can be delivered safely to the subject. Electromagnetic (EM) simulations have usually been performed to assess the electric field and RF energy levels that are experienced by the subject. In order to validate these EM simulations, the distribution of radiofrequency (B1) field can be measured experimentally, and compared with simulation results. Also, the measurement of temperature in phantom and animal models has been used to assess RF heating directly and validate the EM simulations.
Well-characterized phantom models are needed to assess RF heating experimentally. Meat phantoms can be used for RF heating tests, but these are difficult to store and challenging for their shape to be well described. Agar-gel phantoms can also be used for RF heating tests, in which one can control their dielectric properties with use of carefully controlled ingredients, such as NaCl and polyethylene powder to achieve specific conductivity and permittivity values. Once a phantom is made, the dielectric properties can be verified experimentally using an open-ended coaxial cable.
A number of EM simulation methods have been proposed, which help one understand EM field phenomena in high-field MRI. But there are still many questions remaining which need to be further studied, including better characterization of thermal behaviours. In Chapter 3, three simulation methods are compared against experimental thermal elevation measures.
A framework of validating EM simulations using Proton Resonance Frequency Shift (PRF) based MR thermometry in the context of parallel transmit (pTx) MRI is described in Chapter 4. Also described in this chapter is a 3D gradient-echo sequence used to monitor temperature-induced phase shifts, as well as the required image reconstruction techniques and field-stabilisation methods.
The need for personalised SAR models has arisen quickly, especially in ultra-highfield pTx studies. Use of a safety margin of 1.5 (150%) to account for morphometric differences across the population has been reported previously. To reduce the need for overestimation, the development of a personalized SAR models using non-linear registration is described in Chapter 5 and assessed for robustness using three 'standard' models.
Finally, the practical advantages of using the personalised model in pTx MRI are discussed in Chapter 6. With the aid of high computing capacity the personalised model approach could help MRI users reduce safety margins, so that the scanners can operate closer to the true SAR limits representing the subject in the scanner.

Keywords: MRI RF safety
RF heating test
Personalised SAR modeling
Electro-magnetic simulation
Parallel Transmission
Advisor: Jezzard, P
Hess, A
Pox and partisanship: the politics of health in Puerto Rico, 1898-1917

This thesis explores the development of Puerto Rican public health institutions and policy from 1898 to 1917. I ground the research in the major constitutional legislative actions (Foraker Act of 1900, Jones Act of 1917) taken by the United States to highlight both the key political moments in the colonial relationship between the metropole and colony and the accompanying ramifications for the public health institutions on the island. Case studies of epidemic disease outbreaks—smallpox, hookworm disease, and bubonic plague—facilitate an assessment of how political partisanship, international philanthropic groups, and interest group politicking affected the execution of campaigns responding to these diseases. I show that the circulation of personnel, philosophies, materials, and technologies within the American sphere of influence alone resulted in a sanitary imperialism that was a unique and cosmopolitan amalgamation of the latest medical and public health science of the day. I contend that the annexation and administration of Puerto Rico was above all haphazard in the early years of the twentieth century. The narrative that emerges from other historians who argue that highly specific themes or debates were the central issue does not fit the archival record. Such single-factor explanations as race, gender, sexuality, religion, or economic expansion mask the importance of highly particular factors on the ground. This thesis demonstrates that an understanding of the Puerto Rican context requires a more nuanced and even-handed approach than previous literature has provided. Health policy and institution building from 1898 to 1917 is a story of the continuous attempt to disentangle public health from partisan politicking. In large part, public health and disease campaigns were conceptualized as a means of enhancing commercial ties with the international community and improving the economic outlook of the island.

Advisor: Davies, G
Harrison, M
Application of a phase-field model to ferroelectrics

The current work uses a phase-field model to design nanoscale ferroelectric device concepts and to explore nanoscale ferroelectric behaviour. The results are expected to serve initial steps for nanoscale experimentation and to assist in the industrial application of ferroelectrics.
The use of ferroelectrics in nanoscale devices such as sensors or energy harvesters has increased in recent times. This has advanced research interests in nanoscale ferroelectric properties. In the current study, a phase-field model is used as a research tool to explore nanoscale behaviour of barium titanate. The model is first used to design and optimize nano-actuator concepts that generate actuation strains ~0.45%. This strain is four times as large as the strain offered by piezoceramic actuators in market. Next, the model is used to describe how scaling and surface conditions affect the formation of nanoscale polarization patterns, such as vortices. The results demonstrate the dominant effect of surface conditions and explain experimental observations of phase, tetragonality and polarization patterns in ferroelectric nanoparticles. The phase-field model is next extended to three dimensions and is used to test the stability of nanoscale periodic polarization patterns. The results describe the internal stress and electric fields developed in these patterns, and illustrate a mechanism of how complex polarization patterns can be formed under external strain or electric fields. Here, a conceptual design of an energy harvester is also explored.
The current work explores the application of a phase-field model as a design tool to develop nano-actuator and energy harvester concepts. The results on actuation/harvester cycle and the design parameter optimization would assist in developing device prototypes and eventually benefit in industrial fabrication. The phase-field model extended to three dimensions contributes to the study of domain patterns with out-of-plane polarizations and will assist in engineering a more realistic ferroelectric device. The results on the effects of scaling, surface energy and external loads on nanoscale polarization patterns, explains prior experimental observations of polarization patterns and provide useful insights on how to engineer domain configurations for nanoscale applications. Finally, the results motivate research towards developing prospective nanoscale applications from other smart materials, such as relaxors and ferromagnets.

