VictorJuiz/thesis huggingface dataset:
Field theoretical studies of nonequilibrium systems with long-range interactions
Keywords: Electrolytes
Stochastic Field theory
Long-range interactions
Langevin dynamics
Fluctuation-induced forces
Chemotaxis
Renormalisation group theory
Scaling laws

Characterising the effects of correlated fluctuations in nonequilibrium systems is an essential step in modelling many natural and synthetic processes. This thesis uses stochastic and field-theoretical approaches to investigate the rich macroscopic behaviour arising from nonequilibrium fluctuations in two systems: strong electrolytes driven by an external electric field and chemotactic particles with generalised gradient-sensing mechanisms. The common feature shared by these systems is the presence of nonlocal Coulombic interactions among their constituent particles. In electrolytes, these are electrostatic interactions governed by the Poisson equation; in chemotactic systems, on the other hand, diffusing chemical signals secreted by each particle mediate nonlocal interactions, which, in the limit of fast-diffusing signals, are governed by a similar Poisson relation.
In the first case, we study the stochastic dynamics of a driven electrolyte using the Dean-Kawasaki formalism and show that it exhibits scale invariance notwithstanding the Debye screening effects. Accordingly, the correlation functions of the driven electrolyte take power-law forms, in sharp contrast to the exponentially screened correlations in equilibrium electrolytes. These correlations give rise to fluctuation-induced forces between neutral boundaries that confine the electrolyte. In the Casimir geometry, we show that these nontrivial forces are generally long ranged and have transient parts that decay algebraically over time. We also find that the steady-state fluctuation force can be tuned in magnitude and direction by adjusting the external electric field.
In the second case, our focus is on self-chemotactic systems, namely collections of living or synthetic particles that release fast-diffusing chemical signals in their environment while responding to signal gradients by adjusting their motion. Based on scaling analysis and microscopic considerations, we devise a natural generalisation of the conventional Keller-Segel model by incorporating the effect of particle polarity into the stochastic density equations. We examine the associated large-scale properties of the system, first by studying its symmetry properties where we identify an emergent Galilean symmetry, and then through dynamical renormalisation group analysis of its critical state. We find exact scaling exponents, which show that density fluctuations are super-diffusive and the number fluctuations are non-Poissonian.
Investigation into structural and functional relationships of short-chain dehydrogenases and reductases (SDRs) using a compound library
Keywords: short-chain dehydrogenases/reductases
SDR
differential scanning fluorimetry
TM shift
structural genomics
cofactor
DSF
SGC

The short-chain dehydrogenases/reductases (SDR) protein family is one of the largest and most evolutionarily conserved protein superfamilies known to date. SDRs show a remarkable ability to accommodate hundreds of reactions/substrates by using the versatile nucleotide binding domain as their central scaffold. SDRs are implicated in many different disease pathways, and represent a ‘druggable’ enzyme class, which has generated extensive biotechnological and pharmaceutical interest. For 28 human SDR members, the three- dimensional structures have been determined. Despite this, almost 25 % of human SDR members still have unknown functions, and many members lack any chemical descriptors. To address the dearth of ligand knowledge, 28 SDRs were cloned, expressed and purified to further characterise members by the application of differential scanning fluorimetry (DSF). A family annotation through cofactor preference, substrate accommodation and subcellular localisation has shown a few distinctive traits within the SDR family. This in silico approach has led to the creation of a systematic flow chart, which provides a starting point to identify substrate classes for orphan SDRs. Cofactor and inhibitor screening of SDRs by DSF has shown Tm shifts that are in-line with previous experimental data. DSF screening showed the decryption of 6 cofactor preferences for orphan SDRs, five of which have been confirmed in crystal structures. In contrast, screening of substrates in DSF produce little thermal stability (15 % detection rate), rendering it difficult to distinguish specific substrates for orphan SDRs. However, over 70 % of SDRs screened in DSF with known enzyme activity produce thermal shifts with compounds that resemble their substrate structures. This can therefore infer substrate classes for orphan SDRs that compare well with those from computational predictions. DSF screening against a ligand library has led to the discovery of the first small molecule binders for Nmr-like family domain-conatining protein 1 (NMRAL1) and selective inhibitors for Hydroxyprostaglandin dehydrogenase (HPGD). The use of small molecule ligands identified from DSF has also contributed to the success of crystal formation in the case of Hydroxysteroid dehydrogenase-like protein 2 (HSDL2) and Dehydrogenase/reductase SDR family member 2 (DHRS2). Overall this study has provided a platform for ligand screening to further structurally characterise the SDR family.
Modelling the spectra of exoplanets
Keywords: spectral retrieval
astronomy
exoplanets

