VictorJuiz/thesis huggingface dataset:
Asymptotic invariants of infinite discrete groups
Keywords: group
combing
isoperimetric inequality
asymptotic cone

Asymptotic cones. A finitely generated group has a word metric, which one can scale and thereby view the group from increasingly distant vantage points. The group coalesces to an "asymptotic cone" in the limit (this is made precise using techniques of non-standard analysis). The reward is that in place of the discrete group one has a continuous object "that is amenable to attack by geometric (e.g. topological, infinitesimal) machinery" (to quote Gromov).
We give coarse geometric conditions for a metric space X to have N-connected asymptotic cones. These conditions are expressed in terms of certain filling functions concerning filling N-spheres in an appropriately coarse sense.
We interpret the criteria in the case where X is a finitely generated group Γ with a word metric. This leads to upper bounds on filling functions for groups with simply connected cones -- in particular they have linearly bounded filling length functions. We prove that if all the asymptotic cones of Γ are N-connected then Γ is of type FN+1 and we provide N-th order isoperimetric and isodiametric functions. Also we show that the asymptotic cones of a virtually polycyclic group Γ are all contractible if and only if Γ is virtually nilpotent.
Combable groups and almost-convex groups. A combing of a finitely generated group Γ is a normal form; that is a choice of word (a combing line) for each group element that satisfies a geometric constraint: nearby group elements have combing lines that fellow travel. An almost-convexity condition concerns the geometry of closed balls in the Cayley graph for Γ.
We show that even the most mild combability or almost-convexity restrictions on a finitely presented group already force surprisingly strong constraints on the geometry of its word problem. In both cases we obtain an n! isoperimetric function, and upper bounds of ~ n2 on both the minimal isodiametric function and the filling length function.
Variable domain orientations in antigen receptors
Keywords: Protein Engineering
Structural Biology
Computational Biology
Antibodies

Specific recognition of pathogenic molecules by the immune system is mediated by proteins known as antigen receptors. One such component is the antibody. Binding properties of natural and engineered antibodies can be understood by studying the structure of their variable domains, VH and VL. In this thesis we investigate how the two variable domains orientate with respect to one another and therefore influence the geometry of the antigen binding site which is formed between them.
We describe a method which fully characterises the VH-VL orientation in a consistent and absolute sense using five angles and a distance. The ABangle method is used to investigate variable domain orientation in structures collected by our database SAbDab.
Using the ABangle method we compare VH-VL orientation to the corresponding property in a different component of the immune system, the T-cell receptor (TCR). Despite having similar individual domain structures the variable domain orientations of antibodies and TCRs are found to be distinct. This is found to affect an antibody’s ability to mimic TCR specificity.
ABangle's characterisation is used to find determinants of the VH-VL orientation. We identify sequence and structural properties that influence the variable domain pose. A feature based method for predicting VH-VL orientation is presented and assessed. Future directions of this research and its application to the development of antibody therapeutics are described.
Special metric structures and closed forms
Keywords: special metrics
skew-torsion
G2
sugra compactifications
generalised geometry

In recent work, N. Hitchin described special geometries in terms of a variational problem for closed generic p
-forms. In particular, he introduced on 8-manifolds the notion of an integrable PSU(3)
-structure which is defined by a closed and co-closed 3-form. In this thesis, we first investigate this PSU(3)
-geometry further. We give necessary conditions for the existence of a topological PSU(3)
-structure (that is, a reduction of the structure group to PSU(3)
acting through its adjoint representation). We derive various obstructions for the existence of a topological reduction to PSU(3)
. For compact manifolds, we also find sufficient conditions if the PSU(3)
-structure lifts to an SU(3)
-structure. We find non-trivial, (compact) examples of integrable PSU(3)
-structures. Moreover, we give a Riemannian characterisation of topological PSU(3)
-structures through an invariant spinor valued 1-form and show that the PSU(3)
-structure is integrable if and only if the spinor valued 1-form is harmonic with respect to the twisted Dirac operator. Secondly, we define new generalisations of integrable G2
- and Spin(7)
-manifolds which can be transformed by the action of both diffeomorphisms and 2-forms. These are defined by special closed even or odd forms. Contraction on the vector bundle ToplusT∗
defines an inner product of signature (n,n)
, and even or odd forms can then be naturally interpreted as spinors for a spin structure on ToplusT∗
. As such, the special forms we consider induce reductions from Spin(7,7)
or Spin(8,8)
to a stabiliser subgroup conjugate to G2timesG2
or Spin(7)timesSpin(7)
. They also induce a natural Riemannian metric for which we can choose a spin structure. Again we state necessary and sufficient conditions for the existence of such a reduction by means of spinors for a spin structure on T
. We classify topological G2timesG2
-structures up to vertical homotopy. Forms stabilised by G2timesG2
are generic and an integrable structure arises as the critical point of a generalised variational principle. We prove that the integrability conditions on forms imply the existence of two linear metric connections whose torsion is skew, closed and adds to 0. In particular we show these integrability conditions to be equivalent to the supersymmetry equations on spinors in supergravity theory of type IIA/B with NS-NS background fields. We explicitly determine the Ricci-tensor and show that over compact manifolds, only trivial solutions exist. Using the variational approach we derive weaker integrability conditions analogous to weak holonomy G2
. Examples of generalised G2
- and Spin(7)
structures are constructed by the device of T-duality.
The role of catalysts and algae in forming a sustainable solution for a global food and fuel crisis
Keywords: catalysis
biofuels
algae
lifecycle analysis
transport
low carbon
energy security
climate change

