VictorJuiz/thesis huggingface dataset:
Multi-mode coaxial transmon qubits for quantum computing and sensing

Superconducting circuits are well established as a viable candidate for the realisation of quantum computers. Circuits based on the transmon qubit are now ubiquitous, owing to its simple design and reduced control wiring overhead. An issue with transmon qubit-based architectures is the always-on unwanted interactions that impose limits on gate speeds and introduce errors into their operation. In addition, understanding sources of noise and decoherence is essential to the low-error operation quantum computers.
This thesis describes the implementation of a multi-mode superconducting qubit in a coaxial circuit QED architecture. Constructed from three superconducting islands, connected via two Josephson junctions, the device possesses two transmon-like modes with orthogonal field symmetries. The unique polarisation of each mode allows for engineering dissipation and coupling in the system, extending functionality beyond the single-mode transmon. Experimental results on the unit-cell of the two-mode coaxial transmon are presented, demonstrating coherent control and simultaneous dispersive readout of the modes of the device. A predictive theory of charge sensitivity in a multi-mode superconducting qubit is presented, and experimental results in agreement of this theory are shown, observing sensitivity to four charge-parity configurations and two independent gate-charge offsets. The utility of a multi-mode qubit as a charge detector in spatially tracking local-charge drift of ≃ 100 µm length scales is also shown, demonstrating the use of these devices as tools in understanding charge noise in superconducting circuits. Finally, a system of a pair of coupled two-mode coaxial transmons is introduced, demonstrating a highly mode-selective coupling architecture. A suppressed quantum crosstalk of 2 kHz between protected modes of the devices is measured, along with equal single qubit gate fidelities when operated both individually and simultaneously. A first characterisation of a microwave activated conditional phase interaction between computational modes driven via ancillary transitions (AT-MAP) is presented. Whilst not shown in this work, this state-dependent two-qubit interaction can be used to generate entanglement. Combined with the low crosstalk demonstrated, this shows the multi-mode qubit architecture is a promising candidate for the construction of larger scale quantum processors with fast gates and low crosstalk-related errors.

Keywords: charge noise
low-error operation
3D integration
out-of-plane wiring
entanglement generation
crosstalk suppression
coaxmon
qubit
superconducting qubits
circuit QED
high-coherence
transmon
multi-mode qubit
Advisor: Leek, P
Modelling adversarial dynamics in natural and artificial immunity

Immunity is both a lens to understand the ecology of adversarial host-pathogen interactions, but also a lever for clinical intervention in combating infectious disease. This thesis uses mathematical modelling to interrogate both the function and effectiveness of natural immune systems, and how human interventions like vaccination can be best deployed. A defence of the value of this scientific approach in overcoming the empirical and interpretative challenges for these topics is provided in chapter 1.
The first two investigations consider the evolution and functional performance of natural immune systems. Chapter 2 proposes that immune adaptations can plausibly arise from Fisherian selection, and therefore could be maladaptive, and constructs a simple mathematical model of hosts and pathogens to examine this potential mechanism. Chapter 3 assesses the utility of a particular immune adaptation: fever. It models the impact of different proposed thermal strategies of fever in terms of suppressing pathogen temperature-dependent growth, and compares these to the calorimetric costs of heating.
The second two investigations consider how artificial immunity is best deployed, focusing upon vaccination strategies in the COVID-19 pandemic. Chapter 4 considers the risk and benefit of very early emergency use of a vaccine, before its safety and efficacy is known, finding this balance can favour such use for many individuals in the early stages of the COVID-19 pandemic. Chapter 5 investigates another emergency strategy for multiple dose vaccines, prioritising individuals for first doses and the expense of postponing individuals receiving subsequent doses, and when this strategy would be beneficial for public health in terms of risk reduction, disease transmission, and earlier relaxation of non-pharmaceutical interventions.
I conclude with a discussion of broader themes which span across these investigations, and suggestions for further research.

Keywords: mathematical modelling
host-parasite
evolution
vaccine
fever
Advisor: Bonsall, M
A systems theoretical and reflexive law framework for the regulation of religious family life

