VictorJuiz/thesis huggingface dataset:
Quantum enhanced precision measurement and information processing with integrated photonics

Photons have proven to be an effective test-bed for the fundamental concepts and elements of quantum-enhanced technologies. As systems become increasingly complex, however, practical considerations make the traditional approach of bulk optics and free-space propagation progressively more difficult. The major obstacles are the physical space necessary to realise and operate such a complex system, its stability, and maintaining low losses. In order to address these issues, quantum optical technologies can take a cue from their classical counterparts and look towards an integrated architecture to provide miniaturisation, greatly enhanced stability, less alignment, and low loss interfaces between different system components.
In this thesis the feasibility of chip-based waveguides as a platform for metrology and information processing will be explored. In Part I, the necessary criteria for a metrology system to out-perform its classical counterpart will be investigated. It will be found that loss is a major barrier to this aim and, critically, that it is unlikely to have been achieved to date by any experiment which consumes resources of a fixed photon number. The issue of loss will be addressed by developing a scalable heralded source of a class of entangled photonic states which are both robust to losses and practically feasible to prepare. A novel tomographic technique will be developed to characterize these states and it will be explicitly demonstrated how it is possible to beat some bounds on classical performance without being able to out-perform a comparable classical system. Finally, a proof of principle demonstration of a waveguide-based interferometer with an integrated phase-shifter will be undertaken. It will be shown that the device preserves quantum interference, making it suitable for use in quantum-enhanced metrology applications.
In Part II, integrated optics in the context of information processing will be discussed. First, a novel characterization technique will be developed which enables the behaviour of complex circuits to be predicted. The technique is independent of loss in the device being characterized. A method of simulating these circuits will be outlined that takes advantage of the computational speed-up available from parallelisation and sparse matrix operations. A key increase in complexity for integrated photonic systems will be demonstrated by showing quantum interference of three photons from two separate sources in eight spatial modes. The resulting interference has a visibility which beats all possible classical interference visibilities for similar circuits. Finally, a fully integrated waveguide-coupled photon-number-resolving detector will be developed and demonstrated. This proof of concept demonstration will show good resolution of different photon number events. The device will be modelled and routes to high efficiency operation will be explored.

Keywords: quantum information processing
quantum optics
precision measurement
Advisor: Walmsley, I
The mathematics of ship slamming

Motivated by the motion of a ship in a heavy sea, a mathematical model for the vertical impact of a two-dimensional solid body onto a half-space of quiescent, inviscid, incompressible fluid is formulated. No solutions to the full problem are known, but in the case when the impacting body has small deadrise angle (meaning that the angle between the tangent to the profile and the horizontal is everywhere small) a uniformly valid solution is obtained by using the method of matched asymptotic expansions. The pressure on the body is calculated and is in fair agreement with experimental results. The model is generalised for more complicated impacts and the justifications for the model are discussed.
The method is extended to three-dimensional bodies with small deadrise angle and solutions are obtained in some special cases. A variations! formulation of the leading order outer problem is derived, which gives information about the solution and leads to an fixed domain scheme for calculating solutions numerically. A partial linear stability analysis of the outer problem is given which indicates that entry problems are stable but exit problems are unstable to small perturbations.
A mathematical model for the effect of a cushioning air layer between the body and the fluid is presented and analysed both numerically and in appropriate asymptotic limits.
Finally, the limitations of the models are discussed and directions for future work indicated.

