VictorJuiz/thesis huggingface dataset:
Droplet dynamics on superhydrophobic surfaces

Millions of years of evolution have led to a wealth of highly adapted functional surfaces in nature. Among the most fascinating are superhydrophobic surfaces which are highly water-repellent and shed drops very easily owing to their chemical hydrophobicity combined with micropatterning. Superhydrophobic materials have attracted a lot of attention due to their practical applications as ultra-low friction surfaces for ships and pipes, water harvesters, de-humidifiers and cooling systems. At small length scales, where surface tension dominates over gravity, these surfaces show a wealth of phenomena interesting to physicists, such as directional flow, rolling, and drop bouncing.
This thesis focuses on two examples of dynamic drop interactions with micropatterned surfaces and studies them by means of a lattice Boltzmann simulation approach. Inspired by recent experiments, we investigate the phenomenon of the self-propelled bouncing of coalescing droplets. On highly hydrophobic patterned surfaces drop coalescence can lead to an out-of-plane jump of the composite drop. We discuss the importance of energy dissipation to the jumping process and identify an anisotropy of the jumping ability with respect to surface features. We show that Gibbs' pinning is the source of this anisotropy and explain how it leads to the inhibition of coalescence-induced jumping.
The second example we study is the novel phenomenon of pancake bouncing. Conventionally, a drop falling onto a superhydrophobic surface spreads due to its inertia, retracts due to its surface tension, and bounces off the surface. Here we explain a different pathway to bouncing that has been observed in recent experiments: A drop may spread upon impact, but leave the surface whilst still in an elongated shape. This new behaviour, which occurs transiently for certain impact and surface parameters, is due to reversible liquid imbibition into the superhydrophobic substrate. We develop a theoretical model and test it on data from experiments and simulations. The theoretical model is used to explain pancake bouncing in detail.

Keywords: superhydrophobic surfaces
hydrodynamics
fluid dynamics
lattice Boltzmann
wetting
simulations
Advisor: Yeomans, J
Synaptic interaction of hippocampal gabaergic neurones

Current concepts of hippocampal circuitry assume a large population of excitatory principal neurones whose activity is largely governed by a network of local-circuit GABAergic interneurones. The diversity of hippocampal local-circuit neurones and their synaptic control over principal cell activity was investigated in vitro, in order to define their synaptic connections and functional roles.
Single and dual intracellular recordings were made from local-circuit neurones and pyramidal cells in area CA1 of the rat hippocampal slice. Interneurones were tentatively distinguished from pyramidal cells based on their firing as well as their membrane properties. Intracellular labelling of recorded cells with the marker biocytin revealed a diversity of cell types based on differential dendritic and axonal morphology and synaptic connections.
The physiological data revealed that all types of interneurone tested evoked inhibitory postsynaptic potentials (IPSPs) in simultaneously recorded pyramidal cells. The IPSPs had fast rise and decay kinetics and the ones tested pharmacologically, were mediated by GABAA receptors. Similarly, individual interneurones were also shown to innervate other local-circuit interneurones in addition to pyramidal cells, the evoked effects being qualitatively similar in both types of postsynaptic targets.
The postsynaptic effect and functional role of one type of hippocampal interneurone, the basket cell, was investigated in greater detail. Basket cell-evoked IPSPs were reliable, but showed some frequency-dependent attenuation. Moreover, basket cell IPSPs were found to interact with intrinsic pyramidal cell conductances to elicit rebound depolarisations and facilitate action potential generation.
More detailed investigation showed that basket and axo-axonic cells were particularly effective in entraining pyramidal cell firing and sub-threshold membrane potential oscillations. Through these powerfully tuned mechanisms, sub-types of local-circuit interneurone provide a powerful mechanism to synchronise the activity of pyramidal cells.
These results demonstrate a remarkable diversity of GABAergic local-circuit neurones in the hippocampal CA1 area and suggest that specific subtypes of cell mediate different functions.
Doxastic spaces: a new approach to relational beliefs and unstable neglect

This thesis introduces and explores a novel construct for studying human beliefs in social science: doxastic spaces. These flexible analytical devices are demonstrated as capturing three key properties of beliefs which are difficult to depict through other formats: the relational, relative, and reflexive properties of beliefs. The doxastic-space paradigm developed by this thesis is likewise shown to enable new and insightful theories about belief formation and change. Two such theories cultivated herein are quantized evidence theory (QET) and entropy-based social learning (EBSL). These theories prioritise not only the evidential bases of beliefs, but also the cognitive limitations on memory and attention that people face in constructing and updating beliefs about their worlds. Such bases and limitations underscore not only the role that context has to play in sculpting beliefs, but also the reciprocal function of beliefs in helping to determine and demarcate context. Part of that context is discussed as being other people relevant in social judgment and learning situations. And interplay between beliefs and context is used to aid explanation for unstable tendencies in neglectful cognition. The work mixes theoretical and empirical investigation of the doxastic-space framework, and suggests that it may serve social science by working to not only forge deeper comprehension of belief dynamics but also to operate as a platform for interdisciplinary exchange.

