VictorJuiz/thesis huggingface dataset:
Templated self-assembly of the bacterial flagellar motor torque ring in vitro

The Bacterial Flagellar Motor is an ion-driven rotary motor employed by many bacteria for motility and surface sensing, and a model system for the self-assembly and regulation of large protein complexes.
Early in motor biogenesis a ring of the integral membrane protein FliF templates the cytoplasmic assembly of FliG, which subsequently templates transient incorporation of FliM1:FliN3 subunits. FliG, FliM and FliN collectively comprise the C-ring: site of torque generation and directional switching. Switching is regulated by binding of CheY-P to FliM1:FliN3, propagating a co-operative conformational change throughout the entire C-ring. The molecular details of C-ring structure, assembly and dynamics are unclear.
Averaged cryo-EM structures of purified motors feature a curious symmetry mismatch between the FliF ring (~26-fold) and C-ring (~34-fold), while in vivo fluorescence shows a variation in FliM1:FliN3 population with rotation direction that is not resolved in the EM structures. The stoichiometries of FliG/M/N are all disputed, and cannot yet be measured accurately in vivo. More powerful techniques are available in vitro, but it is unclear whether dynamic structural features of the motor survive purification.
Therefore, we aspire to assemble a C-ring in vitro as a platform for in vitro study. Furthermore, by substituting the difficult-to-reconstitute FliF template with a controllable DNA-origami mimic, we envisage studying self-assembly from the bottom up through template remodelling: a novel concept in the study of protein self-assembly.
This thesis describes the development of linear DNA templates mimicking short fragments of the FliF ring. FliG arrangement on these templates is specified by DNA sequence design, and can be quantified with single-molecule fluorescence and native gel electrophoresis. The methods developed here will allow testing of the FliG domain-swap polymerization model as a mechanistic explanation for the symmetry mismatch, and lay the foundations for in vitro construction of a complete C-ring.

Keywords: DNA nanotechnology
Bacterial Flagella Motor
Advisor: Turberfield, A
Berry, R
The shape of things to come: global order and democracy in 1940s international thought

This thesis examines the role of democracy in British, French and American visions of global order in the 1940s. It argues that ‘democracy’ in a global context did not reflect ‘Wilsonian’ or ‘Cosmopolitan’ dreams, nor did it refer to the questions of state representation and institutional accountability that dominate contemporary debates. Instead, it shows that building a ‘democratic’ global order in the 1940s meant, above all, an attempt to address the challenge of democratic modernity, summarised by Karl Polanyi in 1944 as the search for ‘freedom in a complex society’, in the new global environment of the mid-century. This challenge was composed of five core concerns, ranging from the protection of the individual from the modern state and the transformation of democratic participation, to the use of expert planning and modern technology to secure economic justice. Achieving a balance between these competing and at times contradictory imperatives was seen as the key to securing a new democratic order that could resist the temptations of nationalism and totalitarianism and secure peace. Crucially, it was only through the structures of a new global order that, internationalists argued, there could be any chance of success. The task was not an easy one, and the historical investigation shows how the choices and trade-offs internationalists made in relation to these imperatives entailed costs in terms of inclusivity, participation and even rights within visions of democratic global order.
The thesis has both historical and conceptual goals. First, it recovers important ideas about global order that have been largely written out of the history of this period by taking the language of democracy in world order debates seriously and understanding these visions in context. Conceptually, its aim is to contest and transform how we think about global order and democracy in the history of international thought and in the present day. Instead of Cosmopolitan, Wilsonian, liberal or other normative blueprints for a democratic world order, the conclusion argues that we should, following the example of the 1940s, reconceptualise the relationship between global order and democracy today in relation to the persistent dilemmas of democratic modernity. In a global context, these continue to have interlocking domestic and international dimensions and, more importantly, continue to require choices that entail normatively contestable costs in the construction of a democratic global order. Only then, it argues, will it be possible to think about how these shortcomings can be mitigated and whether and what kind of democratic order we want to pursue at all.