This thesis undertakes three separate lifecycle analyses to determine the emissions and fossil energy demand required to process algae biomass into renewable fuel and animal feed. A complete well-to-wheel fuel-cycle analysis is conducted for the production of biodiesel and jet biofuel from algae biomass. The environmental impacts of algae-based fuels for the road transportation and aviation industry are benchmarked against analogue conventional fossil fuels. This thesis demonstrates that algae biofuel production can only realize its inherent environmental advantage of reduced GHG emissions, once every step of the production chain is fully optimized and decarbonized. This includes smart co-product utilization, offsetting fertilizers through wastewater recycling, reusing exhaust gases as additional CO2 source and using decarbonized electricity, heat and indirect energy.
The definition of a Catalyst Sensitivity Index (CSI) demonstrates how catalytic efficiency increases can impact the fossil energy consumption and the greenhouse gas emissions balance of catalyst-dependent processes. The CSI will allow the industry to highlight ‘best practice catalysts’ and draw conclusions for what efficiency gains one could anticipate with higher performance catalysts.
For countries where a decarbonized electricity and heat grid is not available to guarantee low-carbon algae fuel production and the looming resource scarcity around marine feed production has become more pressing, the alternative use of algae for aquafeed production is recommended. This thesis analyses major routes towards the future cost-competitive production of microbial biomass as sustainable fish meal and oil source to meet a global demand for depleting fish feed supplies. A comprehensive economic cost analysis and lifecycle assessment demonstrates the feasibility of replacing global fish meal and fish oil supplies with low-carbon and affordable algae feed by the year 2030. This research reveals how algae feed production has the potential to transform a pressing resource tipping point into a turning point.
Pathogen identification in lower respiratory tract infection
Keywords: empyema
diagnostics
pneumonia
16S rRNA
microbiology
pleural infection

Treatment of lower respiratory tract infection (pneumonia and pleural infection) relies on the use of empirical broad spectrum antibiotics, primarily because reliable pathogen identification occurs infrequently. Another consequence of poor rates of pathogen identification is that our understanding of the microbiology of these infections is incomplete.
This thesis addresses some of these issues by combining the acquisition of high quality lower respiratory tract samples, free from nasooropharyngeal contamination, with novel molecular microbiological techniques in an attempt to increase rates of pathogen identification.
Four main areas are examined;
The role of so-called ‘atypical pneumonia’ bacteria in causing pleural infection. These pathogens have been previously identified in the pleural space infrequently and routine culture usually fails to isolate such bacteria. High sensitivity nested polymerase chain reaction (PCR) is a culture-independent technique which is used to undertake a systematic evaluation for these pathogens in pleural infection samples.
The role of Pneumocystis jirovecii in pleural infection, either as a co-infecting pathogen or in monomicrobial infection. This fungus causes severe pneumonia, particularly in the immunosuppressed, but is increasingly recognised as a co-pathogen in community-acquired pneumonia, and is frequently isolated in the upper and lower respiratory tract in health. A high sensitivity real-time PCR assay is used to examine for this fungus.
Ultra-deep sequencing of the 16S rRNA gene is used to perform a comprehensive microbial survey in samples taken from the multi-centre MIST2 study of pleural infection. The techniques employed allow analysis of polymicrobial samples and give very high taxonomic resolution, whilst incorporating methods to control for potential contamination. Further, these techniques provide confirmation of the results from the ‘atypical’ bacteria nested PCR study.
Bedside ultrasound-guided percutaneous transthoracic needle aspiration (TNA) of consolidated lung is undertaken in patients with pneumonia, as part of the PIPAP study. An evaluation is undertaken of the efficacy and acceptability of TNA. Aspirate samples acquired are also processed using ultra-deep sequencing of the 16S rRNA gene. Other samples obtained as part of the PIPAP study, such as ‘control’ lung aspirates and ‘control’ pleural fluid samples, are similarly processed to enable calculation of sensitivity and specificity of the sequencing methodology.
Development of superconducting bolometer device technology for millimeter-wave cosmology instruments
Keywords: device technology
nanotechnology
lithography
microwave
microfabrication
modelling
millimeter-wave
quantum device physics
detectors
astrophysics
integrated circuit