Keywords: Cognition
Beliefs
Reflexivity
Advisor: Clark, G
Nuclear translation

In bacteria, protein synthesis can occur tightly coupled to transcription. In eukaryotes, it is believed that translation occurs solely in the cytoplasm; I test whether some occurs in nuclei and find: (1) L-azidohomoalanine (Aha) – a methionine analogue (detected by microscopy after attaching a fluorescent tag using ‘click’ chemistry) – is incorporated within 5 s into nuclei in a process sensitive to the translation inhibitor, anisomycin. (2) Puromycin – another inhibitor that end-labels nascent peptides (detected by immuno-fluorescence) – is similarly incorporated in a manner sensitive to a transcriptional inhibitor. (3) CD2 – a non-nuclear protein – is found in nuclei close to the nascent RNA that encodes it (detected by combining indirect immuno-labelling with RNA fluorescence in situ hybridization using intronic probes); faulty (nascent) RNA is destroyed by a quality-control mechanism sensitive to translational inhibitors. I conclude that substantial translation occurs in the nucleus, with some being closely coupled to transcription and the associated proof-reading. Moreover, most peptides made in both the nucleus and cytoplasm are degraded soon after they are made with half-lives of about one minute.
I also collaborated on two additional projects: the purification of mega-complexes (transcription 'factories’) containing RNA polymerases I, II, or III (I used immuno-fluorescence to confirm that each contained the expected constituents), and the demonstration that some ‘factories’ specialize in transcribing genes responding to tumour necrosis factor α – a cytokine that signals through NFκB (I used RNA fluorescence in situ hybridization coupled with immuno-labelling to show active NFκB is found in factories transcribing responsive genes).

Keywords: click chemistry
nonsense-mediated mRNA decay
L-azidohomoalanine
immuno-RNA FISH
proximity ligation assay
transcription factory
intronic translation
CD2
puromycin
Nuclear translation
antibody blocking
nuclear protein synthesis
Copper-catalyzed azide-alkyne cycloaddition
Advisor: Cook, P
Formalisations and applications of business process modelling notation

Business Process Modelling Notation (BPMN) is a standardised diagram notation for modelling interactive workflow processes graphically at the design stage. The primary objective of this thesis is to provide a framework for precise specifications and formal verifications of workflow processes modelled as BPMN diagrams. We provide two behavioural semantics for BPMN in the process algebra Communicating Sequential Processes (CSP). We apply existing CSP refinement orderings to both the refinement of business process diagrams and the verification of behavioural compatibility of business process collaborations. The first semantic model is an untimed model, focusing on the control flow and communication of business processes. The second semantic model extends the first one to capture the timing aspect of behaviour.
We also consider the applications of the semantic models. The secondary objective of this thesis is to apply BPMN and the semantic models to reason about long running empirical studies (e.g. laboratory experiments, clinical trials). We introduce a declarative workflow model Empiricol for recording trials and experiments precisely, and define bidirectional transformation functions between BPMN and Empiricol. Using the transformation functions, we make graphical specification, simulation, automation and verification of trials and experiments possible. We provide two case studies on the applications of BPMN’s formalisations.

Keywords: formal methods
communication sequential processing (CSP)
BPMN
Z Notation
Advisor: Gibbons, J
The impact of association with the EU on domestic industrial policy making

This thesis is a case study of the effects of association with the EU on domestic industrial policy making in Poland during 1990-1995 from a liberal intergovernmentalist perspective, showing how association affected the industrial policy-making autonomy of the Government in relation to other domestic actors in two ways. First, because domestic interests were weak and divided in transition-era Poland, the EU provided political leaders with a sharper focus and allowed them to consolidate domestic support for government industrial policy initiatives. Second, where domestic opposition arose, association helped political leaders to overcome it by giving industrial policy initiatives greater legitimacy and allowing them to be portrayed as "mandatory" for EU membership. The manner in which the Government handled domestic pressure for intervention from state enterprises seeking to avoid painful adjustments and restructuring during the transition offers a prime test of the effects of EU association on industrial policy-making autonomy.
In most areas, the pro-market, pro-competition policies mandated by EU association were incompatible with the nature and level of governmental involvement in industry under socialism, requiring an end to state subsidies and other forms of discretionary support enjoyed by state enterprises for nearly four decades. Incorporating case studies of the steel and textiles sectors, this thesis illustrates how in the context of transition, the Government's commitment to EU association was stronger than for other recent EU members and ensured that the Government would deviate from the course charted in the Association Agreement only in cases of intense domestic pressure, and even then only temporarily. Accordingly, in a new twist to liberal intergovernmentalism, Poland's transitional domestic situation coupled with the country's enduring commitment to eventual EU membership ensured that the effects of association on policy-making autonomy were more pronounced in Poland than in existing member states.
Investigation of varicella zoster virus glycoprotein-specific T cell responses