Keywords: Democratic theory
Global order
Cosmopolitanism
Postwar order
Democratic world order
1940s international thought
Internationalism
Liberal world order
Wilsonianism
Historical international relations
Democracy
Advisor: Hurrell, A
Aerodynamic flow sensing in the desert locust (Schistocerca gregaria)

Insects are richly instrumented with sensors used in flight control. Whilst we have good knowledge of the basic physiology of these structures, in many cases we have only a cursory understanding of the likely stimuli each sensory system receives during flight or why these systems have evolved to perform their particular function. This thesis examines the role and optimisation of arrays of cephalic flow-sensitive hairs, called trichoid sensilla, in the flight control of the desert locust (Schistocerca gregaria). Particle image velocimetry and computational fluid dynamics are used to measure and simulate the airflows being received by the fields of sensilla during flight. The visualisations reveal distinct local flow conditions over each field and how these are modulated differently by perturbations. The geometry of every individual hair is captured using both benchtop and synchrotron based X-ray micro tomography (XMT). These scans enable three-dimensional measurement of each hair’s direction of curvature, which represents the direction of peak sensitivity to airflow. By combining flow stimulus and directional sensitivity data, we provide strong evidence for separate fields being tuned for distinct roles: some as step detectors for monitoring stall at extreme angles of attack, others as graded sensors for angles of attack and sideslip, and possibly for monitoring airspeed. Finally, we examine the flight response of tethered locusts to varying aerodynamic stimuli by changing the angle of sideslip and selectively covering fields of sensilla from oncoming airflow. We demonstrate a clear role for the sensilla in modifying the forces and moments generated under varying sideslip, as well as in changing the underlying natural modes of motion of the system. We reveal the axes about which the locusts are unstable under our experimental conditions, and demonstrate the necessary additional sensory feedback required to stabilise the system fully.
The combined data represent a comprehensive and thorough examination of the complete cephalic flow-sensing system, providing insights applicable to both further biological study on multi-modal flight control and the use of bio-inspired arrays of sensors for manmade applications.

Advisor: Taylor, G
Bomphrey, R
A structure-function study of the TWIK-1 K2P channel

Two-pore domain potassium (K2P) channels play a role in regulating the resting mem- brane potential of cells and therefore play a major role in the function of both excitable and non-excitable cells. One of the K2P family members is the Tandem-pore Weak Inwardly-rectifying Potassium (TWIK-1) channel. It is mostly found in the kidney and heart. However, not much is known about the biophysical properties and regulation of this channel. In the first part of this study, the presence of a hydrophobic cuff at the inner pore side of the channel is identified and characterised. This cuff acts as a barrier to water permeation, and by extension, ion flow through the channel. Using molecular dynamic simulations and electrophysiology, two leucine residues, L146 and L261, were identified as the primary constituents of this hydrophobic cuff. Systematic mutagenesis of these residues reveals that the barrier against pore hydration can be overcome by introducing polar side chains into these positions.
This study also addresses the problem of TWIK-1 functional expression at the surface membrane. Suppression of TWIK-1 functional activity has been thought to be caused by binding of a small ubiquitin-like modifier (SUMO) to a lysine residue in the C-helix (K274). However, it has also been suggested that TWIK-1 at the surface membrane is rapidly internalised into endosomes via the endocytosis pathway. My results suggest that the latter explanation is more likely.
The second major part of this study focused on the structure and function of the amphipathic helix near the c-terminus of the protein. This 'C-helix' lies parallel to the intracellular membrane surface. Using scanning mutagenesis and electrophysiological measurements, a trio of positively-charged residues (K274/R277/K278) that faces the inner pore were identified as playing an important role in the functional expression of TWIK-1 currents by influencing the electrostatic charges at the intracellular pore mouth of TWIK-1. Overall this thesis provides new insights into the structural features which control the functional activity of the TWIK-1 potassium channel.

Advisor: Tucker, S
From cash flows to water flows: An assessment of financial risks to rural water supply sustainability in sub-Saharan Africa

This research examines the collective action and financial dimensions of rural waterpoint sustainability in sub-Saharan Africa. Four interlinking papers empirically evaluate the nature and drivers of financial risks, and how they in turn impact the operational performance of community water supplies. The research is grounded in conceptual and theoretical frameworks pertaining to collective action and common-pool resource management, in particular Ostrom's social-ecological systems framework (Ostrom, 2007), Musgrave & Musgrave's economic good framework (Musgrave & Musgrave, 1973), and Marwell & Oliver’s critical mass theory (Marwell & Oliver, 1993).
The first paper analyses data extracted from national waterpoint inventories in Liberia, Sierra Leone, and Uganda. The remaining three papers draw on primary data from rural Kenya comprising 229 years' worth of water committee financial records, a census of 571 waterpoints, and a survey of 3,361 households. These data were collected during extensive field work campaigns in Kwale, Kenya. Quantitative analyses were carried out by way of advanced statistical techniques, including logistic regression, linear mixed (repeated measure) models, and generalised estimating equations.
Results suggest collection of user fees is a significant determinant of waterpoint sustainability, alongside other institutional, technical, geographical and environmental variables. However, monthly payment arrangements are beset by non-payment and late payment, particularly if rainfall levels are high, group size is large, households are far away, and water is aggressive and unpalatable. Although monthly contribution levels remain relatively stable above a collective payment rate of 60%, there is little evidence of self-sustaining growth beyond this point, and revenue collection is prone to collapse below this collective payment threshold. In comparison, pay-as-you-fetch fees are associated with increased revenue and improved operational performance, but result in a higher proportion of households opting for an unimproved water source.
If the Sustainable Development Goal of universal access to safe water supplies is to be achieved in rural sub-Saharan Africa, strategies are needed to strengthen revenue collection systems and bolster payment incentives. External support and professionalised service delivery models present potential pathways to advance these goals. Policymakers may also need to introduce carefully designed subsidies, or promote self-supply approaches that realign lifecycle costs with users’ willingness-to-pay.