What is the best institutional relationship between law and religion in family life? This question arises in response to a double-bind: some individuals within religious groups experience discrimination in their communities. However, in seeking civil remedies these individuals may be forced to abandon parts of their religious identities: they struggle to express themselves as both religious individuals and bearers of human rights because the systems that mediate their experience of the world make absolutist demands upon them.
This Thesis makes three central contributions based on reflexive law:
First, it identifies reliance on direct, command and control interventions in religious and family life as a common thread across existing models. Despite different conceptual positions on the relationship between law and religion, these interventions have tended to rely on and assume direct forms of State regulation.
Second, it argues that systems are resistant to these direct, external interventions, leading to a trilemma: ineffectiveness, unresponsiveness or incoherence. This Thesis uses the trilemma as an analytical lens to deconstruct the examples of mahr agreements and religious divorce across four example jurisdictions: UK, Canada, India and Israel. This analysis establishes two criteria to structure decisions about the circumstances and manner of State interventions in family life: first, interventions should preserve functional differentiation and communicative freedoms. Second, interventions ought to be justified according to the normative criteria of relational autonomy, substantive equality and care. These criteria – reflexive and normative - are interwoven: reflexivity is underpinned by values and in turn these values are necessary for this vision of a functionally differentiated society.
Third, this Thesis proposes a reflexive model for devising particularised, indirect interventions intended to alter these systems and modify power structures. This Thesis defends an arrangement that promotes bounded self-regulation of religious family life through a decentralised, collaborative and democratically experimental model.

Keywords: systems theory
family law
equality
regulation
human rights
law
religion
reflexive law
comparative
Advisor: Fredman, S
Taylor, R
Active nematics for living matter: from topological defects to tissue organisation

Living matter describes systems which convert chemical energy from their surroundings to grow or to generate active forces. Biological tissues are composed of many anisotropic and active cells, which can exhibit nematic long-range orientational order. The continuous injection of energy on the single-cell level can lead to complex flow patterns on the tissue scale and topological defects in the cell orientation field. This thesis explores different applications of active nematic theories to living systems. By including key biological features in active hydrodynamic models, we investigate the interplay between collective flows, shape formation and topological defects in two- and three-dimensional tissues.
Using continuum simulations, we investigate the morphology of active, self-deforming cell aggregates, where cell-generated active stress drives flows which can deform the surface. The resulting shape dynamics, such as the formation of finger-like protrusions, surface wrinkles or invagination, are reminiscent of many biological processes, ranging from morphogenesis to collective cancer invasion. We explore how spatial variations of active stress affect the dynamics in active nematic systems. We find that activity gradients induce forces which cause cell orientations and topological defects to preferentially align along a particular direction. Based on these results, we subsequently investigate multicellular spheroids, which are spherical cell clusters widely used as model systems for studying tumor dynamics. The competition over limited resources within spheroids generates proliferation gradients, leading to radial cell flows and activity gradients, both of which can affect the orientation axis of cells. As a result, distinct cell alignment patterns emerge within aggregates, which allows us to infer dynamical tissue parameters for different cell types based on experimental measurements of cell orientations inside spheroids. Finally, we motivate a continuum model for two-dimensional tissues, in which the direction of active stress is decoupled from the orientation axis of cell shape. We show that misalignment between active forces and cell shapes in tissues is linked to topological defects in the cell orientation field, both in simulations and experiments. This suggests that the direction of active stress can vary continuously within tissues, which challenges the underlying assumptions of some widely used tissue models.
This thesis demonstrates how physical continuum models of active materials can help us to understand shape formation and collective cell organisation in living matter.

Keywords: tissue mechanics
soft matter
computational fluid dynamics
biophysics
active matter
Advisor: Yeomans, J
Study of the roles of two pore channels (TPCs) in metabolism

Second messengers play roles in communication between and within cells and are critical in various physiological functions at cellular level. As an important second messenger, Ca2+, through spatiotemporal changes in its cytosolic concentration in the cell, regulates multiple physiological processes. One source of cytosolic Ca2+ is the intracellular Ca2+ stores which mainly include the endoplasmic reticulum (ER) and the endolysosomal system. In past decades, research has identified the different triggers and mechanisms of Ca2+ release from different organelles. NAADP, as the most potent trigger, initiates Ca2+ release from the endolysosomal system, and there is evidence that two pore channels (TPCs), a type of cation channel located in endolysosomes, can mediate such Ca2+ release. Much previous research has successfully investigated the functions of TPCs in various physiological and pathological processes. In my studies, I have employed TPC gene-edited animal and cell models to investigate the function of TPCs in metabolism, particularly adipocyte differentiation, and pancreatic digestive enzyme secretion.
Obesity and related metabolic diseases have become a major problem; in the UK they are estimated to affect around 25% of adults and around 20% of children. Drug treatments with a minimum of adverse reactions could be an important tool alongside preventative measures. TPCs were investigated as a potential target for anti-obesity treatment in two different aspects: adipogenesis and lipid absorption. The studies were based on unpublished evidence that Tpcn1-null mice are leaner with less lipid absorption in the intestine; also, the differentiation from mesenchymal stem cells to adipocytes in a Tpcn2 knock-down cell line is significantly reduced.
In this study I showed that pancreatic acinar cells isolated from Tpcn1-null mice have reduced lipase activity, and also that activities of other pancreatic enzymes are reduced. Moreover, Raman spectroscopy of Tpcn1/2 double-knockout pancreatic acinar cells show a reduction in the abundance of cytochrome C, which is the first study that connects TPCs with cytochrome C and should further lead to understanding of the relationship between TPCs and cell apoptosis. With regard to adipocyte differentiation, a shRNA knock-down mesenchymal stem cell model as well as preadipocytes isolated from Tpcn2-null mice showed reduced adipogenesis and the reduction seems to be led by an alteration in cyclic AMP signalling levels that induces Tpcn2 gene expression with calpain as a downstream modulator. In addition, hepatocytes isolated from Tpcn1-null mice were used as a model for SARS-CoV-2 pseudo-virus infection study, and the results showed that TPC1 may have functions in the infection of senile high-fat diet mice, and TPC1 may be regulating expression of TIMP-1 after infection.
The study of TPCs’ role in lipid metabolism has expanded our understanding of this pathophysiological process and could lead to the identification of new therapeutic drug targets for anti-obesity treatment.