T cells are believed to be important in the control of varicella zoster virus (VZV) replication but little is known of T cell epitopes and the relationships between T cell responses, viral load and clinical disease during primary infection.
I initially set to investigate the immune responses to two of the main VZV glycoproteins (gE and gI) using ex vivo and cultured IFNγ ELISpot assays. I identified several novel CD4+ T cell epitopes within gE and gI and characterized the phenotype of gE DRB1*1501 tetramer specific responses in healthy immune donors. I then set out to investigate the function and phenotype of VZV specific T cells in primary infection and their relationship to viral loads and clinical disease severity by using glycoprotein E/DRB1*1501 specific MHC class II tetramers, ex vivo IFNγ ELISpot assays and quantitative real time PCR assays. I compared the frequency and phenotype of specific T cells with virological and clinical outcomes in 32 adult individuals with primary VZV infection.
In healthy immune donors, the gE specific T cells showed a early intermediate stage of differentiation with evidence of recent activation. Patients with acute primary infection had higher VZV/DRB1*1501 tetramer specific T cell responses and expressed markers of activation and effector differentiation. Viral loads were found to be significantly higher in patients with moderate to severe infection compared to those with mild infection (p<0.001). A significant inverse correlation was seen between the viral loads and the ex vivo IFNγ ELISpot responses of the patients (p<0.05, r=-0.64).
These data would be compatible with a role for gE and gl-specific T cells in the control of viral replication during both primary infection and re-activation.

Advisor: Ogg, G
The evolutionary ecology of spiteful bacteriocin production

Understanding the conditions that favour the evolution and maintenance of spiteful bacteriocin production combines two important questions from the fields of social evolution and microbiology. Spiteful behaviours, though, initially thought to be rare represent an important class of interactions between bacteria through the production of bacteriocins. Bacteriocins can be considered spiteful as they are costly to produce (in many cases requiring lysis) and are costly to sensitive bacteria (i.e. they are lethal). However, much about the ecology of spiteful behaviours and bacteriocin production remains unclear. Mathematical models have given us important insights into some conditions that should favour bacteriocin production, but few empirical studies exist supporting these results. In this thesis I use the bacterium Pseudomonas aeruginosa (a prolific producer of bacteriocins), to examine conditions that favour bacteriocin production. I also investigate more specific elements about this system and toxin production in general. I find that bacteriocin production in P. aeruginosa closely follows predictions made from mathematical models under a range of different conditions (e.g. frequency, scale of competition, multiple social traits). I also find that resistance can evolve to bacteriocins and biological mechanisms such as the neutralisation of one’s own toxin can have important consequences. Finally, I consider bacteriocin as a policing trait testing predictions about the role that linkage plays in policing. This work represents a comprehensive study into the importance of bacteriocin production in bacteria.

Keywords: kin selection
social evolution
allelopathy
bacteriocin
Advisor: Buckling, A
A framework of usable and secure system design

Despite existing work on dealing with security and usability concerns during the early stages of design, there has been little work on synthesising the contributions of these fields into processes for specifying and designing systems. Without a better understanding of how to deal with both concerns at an early stage, the design process risks disenfranchising stakeholders, and resulting systems may not be situated in their contexts of use.
The research problem this thesis addresses is how techniques and tools can be integrated and improved to support the design of usable and secure systems. To develop this understanding, we present IRIS (Integrating Requirements and Information Security) --- a framework for specifying usable and secure systems. IRIS considers the system design process from three different perspectives --- Usability, Security, and Requirements --- and guides the selection of techniques towards integrative Security, Usability, and Requirements Engineering processes.
This thesis claims that IRIS is an exemplar for integrating existing techniques and tools towards the design of usable and secure systems. In particular, IRIS makes three significant contributions towards the stated research problem. First, a conceptual model for usable secure Requirements Engineering is presented, upon which the IRIS framework is founded; this meta-model informs changes to elicitation and specification techniques for improved interoperability in the design process. Second, several characteristics of tool-support needed to elicit and specify usable and secure systems are introduced; the CAIRIS (Computer Aided Integration of Requirements and Information Security) software tool is presented to illustrate how these characteristics can be embodied. Third, we describe how the results of applying IRIS can be used to improve the design of existing User-Centered Design techniques for secure systems design.
We validate the thesis by applying the IRIS framework to three case studies. In the first, IRIS is used to specify requirements for a software repository used by a UK water company. In the second, IRIS is used to specify security requirements for a meta-data repository supporting the sharing of medical research data. In the final case study, IRIS is used to analyse a proposed security policy at a UK water company, and identify missing policy requirements. In each case study, IRIS is applied within the context of an Action Research intervention, where findings and lessons from one case study are fed into the action plan of the next.