Advisor: Ockendon, J
LRL genes are ancient regulators of tip-growing rooting cell development in land plants

Evolution of developmental genes is an important mechanism for plant morphological evolution. The LRL genes are an ancient group of bHLH transcription factors that positively regulate root hair development in angiosperms. Here I show that, in the moss Physcomitrella patens, two LRL genes are present and they positively regulate rhizoid and caulonema (a rhizoid-like cell type) development. GUS-transcriptional reporter plants show that both PpLRL1 and PpLRL2 are expressed in tissues giving rise to caulonemata. Loss-of-function mutants in either PpLRL1 or PpLRL2 led to defective rhizoid and caulonema development, and the Pplrl1 Pplrl2 double loss-of-function mutants completely lack rhizoids and caulonemata. Consistent with this, gain-of-function mutants show enhanced rhizoid and caulonema development. In addition, I show that the stimulatory effects of auxin and low phosphate on the development of rhizoids and/or caulonemata required PpLRL gene function. Together, these results show that LRL genes are conserved, positive regulators in tip-growing rooting cell development in land plants. To elucidate whether LRL genes belong to part of a conserved gene network, I use qRT-PCR to determine the transcriptional interaction between LRL genes and the Class I RSL genes, which is another group of conserved regulators of rhizoids and root hairs. Comparing the LRL-RSL network between P. patens and A. thaliana reveals that LRL and Class I RSL genes are transcriptionally independent of each other in P. patens but one LRL gene is transcriptionally downstream of Class I RSL genes in A. thaliana. This suggests that the gene network controlling tip-growing rooting cell development has changed since mosses and angiosperms last shared a common ancestor.

Keywords: LRL genes
roots
rhizoids
evo-devo
auxin
Advisor: Dolan, L
Harberd, N
MRI and histological analysis of brain metastasis and the effect of systemic inflammation

Background
Brain metastasis is a leading cause of cancer mortality and affects 20-40% of all cancer patients. The BBB is responsible for isolation and protection of the brain parenchyma from many diagnostic and therapeutic agents. New molecular agents that target tumour-associated VCAM-1 expression on the brain endothelium show improvements in the early diagnosis of brain metastasis. The vascular endothelium of the CNS plays an important role in the maintenance of the brain microenvironment and possibly aids the extravasation of tumour cells via expression of CAMs.
Aims
Using the breast carcinoma-derived 4T1 cell line, syngeneic to BALB/c mice, this work aimed (i) to determine the level of colocalisation between VCAM-1 expression at sites of brain metastasis and the presence of VCAM-MPIO-induced hypointensities in MR datasets; (ii) to describe the normal developmental characteristics of the intracardial BALB/c-4T1 brain metastatic model in the absence of overt inflammation; (iii) to test the effects of an adenovirus-induced systemic inflammatory challenge on metastatic uptake and development in the brain.
Results
The level of correspondence of VCAM-MPIO-derived hypointensities with VCAM-1 expression at the tumour site was found to be dependent on the size of metastasis. An improved method for detection of VCAM-MPIO hypointensities using an automated method has been presented. Tumours were found to develop preferentially on venous rather than arteriolar blood vessels, and showed greater and lesser abundance in different anatomical brain regions. Adenovirus injection was found to cause an upregulation of a range of peripheral pro-inflammatory cytokines, and expression of VCAM-1 on cerebral vasculature, preferentially on arteriolar blood vessels. Both pre- and post-treatment with adenovirus caused a two-fold reduction in tumour numbers and altered developmental characteristics of established tumours, although no significant differences were observed in VCAM-MPIO hypointensities in MR datasets.
Conclusions
The development of molecular MRI approaches to target VCAM-1 expression at the site of brain metastases has improved the sensitivity of tumour detection. 4T1-GFP metastasis to the brain is specific both to anatomical sites and to regions of the vascular bed, suggesting differences in vascular morphology and/or signalling dynamics in these locations. The changes in tumour number and morphology as a result of systemic inflammation suggest an anti-tumour effect of adenoviral treatment and, given the role of the systemic immune system and its importance in the development of immunotherapies, possible future directions for research.