Advisor: Parrington, J
Lei, M
Driven colloidal particles in optical potential energy landscapes

The structure and dynamics of colloidal particles in optical potential energy landscapes is studied. Experiments use paramagnetic or optically anisotropic colloidal particles interacting with lines or pairs of time-dependent optical traps. First, the pairwise interactions of the paramagnetic particles are measured using pairs of optical traps. We test a novel data analysis method under various conditions and calculate the magnetic susceptibility of the particles. Next, we measure the structure and dynamics of chains of paramagnetic colloids in a sinusoidal optical potential of varying depth. At well defined chain lengths, we observe a transition from an asymmetric, strongly pinned state to a free-sliding, symmetric state as the optical potential decreases. We then analyse the frictional dynamics of the same system under a constant driving force and observe a transition from low to high friction as the optical potential increases. We model the dynamics of the chains in the low and high friction regimes. The simple hard sphere model developed for the high friction regime is used to derive an equation which predicts the transition point from low to high friction. Next, we drive the chains through a time-dependent optical potential with an oscillating depth. We analyse the synchronisation of the chain’s motion to the oscillations of the potential and characterise the dynamics, observing a novel mode of motion involving the simultaneous nucleation of kinks and anti-kinks. Finally, we study the dynamics of a single optically anisotropic dumbbell particle interacting with a repulsive optical trap controlled by a time-delayed feedback protocol. We observe a transition from diffusive to driven dynamics which is modelled using delay-differential equations. We find that this transition coincides with the maximum work done on the particle and a local minimum in the mutual information between the particle and the trap.

Keywords: Aubry transition
driven systems
Frenkel Kontrova model
colloids
kinks
soft matter
feedback
friction
optical traps
Advisor: Dullens, R
Who reforms? The political economy of digital infrastructure

Social protection schemes and cash transfer payments are playing an increasingly central role in the strategies of low-income countries to tackle poverty. However, weak systems of government delivery (especially in rural areas) continue to constrain the effectiveness of these programs in improving the lives of the world’s poorest people. In this context, a growing literature demonstrates that digital infrastructure, such as secure payments systems to distribute government transfers directly into financial accounts controlled by program recipients, can dramatically reduce diversion of social protection payments by local intermediaries, disrupt systems of political patronage and improve democratic accountability by creating transparency and empowering beneficiaries.
But this presents a puzzle: in environments where incumbents may benefit from delivery systems that are distorted by clientelism, rent-seeking or the politicisation of social protection programs, when and why would politicians choose to implement policy reforms that disintermediate partisan actors from the administration of social spending and forfeit potentially powerful sources of electoral advantage?
I offer and test a theory of variation in reform outcomes, arguing that the digitisation of entitlements is not simply a technocratic, politically-neutral solution to logistical issues of distribution that can be easily explained by levels of national economic development or technological savviness. Digital infrastructure can be an important form of state capacity that allows governments to directly reach their citizens, and its absence can be a strategic choice prolonging the access of incumbents to resources and power. I find that the interaction of political economy factors, namely electoral competition and pre-existing clientelism, can influence the timing and extent to which political actors will distribute benefits to citizens digitally: when clientelism is prevalent and competition is high, reform is less likely as incumbents attempt to preserve all sources of advantage when they compete with challengers for power.
At the subnational level, in addition to these dynamics, incumbents in federal democracies often face a trade-off between aligning with a central reformist government and disintermediating their own local networks of patronage. In these circumstances, the extent to which subnational politicians share the partisan identity of the central government significantly influences reform timing and implementation, as can the degree to which state-level incumbents are enmeshed with local networks of brokers.
I find empirical support for these hypotheses at the cross-country and subnational levels, exploring global variation as well as disparities in state-level outcomes in the context of the world’s largest social protection system in India. Using original data sets and mixed methods, I investigate whether politics matters in the adoption of digital infrastructure to improve government service delivery.