Keywords: HCI
Requirements Engineering
Information Security
Advisor: Flechais, I
Production of cold atoms via photdissociation of small molecules

This thesis describes the development of a relatively novel technique for the gen- eration and subsequent trapping of cold species. Molecules in a pulsed supersonic expansion are photolysed, such that the centre-of-mass velocity vector of one of the fragments is equal in magnitude but opposed in orientation to the lab-frame velocity of the precursor molecule. This technique, known as ‘Photostop’, leaves a fraction of the fragments with a narrow velocity distribution, centered around zero velocity in the lab-frame. They can be shown to have zero velocity by changing the time between photodissociation and ionisation; fragments with a high kinetic energy will leave the ionisation volume prior to interrogation. The underlying velocity distribu- tion is uncovered by using the velocity-map imaging technique, and the temperature of the fragments can be determined.
The method was originally optimised for the molecular case. Cold NO has been produced from the dissociation of NO₂ molecules, and a single rotational state has been shown to remain in the ionisation volume 10 μs after dissociation, implying a sample temperature of 1.17 K. Using the optimised experimental conditions de- rived from the velocity cancellation of NO, the atomic case is demonstrated for the dissociation of Br₂ to give zero-velocity Br fragments. The Br atoms are seen for delay times in excess of 100 μs, showing the greater applicability of the method to the atomic case. The temperature of the residual atoms is shown to be in the milliKelvin regime, as determined through detailed Monte Carlo simulation of the motion of the stopped atoms. The possibility of trapping the ultracold Br atoms in a magnetic field is explored, and a quadrupolar trap created between two per- manent bar magnets is demonstrated to confine the atoms spatially, within the ion extraction optics, for delays in excess of 1 ms.
The Photostop technique is intended to be a stepping stone on the way to widening the number of chemical species available for study in the ultracold regime. The possibility of improvements to the experiment is considered, in order to increase the efficiency of the experiment such that the number density becomes high enough to be viable as a source of atoms for use in cold chemical reactive studies. The possibility of extending the method so as to be used as a tunable velocity source of atoms is also discussed.

Keywords: photodissociation
cold
lasers
atoms
bromine
ultracold
Advisor: Softley, T
The complexity of counting problems

This thesis is concerned with the computational complexity of several counting problems occurring in graph theory, all of which are related directly to the Tutte polynomial. The Tutte polynomial contains as specialisations many fundamental quantities. Among these are the partition function of the Ising and Potts models on the graph and the reliability probability as well as basic combinatorial functions such as the chromatic and flow polynomials.
Polynomial-time computable recurrence relations are given for the Tutte polynomial of the complete graphs and complete bipartite graphs, which can be solved at certain points. The flow polynomials of a particular family of cubic graphs are shown to have arbitrarily large zeros, in contrast to the conjectured behaviour of the zeros of the chromatic and reliability polynomials.
The main results of the thesis are the following:
Theorem: For any positive (constant) integers i, j and k, computing the coefficient of xi yi in the Tutte polynomial of an arbitrary graph is #P-complete. However, it can be checked in polynomial time whether the coefficient is less than k.
The complexity of evaluating the Tutte polynomial modulo a prime is also considered, and some partial results are given.
Turning to approximation, a polynomial-time uniform generator for forests of dense graphs is given. Using this, a fully polynomial randomised approximation scheme (fpras) for the number of forests of a dense graph is created. This leads to the following generalisation:
Theorem: For any rational x ≥ 1, there exists a fully polynomial randomised approximation scheme for evaluating the Tutte polynomial of dense graphs at the point (x,1).

Advisor: Welsh, D
The politics of change : explaining capital punishment reform in China

The thesis seeks to enhance understanding of the recent reform of capital punishment law, policies and institutions in China by studying its causes, significance, and limits. The research surveys the reform initiated by China’s top judiciary – the Supreme People’s Court - around 2006-2007. It demonstrates a changing domestic socio-political context, within which the external and internal impetus to reform is inevitable. Drawn from elite interview evidence with penal policy makers including judges, prosecutors, and legislators, the thesis concludes that Europe-inspired, cross-border abolitionist sentiments created motivation for change in China through soft mechanisms of shaming and persuasion, albeit to a limited degree. In the domestic realm, the research identified three pairs of interrelated tensions – the contradiction between elites and the public, the conflict between political intervention and judicial autonomy, and the divergent interests and priorities between top judicial organs and lower courts. These tensions are useful social, political and legal indicators to explain why and how China reformed its capital punishment machinery.

Keywords: China
Reform
the Death Penalty
Human rights
Advisor: Hoyle, C