Keywords: CNS
blood-brain barrier
image analysis
immunology
metastasis
Advisor: Sibson, N
Anthony, D
Diversity of silica-scaled protists

This thesis investigates the diversity of two silica-scaled protist groups, Paraphysomonadida and Thaumatomonadida by light and electron microscopical observations and sequencing (rDNA) on novel clonal cultures. Despite these groups of protist dominating pelagic, littoral as well as inland freshwater and soil habitats, they are taxonomically poorly understood to the extent that any progress in ecological theory is hampered. Now that environmental DNA sequencing is being carried out faster than we can characterise protists from culture it is important that we understand how molecular and physical diversity match up, especially because so many protists are morphospecies.
Nearly one hundred isolates were cultured on which both morphological and molecular data was carried out in parallel to reveal around 50 new species of protist from eight different genera: two heterokont genera, Paraphysomonas and Incisomonas n. gen., and six cercozoan genera, Thaumatomonas, Allas, Reckertia, Thaumatospina n. gen., Cowlomonas n. gen., and Scutellomonas n. gen.
These data make major contributions to taxonomy and understanding aspects of protist diversity where previously morphological diversity was heavily biased towards over- generalized morphotypes. This thesis quickly showed that gross lumping of morphospecies was true of Paraphysomonas, for which many of the isolates cultured herein might have been regarded as one species (not more than 20). The many cultured isolates exhibited varied cell and scale morphology, and by sequencing (rDNA), it was possible to see the evolution of scale morphology map on to trees. This marriage of molecular and morphological data made it possible to view distinct groups of species that shared scale detail that might have otherwise been overlooked had either method been used alone.
This research has shed significant light on how scale morphology can be used as reliable taxonomic marker for protists, the insights of which can be applied to make taxonomic improvements to other silica-scaled protist groups.

Keywords: TEM
EM
secondary structure
algae
phylogeny
protists
biology
light microscopy
18S
ITS2
ribosome
SSU
microscopy
electron microscopy
ultrastructure
SEM
taxonomy
Advisor: Cavalier-Smith, T
Tory economic discourse from the age of restriction to the rise of Disraeli: 1797-1850

In 1797 Pitt the Younger's war-time government promulgated the Restriction Act which suspended cash payments from the Bank of England, with the proviso that soon after the restoration of peace, the payments would be resumed and the ancient metallic standard of nation restored. Contemporary accounts from the period, as well as current historiography, acknowledge Great Britain experienced great prosperity during this Age of Restriction: the question was whether it was built on a true and solid foundation.
The conservative understanding of the consequences of a resumption of specie payments informed their subsequent position in favor of protection in agriculture. Indeed, there is considerably evidence that the Corn Laws were a second-choice policy prescription to counter the deflationary effects of the gold standard, the true solution, as the conservatives argued, was a more expansive currency system like bimetallism or a free-banking system like Scotland’s, founded upon a variant of the real bills doctrine. The irony is that while the conservatives were more pro-free market on the margins of money and banking, their response to bullionism called for more government intervention to counteract the pernicious effects generated by government activity in the first instance. This paper presents these arguments as a conservative bid for the support of the "productive classes" of the nation, which alters the way the Tories should be understood, and sheds light on an important group of people about whom scholars still know very little.

Keywords: currency
Bank of England
government
banking
conservatism
Advisor: Offer, A
Muon capture schemes for the neutrino factory