Advisor: Hope, R
Robust and stochastic MPC of uncertain-parameter systems

Constraint handling is difficult in model predictive control (MPC) of linear differential inclusions (LDIs) and linear parameter varying (LPV) systems. The designer is faced with a choice of using conservative bounds that may give poor performance, or accurate ones that require heavy online computation. This thesis presents a framework to achieve a more flexible trade-off between these two extremes by using a state tube, a sequence of parametrised polyhedra that is guaranteed to contain the future state.
To define controllers using a tube, one must ensure that the polyhedra are a sub-set of the region defined by constraints. Necessary and sufficient conditions for these subset relations follow from duality theory, and it is possible to apply these conditions to constrain predicted system states and inputs with only a little conservatism. This leads to a general method of MPC design for uncertain-parameter systems. The resulting controllers have strong theoretical properties, can be implemented using standard algorithms and outperform existing techniques.
Crucially, the online optimisation used in the controller is a convex problem with a number of constraints and variables that increases only linearly with the length of the prediction horizon. This holds true for both LDI and LPV systems. For the latter it is possible to optimise over a class of gain-scheduled control policies to improve performance, with a similar linear increase in problem size.
The framework extends to stochastic LDIs with chance constraints, for which there are efficient suboptimal methods using online sampling. Sample approximations of chance constraint-admissible sets are generally not positively invariant, which motivates the novel concept of ‘sample-admissible’ sets with this property to ensure recursive feasibility when using sampling methods. The thesis concludes by introducing a simple, convex alternative to chance-constrained MPC that applies a robust bound to the time average of constraint violations in closed-loop.

Keywords: Stochastic
Robust
Optimal
Tube MPC
Convex
Control
Receding-horizon
Constraints
MPC
Optimisation
Advisor: Cannon, M
Kouvaritakis, B
Exploring and classifying the transient radio sky

Observations of the transient radio sky provide an insight into the most dynamic and energetic events in the Universe. The exploration of transient and variable sources, for a long time primarily focused on higher frequencies, has recently been extended to the long wavelength regime, with the development of facilities such as the Low Frequency Array (LOFAR).
In this work I describe the general design of LOFAR as well as details of the commissioning work performed during the early stages of operation. Secondly, I perform an analysis of the first dedicated LOFAR transient survey -- the Radio Sky Monitor. The investigation is focused on exploring 30 seconds time-scale images and allows us to place an upper limit on the expected areal densities of fast radio transients in the low frequency sky. It also provides spectral index constraints on the previously found, first LOFAR transient event.
I also investigate the relation between the radio luminosities and variability time-scales across a wide range of sources – from nearby flare stars to distant supermassive black holes. The results are discussed in context of the potential use as a classification method, as well as in comparison with the expected brightness temperature of the events. The relation is used as a base for building a tool which classifies (with a given probability) an observed event, depending on the measured rise/decline rates of the flare. It includes the automatic selection of flares and takes into account the estimated areal densities of different classes of objects.
Lastly, I discuss the results of the luminosity – time-scale correlation in context of the estimation of the kinetic power, as well as future prospects of implementing the presented classification method into an automated transient detection pipeline for instruments such as MeerKAT and the Square Kilometer Array.