Extrasolar planets (exoplanets) are planetary-mass objects that orbit different stars in our galaxy. To date, there have been over 4000 of these objects discovered, with a bias towards objects that transit their host star. This thesis focuses on interpreting the emission spectra of hot to ultra-hot Jupiter exoplanets. These are Jupiter-sized objects which orbit close to their host star, resulting in high effective temperatures and a tidally-locked orbital configuration.
The study of the emission spectra of exoplanets lets us probe the vertical chemical and thermal structure of the planet's atmosphere. The majority of the current observations are of hot to ultra-hot Jupiter planets, as the day-side flux is readily measurable with current telescopes. Therefore the first part of the thesis focuses on upgrading the NEMESIS model to calculate H− opacities and implementing a temperature-pressure parameterisation that can handle temperature profiles that can span the parameter space that contain non-inverted and inverted profiles.
These objects exhibit large day-night contrasts due to their tidally-locked nature, and it has been shown that this is detectable with current observations. We explore in this thesis the biases that can arise when studying an exoplanet with a non homogeneous thermal structure. We find that if we assume the thermal structure to be uniform on the disc, this can lead to spurious detection of molecules. We show that by retrieving the nightside and the dayside of the planet simultaneous we can perform an unbiased retrieval. We find that if the nightside contribution is small enough, a simple dilution factor can be used to account for the spatial inhomogeneity of the atmosphere.
Finally, we explore how scattering clouds can affect the way we interpret the emission spectra of cloudy exoplanets. We show that using a model that does not contain scattering to study the emission spectra of a cloudy exoplanet can lead to incorrectly inferred chemical abundances and also an erroneous detection of a thermal inversion. To provide a more agnostic approach to the modelling of clouds, in this thesis we have developed a novel technique to retrieve the cloud scattering properties, namely the single scattering albedo, which approximately encapsulates the real and imaginary refractive index spectra and the particle size of the cloud condensing species.
This thesis has broader impacts on the exoplanet community. The tools developed for hot and large planets will ensure that when moving to study smaller and cooler objects in the future, we can trust that our techniques are well verified.
Precision in the understanding and treatment of paranoia
Keywords: implementation
parenting
virtual reality
delusions
paranoia
compassion
psychosis

Improvements are needed in the effectiveness and accessibility of cognitive behavioural therapy (CBT) for psychosis. One route to improving efficacy is to take a translational approach, focussing on one proposed causal mechanism at a time, and testing specific therapeutic techniques that may help to modify this mechanism. This thesis aims for precision at multiple stages. First, through focussing on a single psychotic experience, paranoia, and a single putative causal mechanism, negative cognition. Second, through testing interventions that target specific aspects of negative cognition in order to reduce paranoia. Third, through conducting studies using a manipulation method to gain precise causal evidence. Finally, using immersive virtual reality (VR) to accurately measure paranoia, train therapeutic techniques in a controlled setting, and, when automated, increase access to evidence-based therapy. Chapter 1 introduces these conceptual and methodological approaches to precision. A systematic review (Chapter 2) found that the manipulation method has to date been infrequently used in psychosis research. Chapters 3, 4, and 5 each report a study that combines the three approaches – specificity, manipulation, and VR. Chapter 3 found that training in compassionate coach imagery, practised in VR social environments, caused significant reductions in paranoia mediated by increases in self-compassion. Chapter 4 found that training in loving kindness meditation, practised in VR, caused significant reductions in paranoia that were mediated by increases in compassion for others. Chapter 5, in contrast, found that altering body posture prior to entering VR had a negligible effect on increasing feelings of power, and no subsequent effect on paranoia. Following this experimental work on modifying negative beliefs, Chapter 6 considered how such beliefs might form in the first place. Using a large epidemiologically representative adolescent sample and a smaller adult sample it was found that parental verbal and physical abuse, over-control, and lack of care were significantly associated with paranoia and negative self and other beliefs. Network analysis did not find that the relationship between parenting and paranoia was mediated by negative self and other beliefs. Finally, given the limited access to CBT for psychosis, Chapter 7 explored the feasibility of implementing automated VR therapy onto psychiatric inpatient wards. A thematic analysis of qualitative data found that both patients and staff believed VR would be beneficial in this setting, but that certain practical barriers needed to be overcome. Overall, this thesis provides initial evidence of the benefits in taking an early-stage translational approach to treatment development for paranoia, showing that even single therapeutic interventions can bring about large effects, and these techniques can now be tested in clinical populations.
Beauty work: consumption, gender and hope in Yaounde, Cameroon
Keywords: West Africa
beauty and fashion
young women
photography