The Cold-Electron Bolometer (CEB) is a sensitive detector of millimeter-wave radiation, in which tunnel junctions are used as temperature sensors of a nanoscale normal metal strip absorber. The absorber is fed by an antenna via two Superconductor-Insulator-Normal metal (SIN) tunnel junctions, fabricated at both ends of the absorber. Incoming photons excite electrons, heating the whole electron system. The incoming RF power is determined by measuring the tunneling current through the SIN junctions. Since electrons at highest energy levels escape the absorber through the tunnel junctions, it causes cooling of the absorber. This electron cooling provides electro-thermal feedback that makes the saturation power of a CEB well above that of other types of millimeter-wave receivers. The key features of CEB detectors are high sensitivity, large dynamic range, fast response, easy integration in arrays on planar substrates, and simple readout. The high dynamic range allows the detector to operate under relatively high background levels.
In this thesis, we present the development and successful operation of CEB, focusing on the fabrication technology and different implementations of the CEB for efficient detection of electromagnetic signals. We present the CEB detector integrated across a unilateral finline deposited on a planar substrate. We have measured the finline-integrated CEB performance at 280-315 mK using a calibrated black-body source mounted inside the cryostat. The results have demonstrated strong response to the incoming RF power and reasonable sensitivity. We also present CEB devices fabricated with advanced technologies and integrated in log-periodic, double-dipole and cross-slot antennas. The measured CEB performance satisfied the requirements of the balloon-borne experiment BOOMERANG and could be considered for future balloon-borne and ground-based instruments.
In this thesis we also investigated a planar phase switch integrated in a back-to-back finline for modulating the polarization of weak electromagnetic signals. We examine the switching characteristics and demonstrate that the switching speed of the device is well above the speed required for phase modulation in astronomical instruments. We also investigated the combination of a detector and a superconducting phase switch for modulating the polarization of electromagnetic radiation.
Exploiting parallelism in decomposition methods for constraint satisfaction
Keywords: constraint satisfaction
divide and conquer
Boolean conjunctive query
LOGCFL
hypertree decomposition
parallel algorithms

Constraint Satisfaction Problems (CSPs) are NP-complete in general, however, there are many tractable subclasses that rely on the restriction of the structure of their underlying hypergraphs. It is a well-known fact, for instance, that CSPs whose underlying hypergraph is acyclic are tractable. Trying to deﬁne “nearly acyclic” hypergraphs led to the deﬁnition of various hypergraph decomposition methods. An important member in this class is the hypertree decomposition method, introduced by Gottlob et al. It possesses the property that CSPs falling into this class can be solved eﬃciently, and that hypergraphs in this class can be recognized efﬁciently as well. Apart from polynomial tractability, complexity analysis has shown, that both afore-mentioned problems lie in the low complexity class LOGCFL and are thus moreover eﬃciently parallelizable. A parallel algorithm has been proposed for the “evaluation problem”, however all algorithms for the “recognition problem” presented to date are sequential.
The main contribution of this dissertation is the creation of an object oriented programming library including a task scheduler which allows the parallelization of a whole range of computational problems, fulﬁlling certain complexity-theoretic restrictions. This library merely requires the programmer to provide the implementation of several classes and methods, representing a general alternating algorithm, while the mechanics of the task scheduler remain hidden. In particular, we use this library to create an eﬃcient parallel algorithm, which computes hypertree decompositions of a ﬁxed width.
Another result of a more theoretical nature is the deﬁnition of a new type of decomposition method, called Balanced Decompositions. Solving CSPs of bounded balanced width and recognizing such hypergraphs is only quasi-polynomial, however still parallelizable to a certain extent. A complexity-theoretic analysis leads to the deﬁnition of a new complexity class hierarchy, called the DC-hierarchy, with the ﬁrst class in this hierarchy, DC1 , precisely capturing the complexity of solving CSPs of bounded balanced width.
Unemployment persistence: theoretical and empirical developments
Keywords: persistence
heterogeneity
unemployment persistence
screening
state dependence
unemployment