Keywords: governance
economic development
clientelism
corruption
Advisor: Rueda, D
Harding, R
Test preparation: an integrated thesis of a meta-analysis and studies on students' strategies

This integrated thesis investigates the effect of test preparation in educational contexts as well as students’ usage of strategies when they prepare for tests. One meta-analysis and four (quasi-) experimental studies were included in the thesis, constituting three research papers. In addition to the main findings reported in the three papers, some cross-experimental analyses were added to further contribute to the overall interpretation of research findings.
The meta-analysis of test preparation effects on large-scale educational tests suggested that students’ test performance can be significantly improved by test preparation. The breadth of test preparation intervention, workbooks, training test-taking skills and test preparation management strategies were found to be significant moderators of test preparation effect. However, the meta-analysis found little evidence to support the notion that testing (i.e., the use of sample items and practice tests) has a superior impact on test performance over other practices (i.e., lecture or restudy), contrary to the solid testing effect reported in the literature.
The effects of testing and restudy strategies for test preparation were further explored across four (quasi-) experiments, which were conducted in an educational psychology course in a teacher training college in China. The first three (quasi-) experiments manipulated three variables: test preparation strategies, the stakes of the test preparation setting, and metacognitive training and practices. How these variables affected students’ performance on post-tests and delayed course tests were investigated. Under high-stakes settings, testing with feedback had significant effects on both post-tests and delayed course tests compared with the control group while restudy only outperformed the control on post-tests. Embedding metacognitive training and monitoring and control tasks during test preparation did not significantly boost the effects. The fourth quasi-experiment simulated a more realistic test preparation condition where students could choose either testing or restudy to study the materials multiple times. Students tended to use one-time testing more often, and they were reluctant to restudy a topic repeatedly. Both quantitative and qualitative analyses suggested that students’ strategy uses were predicted by their confidence and the question type. Chinese students in this research could recognise both the direct and indirect effects of testing practice, which seems to be culturally distinctive. However, additional analyses revealed that students’ blended use of the two strategies failed to enlarge the test preparation effect. Across the four experiments, students with lower prior attainment seem to benefit more from the test preparation interventions.

Keywords: experimental studies
Chinese students
test preparation
learning strategies
meta-analysis
high-stakes tests
Training and validation of a human ventricular cardiac action potential model to predict action potential duration response to acute inhibition of two major ionic currents

Drugs can perturb the electrical activity of cardiac muscle cells, which may lead to cardiac adverse events. The inhibition of a potassium current (IKr) has been shown to prolong the cellular and ventricular repolarisation time, respectively characterised by the action potential (AP) duration (APD) and the QT interval on the ECG, promoting arrhythmia. The in vitro characterisation of IKr inhibition is a key part of pre-clinical cardiac safety assessment for drug candidates. The proarrhythmic risk is further evaluated clinically, with particular focus on QT.
The inhibition of a calcium current (ICaL) can mitigate the prolongation of APD and QT induced by IKr inhibition. Because pre-clinical and clinical guidelines are based on different endpoints, compounds inhibiting both IKr and ICaL may be incorrectly deemed proarrhythmic pre-clinically, in which case compounds with a potentially advantageous risk/benefit ratio may not reach the patient.
Biophysically-detailed models of the cardiac AP have emerged as tools linking in vitro observations with in vivo proarrhythmic risk. This thesis establishes a framework to integrate newly generated experimental data into the development of a novel predictive AP model.
New data were generated ex vivo in adult human ventricular tissue to investigate the relationship between drug-induced changes in APD, IKr inhibition, and ICaL inhibition. A framework was developed to calibrate an AP model to this new data, with particular considerations for limitations on the data and on the understanding of mechanisms underlying the AP. Using this framework, a new AP model was calibrated, achieving improved predictions of drug-induced changes in APD in comparison with previous AP models.
Accurately predicting the changes in APD from in vitro experiments is the first step towards reliable predictions of drug-induced changes in clinically-relevant biomarkers. This work therefore contributes to a greater integration of in vitro experiments and in silico tools, and to enhanced pre-clinical predictions of the cardiac safety assessment of new compounds.

Keywords: model calibration
quantitative systems pharmacology
computational biology
cardiac safety
Advisor: Wang, K
Clerx, M
Mirams, G
Gavaghan, D
Polonchuk, L