Against the backdrop of trade and media liberalisation following the end of the Cold War, this dissertation examines visual self-fashioning among young Bamileke women struggling to attain social adulthood in Yaoundé, Cameroon. It asks why young women living in precarious conditions invest in beauty, dress and photographs of themselves to the extent they do. In order to answer this question, the thesis, moves beyond semiotic understandings of consumption and analyses self-fashioning in embodied and material terms. From this perspective, investments in beauty, dress and photographs not only index dreams and imaginations, but emerge as a set of skills and embodied knowledge that I propose to call “beauty work”. Each chapter examines different skills and collectively illustrate how, through their investments, young women can alter their social positions and create upward paths of social mobility. Thus, for young women beauty, dress and photographs became means by which to fashion and refashion social adulthood in a social, economic and political context where other paths—as employment and education—are compromised.
In developing the notion of beauty work, this thesis contributes to the anthropological and Africanist literature on consumption, gender and hope. First, it challenges understanding of consumption as imitation in semiotic terms and argues for an understanding of imitation as valued skills and embodied knowledge in relation to notions of personhood. Second, insofar as beauty work encompasses skills, it reveals women as industrious. Thus, this thesis challenges understandings of beauty work in terms of empowerment versus resistance and instead discusses how female aesthetic subjectivities through beauty work are being made. The discussion foregrounds notion of femininity as a skill for crafting surface and in doing so illustrates how beauty work defies patriarchal and colonial regimes of recognition. Third, insofar as beauty work relies on newness, it redirects the temporality of embodied knowledge to the not-yet. Thus, this thesis argues, visual self-fashioning is performative of embodied hope when young women dress and photograph themselves to fashion social adulthood. Together the three arguments by drawing out the key role of the body, skills and the senses offer a new approach to understanding of investments in consumer capitalism for young women from Western Africa in particular, and in doing so illuminate workings of aesthetic capitalism in general.
Time-parallelisation techniques with applications to plasma simulation
Keywords: circulant preconditioning
computational fluid dynamics
multigrid
high-performance computing
block preconditioning
parallel-in-time methods

Parallel-in-time (PinT) methods have become an increasingly popular tool in the numerical solution of time-dependent Partial Differential Equations (PDEs), in light of their potential for extracting additional concurrency when spatial parallelism saturates. Particularly complex applications, such as the ones involving plasma simulations for fusion research, would benefit greatly from the implementation of such methods, given the large computational time usually necessary for the numerical solution of their governing equations.
In the first part of this thesis, we develop the concept of Space-Time Block Preconditioning (STBP), a technique for simplifying the task of time-parallelising the solution of a whole system of PDEs by reducing it to that of inverting space-time operators acting on single variables only, which are more amenable to be tackled by PinT algorithms. This technique borrows from block preconditioning strategies developed for spatial operators in the framework of time-stepping algorithms, and extends them to the whole space-time setting. After illustrating the guiding principles behind STBP, we measure its effectiveness with applications in fluid dynamics and magnetohydrodynamics. In both cases, the resulting pre-conditioners show excellent scaling properties with respect to mesh refinement, and their applications come at little-to-no overhead cost in terms of iterations to convergence with respect to their time-stepping counterpart, thus providing evidence for their potential parallel efficiency.
Ultimately, however, the parallel performance of a space-time block preconditioner depends on that of its internal components, which still rely on already-existing PinT methods. This might become an issue when dealing with advection-dominated or hyperbolic equations, as classical PinT algorithms have shown to struggle in this case. For this reason, the second part of this thesis is dedicated to investigating the causes behind this degradation in performance, as well as to study more recent PinT approaches for overcoming this limitation.
The stranger within: creating imagined communities in settler contexts: American New Orleans and Russian Odessa, 1803-1862
Keywords: transnational history
global history
Louisiana purchase
France
United States
diaspora
settler city
Anglo-American War
Mississippi
French
American Civil War
Black Sea
migration
port city
Crimean War
urban history
bilingual
settlement
creoles
language
New Orleans
imagined community
1812 invasion of Russia
comparative history
Odessa
Napoleon
Russian Empire