Keywords: Ferroelectrics
Energy Harvesters
Phase-field model
Vortex patterns
Actuators
Advisor: Huber, J
Continuum modelling and numerical approaches for energy minimisation in diblock copolymers

We use a continuum phase field model to study pattern formation in Diblock Copolymers (DBCs), with an emphasis on terracing in thin films.
Phase separation in DBCs is an important process in nanotechnology that yields an array of highly regular structures on very fine length scales that are of enormous utility. Terraces are ubiquitous in thin film DBC melts. It was long believed that modelling these structures was an intractable problem, but recent attempts to do so using the Self Consistent (Mean) Field Theory (SCFT) were successful.
In this thesis, we use the simpler and more flexible Ohta-Kawasaki (non-local Cahn-Hilliard) Density Functional Theory (DFT) model, derived from the SCFT, with obstacle homogeneous, and long-range energy components. Our main result is that such models can be used to capture terraces in the simplified 2D scenarios we examine, and that these structures form as an inevitable consequence of a simple energy minimisation process.
We consider a 2-phase model for DBC micro-structure evolution, which we analyse rigorously and comprehensively. We study stationary and dynamic (gradient flow) variants of the problem, using the latter as the basis for an efficient but provably convergent numerical method for simulating DBC evolution. Our theoretical analysis and numerical method are based on a common Moreau-Yosida regularisation of the homogeneous energy component. We use the Semi-Smooth Newton (SSN) method to resolve the non-linearities in our numerical method. Comprehensive numerical experiments confirm our theoretical predictions, including a Method of Manufactured Solutions (MMS) test for the order of convergence. We propose a complete specification of the equally spaced global energy minimisers of the symmetric, 2-phase problem in 1D, and offer a practical algorithm for finding them. We explicitly characterise the Order-Disorder Transition (ODT) in parameter space.
We extend our 2-phase model and methods to a 3-phase situation involving a copolymer/homopolymer blend, in which the free surface of the copolymer can adjust to form terraces. We develop energy estimates for energy-minimising 1D morphologies in the sharp interface limit, which we then combine via a double-tangent construction to analyse low energy, 2D structures. We argue that thin films with terraces have a lower free energy than their flat counterparts. Time-dependent numerical simulations in 2D confirm these predictions and provide insight into the evolution of these structures. We replicate and extend recent SCFT results, by performing a numerical experiment in which a terrace forms from a flat initial state.
The model, tools and methods developed in this thesis should serve as a solid foundation for researching more complex, multi-step 3D terraces.

Keywords: Phase field modelling
Energy minimisation
Gradient flows
Asymptotic analysis
Optimization
Finite element methods
Variational inequalties
Non-linear partial differential equations
High performance/parallel computing
Advisor: Kay, D
Muench, A
The making of labour precariousness in post-1949 China

If Marxists are right, why did Mao’s China witness a prevalence of precarious labour? If mainstream modernization theorists are right, why has post-Mao China seen a growth of precarious workers? In the light of these paradoxes, this thesis asks: what are the mechanisms that generate labour precariousness in post-1949 China?
Drawing upon insights from Marxism, mainstream economics, Polanyianism, and the theory of primitive socialist accumulation, this thesis develops a theoretical framework to study the origins of labour precariousness in post-1949 China. Briefly, exploitation and exclusion are two major mechanisms that generate labour precariousness. Both the state and the market can exercise these mechanisms. Both mechanisms operate in spheres of production and social reproduction.
By applying this framework to the analyses of data mainly collected from archives and fieldwork, this thesis has the following findings. Under the exclusion-centred precarization regime in Mao’ era, to reconcile the contradiction between primitive accumulation and political legitimacy, the state built up a system of social exclusion. One’s location in this system determined one’s conditions of precariousness. The rigidity of this system was primarily mediated by the alternation between centralization and decentralization of industrialization, as well as by employment policies and labour movements. Under the exploitation-centred precarization regime in reform China, the previous social exclusion system has been curtailed and the extent of exploitation, in spheres of both production and social reproduction, defines one’s conditions of precariousness. The magnitude of exploitation has been modulated primarily by labour regulation, and by labour movements as well.
On top of these findings, this thesis also extends the extant literature by unveiling the continuities and discontinuities of labour precariousness practices and mechanisms in post-1949 China, and by contributing to two debates in this field. It shows that in the Chinese experience precarization is a process of proletarian unification and formalization is a limited remedy for labour precariousness.

Keywords: precarious workers
history
China
Advisor: Murphy, R