The proposed neutrino factory, a facility for precision measurements of neutrino oscillations, requires directional neutrino beams to reach the required sensitivities. Among the few sources of such beams is the decay of muons travelling at relativistic speeds, therefore an intense source of muons and subsequent rapid acceleration must be designed so they can reach the required energy before decaying. This thesis considers several stages in this process: pions are produced from a proton beam hitting a target and pion yield optima are determined as a function of target design parameters and the proton energy. Issues related to producing the original proton beam are also discussed. The pions decay to a beam of muons, confined by a channel of solenoids and other components known as the muon front end. A design for this is found that meets the requirement of 10^21 muons per operational year [1]. The computer code MARS15 [2] is used to simulate the target, with benchmarks against GEANT4 [3] and initial results from the HARP experiment [4]. The author's code Muon1 [5] is used for muon tracking, with its techniques also explained in the thesis. To find the highest-yielding arrangement of magnets and accelerating components from the target onwards, Muon1 incorporates an optimisation feature where almost all parameters of the beamline can be varied. This produces a high-dimensionality search space where the best muon yield is sought using a genetic algorithm. As each individual evaluation of a design is itself a time-consuming simulation with tens of thousands of particles, the code has been deployed as a distributed computing project that is able to perform millions of simulations per optimisation. [1] "GROUP REPORT: Physics at a Neutrino Factory", C. Albright et al. (Eds. S. Geer and H. Schellman), Report to the Fermilab Directorate, FERMILAB-FN-692, hep-ex/0008064 (2000). [2] "The MARS Code System" version 15.07, by N.V. Mokhov, available from http://www-ap.fnal.gov/MARS/ [3] "GEANT4 - a simulation toolkit", S. Agostinelli et al., Nuclear Instruments and Methods A 506, pp.250-303 (2003), available from http://geant4.web.cern.ch/geant4/ [4] "Status and prospects of the HARP experiment", M. Ellis, J. Phys. G 29, pp.1613-1620 (2003). [5] Muon1 Distributed Particle Accelerator Design project website, http://stephenbrooks.org/muon1

Keywords: particle physics
physics
particle accelerators
Advisor: Prior, C
Cobb, J
Application of stochastic models to radiation chemistry

This thesis addresses one area of major interest in reaction kinetics, the theoretical description of recombination in nonhomogeneous systems. The reaction of the highly reactive particles formed by the passage of ionising radiation through a medium is an important example of this type of system.
Stochastic effects are apparent in every stage of the development of a radiolysis system: in the interaction between the radiation and the medium and in the diffusion and reaction processes that follow. Conventional models for nonhomogeneous kinetics in radiation chemistry are based upon a deterministic analysis. These models are appraised together with an alternative stochastic approach. Three stochastic methods are discussed: a full Monte Carlo simulation of the diffusion and reaction and two approximate models based upon an independent pairs approximation.
It is important that any kinetic model accurately describes the system it purports to represent and this can only be assured by extensive validation. The stochastic models are developed to encompass the diffusion-controlled reactions of ions and radicals and to include the effects of a bulk electrolyte upon the reactions between ions. To model a realistic radiation chemistry reaction scheme, it is necessary to consider reactions that are not fully diffusion-controlled. The radiation boundary condition is introduced and used to extend stochastic modelling to partially diffusion-controlled reactions. Recombination in an anisotropic environment is also considered.
Although a complete analysis of the chemistry of a radiolysis system requires a complex reaction scheme, the scheme can be simplified, in acid and in alkali, by the use of an instantaneous scavenging approximation. In acid, this approximation produces a simple three reaction mechanism based upon five species: H, OH, H2 , H20 and H202 . The acid system is used to demonstrate the stochastic treatment of realistic kinetics. The instantaneous scavenging approximation is examined in detail and techniques are developed for the explicit modelling of reactions with a homogeneously distributed scavenger.
A stochastic treatment of nonhomogeneous reaction kinetics requires a description of the initial spatial distribution of the reacting particles. A rudimentary Monte Carlo simulation is used to determine a simple distribution of clusters of reactive particles similar to that found along the path of a high energy electron in water. This distribution provides a suitable basis for kinetic simulation. The kinetics of a more detailed idealised track structure are also considered and the stochastic and deterministic kinetics of extended particle distributions are discussed.
The abbé de Choisy (1644-1724)

The aim of this thesis is to study critically the works of François-Timoléon, abbé de Choisy (1644-1724) against their historical background, and to present this study in the context or the author's life. It consists of an. introduction followed by seven chapters, the first of which is concerned with biography and bibliography, and the last of which forms a conclusion. In the introduction, I point out that I have chosen four works by Choisy, because of the light that they throw on the writer and his times, for more detailed study, but in so doing have also taken into con- sideration the rest or his output.
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Art and conversation: disturbation in public space