The nineteenth century was marked by imperial competition on a global scale, both though oversea trading ventures and movements of colonisation across continents. Diasporic communities played a central role in empire-making, and their participation in settler colonialism encourages historical inquiries from below. These communities also participated in the creation of informal empires: such was the case of French political and economic émigrés, who settled within the recent territorial gains of other nations and became in turn actors of colonisation. Strangers within their own host communities, they rose to prominence primarily in urban settings, where they could rely on political opportunities and networks that granted them power and influence. In the United States, the Louisiana Purchase and the opening of Western lands to American settlement transformed the formerly marginal role of New Orleans’ francophone Creoles. They became an ambiguous internal other, both aiding and challenging American rule. In the Russian Empire, the conquest and settlement of the Black Sea shores was overseen by French administrators and traders. Most settled in the new city of Odessa and created an urban order that set the city apart from customary Russian rule. Early Odessa and New Orleans were both marked by the influence of francophone groups, located at the intersection with wider immigration patterns, logics of urban growth, and the combination of national politics with empire-building. All contributed to the creation of cities on the margin, estranged from their own nations. This thesis proposes a Francophone and Frenchified ethos as a valuable social currency, which directed the development of key urban institutions such as churches, schools, and newspapers. From the 1800s to the mid-century, that French paradigm was trialled through national and international events, which detached the purposes and meaning of Frenchness from France itself. French attributes – through language and practices – became transformative tools that were a central feature of early New Orleans and Odessa. The two cities witnessed the development of a re-invented Frenchness outside of a formal French realm, which created a flexible category that was only valid within their respective cityscapes. This research points to the multiplicity of actors and scales in each urban context, as well as to the layering of meanings of concepts of Frenchness, historical agency, and empire. Ultimately, the findings of the thesis open promising avenues for the further study of diasporic imperialisms and the function of language and cultural institutions in both supporting and challenging state-driven colonial projects.
Modelling seafaring in Iron Age Atlantic Europe
Keywords: Maritime Archaeology
Agent-Based Modelling
Landscape Archaeology
Iron Age
Visibility Analysis
Navigation
Movement Analysis

The extent to which a European ‘Atlantic Zone’ was connected by maritime links in the Iron Age is debatable, as direct evidence is fragmentary and no accounts from contemporary inhabitants of Atlantic Europe survive. This thesis contributes to this debate by developing a new navigation model and deploying the model in the western English Channel. This thesis seeks to understand (1) whether proposed routes across the Channel would have been viable and whether other alternatives may have existed, (2) whether or not promontory forts could have been used as landmarks for navigator, and (3) how aspects of navigation – such as speed potential, landmarks, and ability to read conditions – may have affected Channel crossings. The model developed for this analysis is a fully agent-based model, in which simulated navigators follow a set of instructions without input from a human operator. A model that allows simulated ships to go off-course and potentially not reach their destinations can be used to evaluate routes in terms of risk and reliability.
The main analysis here consists of a comprehensive survey of simulated Channel crossings from March-September 2018. The results of this analysis suggest that crossings were most successful in brief windows, critique pre-existing schemes of Channel crossing, and evaluate whether certain coastal ‘nodes’ may have been more or less useful as points of departure across the Channel. Case studies focus on (1) the identification of a Continental node ‘corresponding’ to Hengistbury Head, and the potential of Guernsey as a ‘staging port’ for northbound voyages; (2) the connection between Iron Age settlements at Le Yaudet and Mount Batten, and the relative effects of parameter inputs to the model; and (3) the visibility of landmarks at the end of the Cornish and Breton peninsulas. These results demonstrate the value of the model for future analysis and its potential for further development.
Homemaker or breadwinner? A cross-sectional analysis of parental leave policies and their impact on gender role attitudes across European countries.
Keywords: gender role attitudes
parental leave
female labour force participation
policy feedback
gendered division of labour

Despite the widespread increase in female labour force participation, gender role attitudes towards the gendered division of labour remain diversified with stark variations across Europe. Given the significance of parental leave policies in shaping the division of labour between parents, this study examines how parental leave policies influence the formation of gender role attitudes across Europe. Drawing on time series, cross-sectional data from the European Value Study (EVS), and the Organisation for Economic Co-operation and Development (OECD) family database, I study the effects of three parental leave design dimensions, (1) duration, (2) compensation, and (3) flexibility across countries and across time (1990-2017). The results suggest that an increase in the duration of parental leave for fathers as well as a flexible parental leave design that allows parents to split the parental leave have both a strong and positive effect on the formation of egalitarian gender role attitudes. However, an increase in the duration of parental leave for mothers carries a negative effect on the formation of egalitarian gender role attitudes. Further, this study points towards a new emerging cleavage across European countries with some moving further towards a dual-earner model and others reversing the egalitarian advancements and resorting to a more traditional gendered division of labour. The broad perspective on cross-country differences as well as the usage of new evidence on gender role attitudes gives new insights on the debate over the relationship between macro-level policies and their impact through policy feedback on micro-level gender role attitudes.