This thesis presents three chapters on the subject of unemployment persistence. Two of the chapters are empirically focussed and the other is a purely theoretic work. Unemployment persistence is defined as the existence of serial correlation in individual employment outcomes.
The first chapter finds evidence for unemployment persistence among men and women in the Australian youth labour market. Individual labour market dynamics are analysed using the Australian Longitudinal Survey. The analytic framework used is a Random Effects Probit model, incorporating lagged employment status as an explanatory variable status. Results support a “scarring” effect of unemployment upon individuals’ future employment prospects.
The second chapter provides decision-theoretic foundations for unemployment persistence, based upon heterogeneous intrinsic productivity among workers. A representative firm is assumed to receive an imperfectly precise signal of worker ability every period, and re-forms its beliefs every period using a Bayesian updating method. A model of the dynamic behaviour of optimal employment decisions by the firm is constructed. It is shown that under certain circumstances workers of all productivities may be “scarred” in the eyes of the firm by past unemployment, due to the firm’s being unwilling to hire from an unemployment pool of dubious quality.
The third chapter presents a detailed investigation into how to measure unemployment persistence within the UK. The chapter presents several modelling strategies capable of being used to analyse panel data of a binary nature, and discusses how to decide which methods are most appropriate in particular environments. Panel data on men from the British Household Panel Survey are used to estimate a structural state dependence equation in employment status, where lagged employment status is used as an explanatory variable. Particular attention is given to controlling for unobserved heterogeneity between individuals. The empirical results indicate strong evidence of unemployment persistence.
Strategies of sensation and the transformation of the Press, 1860-1880: Mary Braddon, Florence Marryat and Ellen Wood, female author-editors, and the sensation phenomenon in mid-Victorian magazine publishing
Keywords: sensation fiction
Victorian literature
editorship
women's writing
periodical press

This thesis examines the processes of writerly and editorial literary production undertaken by women sensation authors in the 1860s and 1870s. This focus represents a shift from the prevailing critical emphasis on the consumption of sensation fiction to the realm of production and therein allows the thesis to analyse the ways in which sensation operates as a set of rhetorical and linguistic strategies for women writers in the changing publishing conditions of mid-to-late Victorian society. I consider the ways in which sensation is an idiom that permeates all aspects of magazine publishing in this period and demonstrate how it could be adapted and become an empowering discourse for women writers and editors. Furthermore, this thesis sees sensation as an important component in the transformation of the press in the 1860s and 1870s. By analysing the specific ways in which sensational strategies were appropriated and transformed, this thesis reassesses the role of sensation in the creation of women’s writing in the second half of the nineteenth century, and consider its legacies in later ‘New Woman’ writers. I achieve this by examining three women editors, who were part of the transformation of magazine publishing in the period. Mary Elizabeth Braddon (1835-1915), Ellen (Mrs. Henry) Wood (1814-1887), and Florence Marryat (1837-1899) all operated as writers and editors in the mid-to-late nineteenth century. They produced varying types of sensational fiction that they serialised in their own monthly magazines, Belgravia, Argosy, and London Society respectively. Sensation provided a dynamic and flexible means for these women author-editors to assert their status in the context of the expansion of the press in the 1860s and 1870s. I argue that their work invites a more fluid and generous critical definition of sensation.
Modelling innovation diffusion in complex energy-transport systems
Keywords: sustainable energy
innovation
complexity

Global sustainable energy and environmental policies have increased the need to understand how new energy innovations diffuse into the market. The transport sector is currently a major source of unsustainable energy use contributing ~20-25% global CO2 emissions. Although the potential benefits of alternative fuel vehicle (AFV) technologies to reduce CO2 emissions and fossil fuel dependency have been demonstrated, many uncertainties exist in their market diffusion. It is also not well understood how policy can influence rapid diffusion of AFVs. To transition to a more sustainable energy-transport system, we need to understand the market conditions and factors necessary for triggering widespread adoption of new energy innovations such as AFVs.
Modelling the diffusion of innovations is one way to explain why some ideas and technologies spread through society successfully, while others do not. These diffusion processes are characterized by non-linear interactions between heterogeneous agents in complex networked systems. Diffusion theory has typically been applied to consumer durable goods but has found less application to new energy and environmental innovations. There is much scope for advanced diffusion methods to inform energy policy. This depends upon understanding how consumer behaviour and technologies interact and can influence each other over time. There is also need to understand the underlying mechanisms that influence adoption behaviour among heterogeneous agents.
This thesis tackles the above issues using a combination of empirical data analysis, scenarios, and simulation modelling as follows: 1) We first develop the empirical basis for assessing innovation diffusion from a technology-behavioural perspective, where we explicitly account for interactions between consumer preferences and technological performance across different spatial and temporal scales; 2) Scenarios are then used to disaggregate consumer markets and analyze the technological and behavioural factors that might trigger large-scale adoption of AFVs; 3) We then case-analyze the UK transport sector and develop a model of the dynamics between how vehicle technologies and consumer preferences can change and influence the diffusion process; 4) Finally, we develop exploratory simulations to assess how social network effects can influence individual adoption behaviour; 5) We close with policy implications of our findings, contributions and limitations of the thesis, and possible avenues for taking the research forward.