Arthur C. Danto introduced the term “disturbation” in 1985 to denote artworks that confront audiences with the materials of reality in order to produce reactions that are continuous with those of real life. Danto argued that disturbational art dissolve the distance between representation and reality opened up by Platonic metaphysics and by the insertion of theatrical distance, returning art to its mimetic and magical phase.
The thesis uses Danto’s conceptual framework to develop a critical account of artworks that use politics as the medium for their disturbational content by creating relationships with audiences that provoke the re-realization of attitudes, experiences and identities that have been suppressed. In Shibboleth (2007) by Doris Salcedo, disturbation takes the form of the ‘political uncanny’ and in the case of Domestic Tension (2007) by Wafaa Bilal, it takes the form of the ‘political abject’.
The thesis argues that Shibboleth confronted audiences with “the return of the repressed” through a disturbational process of interaction with the space of the Turbine Hall at Tate Modern. Departing from existing readings of Salcedo’s work, the thesis proposes that the installation provoked the experience of the political uncanny by physically enacting suppressed historical, economic and political divisions constructed upon a friend/enemy form of relationship.
Likewise, the thesis argues that the use of virtual electronic media in the process of participation in Domestic Tension radically altered the structure of collaborative activities by its production of the abject through the detachment conferred by distance and anonymity. The degree of self-censorship and accountability that exists in face to face interactions was nullified by the process of remote participation which encouraged deindividuation and anti-social or dehumanizing behavior. The tendency towards dehumanization becomes intensified when the artwork’s content is political, thereby provoking hostile and distancing effects refracted by contemporary geopolitics.

Keywords: contemporary art theory
Advisor: Catling, B
Bull, M
Potential mechanisms in MuSK-myasthenia gravis

Autoimmunity is a failure to tolerate circulating or cell surface expressed self antigens,leading to activation of the immune system and attack of self tissues. Muscle-specific kinase (MuSK) myasthenia gravis (MG) is a disease caused by antibodies to MuSK and hallmarked by fatigable muscle weakness. MuSK is a tyrosine kinase that interacts with low-density lipoprotein receptor-related protein 4 (LRP4), resulting in maintenance of the high density of acetylcholine receptors (AChRs) at the neuromuscular junction; this high density is essential for efficient transmission of signals from nerve to muscle, and MuSK antibodies impair this transmission. MuSK antibodies are predominantly IgG4, a subclass that does not induce immunological damage. Thus how these antibodies cause neuromuscular junction dysfunction is not clear. Potential mechanisms of the MuSK antibodies were explored in in vitro experiments.
Plasmas from fourteen MuSK-MG patients were studied. IgG antibodies and IgG subclass profiles were measured with flow cytometry. Total IgG, Fabs, IgG4 and IgG1-3 subclass antibodies were prepared and purified; these were used to investigate the effects on MuSK surface expression, binding of LRP4 to MuSK, and agrin-LRP4-MuSK-induced AChR clustering in C2C12 mouse myotubes.
No evidence for MuSK endocytosis by MuSK IgG, IgG1-3 or IgG4 antibodies was found. The predominant IgG4 subclass, and the monovalent IgG Fabs, blocked binding between LRP4 and MuSK but both IgG4 and IgG1-3 subclass antibodies were equally able to disperse pre-formed and newly-induced AChR clusters in C2C12 myotubes.
The block of LRP4-MuSK interaction by IgG4 antibodies is likely to be a major pathogenic mechanism in MuSK-MG, which may lead to disrupted signal transduction, reduced AChR aggregation and neuromuscular transmission failure at the neuromuscular junction. In addition, MuSK IgG1-3, until now described as nonpathogenic, may also contribute to the reduced AChR density and neuromuscular dysfunction in MuSK-MG. These results provide new evidence concerning the pathogenic antibodies and their mechanisms in MuSK-MG.

Keywords: IgG4
LRP4
neuroimmunology
neuromuscular junction
MuSK
myasthenia gravis
Advisor: Vincent, A
Cossins, JA