Keywords: Radio transients
Synchrotron emission
Radio variables
Radio sources classification
Advisor: Fender, R
Multifrequency search &amp; classification of the transient radio sky

The radio sky can exhibit dynamic changes that provide an excellent opportunity to study the most exotic events in the Universe. In recent years the development and completion of advanced radio facilities has enabled the transient radio sky to be probed to unprecedented levels, especially at low frequencies with telescopes such as the Low-Frequency Array (LOFAR) revolutionising observations in this regime.
This work primarily focuses on the detection of radio transients both at low and high frequencies. I describe the analysis of a 60 MHz LOFAR monitoring campaign centred at the North Celestial Pole, and report the discovery of the first LOFAR transient source. I also present the initial transient search of the CHILES survey that was performed with the VLA at 1.4 GHz, supported by simultaneous optical observations. Three strong transient candidates are discussed along with identifying a further 72 possible candidates.
Furthermore, I investigate the relation between the radio and optical flux properties of known transient and variable sources, with the aim of developing a classification method for these types of events. I show that from just radio and optical flux measurements, it is possible to separate certain classes of objects, with additional information provided by analysing how individual classes evolve in the radio and optical parameter space over time.
Lastly, I explore the future prospects of the LOFAR and CHILES transient searches, detailing what techniques could be used to further define the transient parameter space. I also discuss how the radio and optical classification method can be advanced and incorporated into automatic transient pipelines, which may be a necessity in the future Square Kilometre Array era.

Keywords: radio transients
radio variables
LOFAR
transient classification
Advisor: Fender, R
Small-island interactions: pottery from Roman Malta

This thesis is an investigation of Roman pottery from the Maltese islands from the 1st century BC to the mid-4th century AD, and how pottery can help assess Malta's economic role in the wider central Mediterranean region. The archipelago’s locally produced vessels, its range of ceramic exports, and the quantification of the types of amphorae, fine, and cooking wares the islands imported, were studied and the data were used to compare with the pottery available from the small islands of Pantelleria, Lampedusa and the Kerkennah isles.
The aim is to revisit the theme of the economic role of the Maltese islands and other similar-sized islands in the region by moving away from the tradition of unilateral and monographic narratives, which more often than not, omit the wealth of information that can be garnered from pottery. In the first instance, a detailed study of three complete and new ceramic assemblages, including amphorae, fine, cooking and coarse wares, was undertaken. The opportunity to quantify identifiable imports and compare them with local products—the first of its kind for fine, cooking and coarse wares—provided valuable proxy data for comparing Malta with neighbouring islands and centres, and demonstrated what proportion of ceramic vessels were locally supplied, and how these changed over time. These data were also fed into a series of network analyses, which plotted the common pottery links shared between small-island and mainland sites in the region. The analyses were interpreted in conjunction with a critique of existing pottery quantification methods, and the potential acceptance for utilising all known pottery data irrespective of the quality and quantity of the published data available. Most importantly, the import trends obtained from this study were incorporated into the existing narrative of how small islands and their local industries featured in the central Mediterranean’s regional economy, highlighting the types of archaeologically visible industries that existed; how these developed symbiotically alongside other larger supply networks; and what effect this might have had on the integration of small islands in the Roman Mediterranean.

Advisor: Wilson, A
Endogenous institutionalism and the puzzle of gender quotas: insights from Latin America

Given their potential to negatively impact men’s goal of staying in office, can gender quotas be aligned with the preferences of male legislators who adopt the policy? In other words, does the rapid spread of gender quotas worldwide challenge notions of the rationality of legislators as career-driven individuals? These are the main questions that drive this thesis. To answer these questions, I develop a prospect theory-based framework that accounts for how electoral security and political ambition impact legislators’ behaviour in influencing the strength of gender quota designs. I argue that, faced with growing pressures to adopt gender quotas, male parliamentarians engage in the risk-taking process of assenting with gender quotas, meanwhile seeking to minimize the potential costs of the policy to their future careers by actively weakening quota designs.
To evaluate the plausibility of my theory, I employ a series of multi-method and multi-level analyses presented across five substantive chapters, each of which is respectively based on: 1) a cross-sectional analysis of Latin America countries; 2) an elite survey experiment with Brazilian state legislators; and, in-depth process tracing of the cases of gender quota adoption in 3) Costa Rica; 4) Brazil; and, 5) Chile.
The work makes three main contributions. Firstly, although previously identified, the resistance of male legislators towards gender quotas had never been systematically analysed in a comparative manner; focusing on the behaviour of male incumbents is thus a relevant contribution. Secondly, although various authors have provided explanations for the origins of gender quota adoptions, no work had ever comparatively assessed sources of the variation in gender quota designs. Thus, I move the study of gender quotas beyond the binary choice of adoption. Thirdly, I show that the static assumptions of endogenous institutionalism need to be modified by the introduction of risk, which can only be achieved by integrating the insights of prospect theory.

Advisor: Power, T
Doyle, D