VictorJuiz/thesis huggingface dataset:
Graph colourings and games
Keywords: graph colouring
games on graphs
computational complexity
algorithms
graph theory
parameterised complexity

Graph colourings and combinatorial games are two very widely studied topics in discrete mathematics. This thesis addresses the computational complexity of a range of problems falling within one or both of these subjects.
Much of the thesis is concerned with the computational complexity of problems related to the combinatorial game (Free-)Flood-It, in which players aim to make a coloured graph monochromatic ("flood" the graph) with the minimum possible number of flooding operations; such problems are known to be computationally hard in many cases. We begin by proving some general structural results about the behaviour of the game, including a powerful characterisation of the number of moves required to flood a graph in terms of the number of moves required to flood its spanning trees; these structural results are then applied to prove tractability results about a number of flood-filling problems. We also consider the computational complexity of flood-filling problems when the game is played on a rectangular grid of fixed height (focussing in particular on 3xn and 2xn grids), answering an open question of Clifford, Jalsenius, Montanaro and Sach.
The final chapter concerns the parameterised complexity of list problems on graphs of bounded treewidth. We prove structural results determining the list edge chromatic number and list total chromatic number of graphs with bounded treewidth and large maximum degree, which are special cases of the List (Edge) Colouring Conjecture and Total Colouring Conjecture respectively. Using these results, we show that the problem of determining either of these quantities is fixed parameter tractable, parameterised by the treewidth of the input graph. Finally, we analyse a list version of the Hamilton Path problem, and prove it to be W[1]-hard when parameterised by the pathwidth of the input graph. These results answer two open questions of Fellows, Fomin, Lokshtanov, Rosamond, Saurabh, Szeider and Thomassen.
A theoretical investigation of gas source growth of the Si(001) surface
Keywords: Si(001)
tight binding
density functional theory

The growth of the Si(001) surface from gas sources such as disilane is technologically important, as well as scientifically interesting. The aspects of growth covered are: the clean surface, its defects and steps; the action of bismuth, a surfactant; the diffusion behaviour of hydrogen in different environments; and the entire pathway for formation of a new layer of silicon from adsorption of fragments of disilane to nucleation of dimer strings. The theoretical methods used, density functional theory and tight binding, are described. Four linear scaling tight binding methods are compared. The construction of the tight binding parameterisations used is also explained.
The structure of the most common defect on the Si(001) surface is identified by comparison of the electronic structure with scanning tunneling microscopy (STM) images. The energy and structure of steps is calculated, and their kinking behaviour is modelled, achieving good agreement with experimental results.
Two unusual features which form when bismuth is placed on the surface and annealed are investigated. The first has possible applications as a quantum wire, and its structure and growth are described. The second relates to a controversial area in the field; a structure is proposed which fits all available experimental evidence.
The behaviour of hydrogen is vital to understanding growth, as large amounts are deposited during disilane growth. After validating the tight binding parameterisation against DFT and experiment for the system of a single hydrogen diffusing on the clean Si(001) surface, the barriers for diffusion on the saturated surface, down a step and away from a defect are found, and prove to be in good agreement with available experimental data.
The pathway for the formation of a new layer of silicon from disilane is described step by step, giving barriers and structures for all events. The interaction with experiment is highlighted, and demonstrates that great benefit accrues from such close work, and that the atomistic modelling techniques used in the thesis produce results in close agreement with reality.
Incremental sheet forming process : control and modelling
Keywords: Incremental sheet forming
variational inequalities
finite element method
model predictive control
computational mechanics

Incremental Sheet Forming (ISF) is a progressive metal forming process, where the deformation occurs locally around the point of contact between a tool and the metal sheet. The final work-piece is formed cumulatively by the movements of the tool, which is usually attached to a CNC milling machine. The ISF process is dieless in nature and capable of producing different parts of geometries with a universal tool. The tooling cost of ISF can be as low as 5–10% compared to the conventional sheet metal forming processes. On the laboratory scale, the accuracy of the parts created by ISF is between ±1.5 mm and ±3mm. However, in order for ISF to be competitive with a stamping process, an accuracy of below ±1.0 mm and more realistically below ±0.2 mm would be needed. In this work, we first studied the ISF deformation process by a simplified phenomenal linear model and employed a predictive controller to obtain an optimised tool trajectory in the sense of minimising the geometrical deviations between the targeted shape and the shape made by the ISF process. The algorithm is implemented at a rig in Cambridge University and the experimental results demonstrate the ability of the model predictive controller (MPC) strategy. We can achieve the deviation errors around ±0.2 mm for a number of simple geometrical shapes with our controller. The limitations of the underlying linear model for a highly nonlinear problem lead us to study the ISF process by a physics based model. We use the elastoplastic constitutive relation to model the material law and the contact mechanics with Signorini’s type of boundary conditions to model the process, resulting in an infinite dimensional system described by a partial differential equation. We further developed the computational method to solve the proposed mathematical model by using an augmented Lagrangian method in function space and discretising by finite element method. The preliminary results demonstrate the possibility of using this model for optimal controller design.
A dialogue across paradigms. The European Commission’s autonomous power within the open method of coordination
Keywords: Open Method of Coordination
European Commission
Child Poverty and Social Exclusion
European Union
European Employment Strategy
Quality in Work

This research project seeks to gauge the autonomous power of the European Commission within the Open Method of Coordination (OMC), a new mode of governance coined at the Lisbon European Council in March 2000 and based on the principle of the voluntary cooperation of Member States. Two cases form the basis of this inquiry, namely, quality in work, a policy issue addressed under the banner of the European Employment Strategy, and child poverty and social exclusion, a key item on the agenda of the OMC for Social Inclusion. A primary impetus at the heart of this project is one of ontological pluralism. Rejecting a zero-sum interpretation of the rationalist/constructivist debate, this study constitutes a plea for a conversation across paradigms. The domain-of-application model employed here works by preserving the integrity of individual theories while specifying a particular scope condition under which constructivist and rationalist insights are likely to prevail. Selecting two cases on the basis of the critical scope condition of issue sensitivity, a central postulate informing this integrative research design is that high issue sensitivity (quality in work) invites strategic interaction among pre-constituted social actors driven by a behavioural logic of utility-maximization, while low issue sensitivity (child poverty and social exclusion) allows for a fundamentally norm-guided behaviour.
Concretely, in effecting this theoretical dialogue, two sets of causal hypotheses are examined. On the one hand, rational choice institutionalism (principal-agent theory) offers a number of suppositions about the Commission’s institutional power, that is, its ability to transform the conditions of action of self-seeking national governments. On the other hand, sociological institutionalism conceptualizes the Commission’s productive power (i.e. its power to constitute the interests and identities of individual agents) through the lens of discourse analysis.
Testing theoretical predictions against collected data makes plain the superior explanatory value of independent variables and causal mechanisms of rationalist lineage in capturing the essence of the Commission’s autonomous power in the case of quality in work and the congruity of sociological institutionalism’s original conjectures in the area of child poverty and social exclusion. Crucially, this strict correspondence corroborates the pertinence of the critical scope condition of issue sensitivity in delineating the explanatory ambit of both theories and attests to the co-existence of different forms of autonomous power wielded by the Commission within the framework of the OMC.
Loss of chaperone protein in human cancer
Keywords: angiogenesis
heat shock proteins
TRAP1
JMY

TRAP1 is a Heat Shock Protein (HSP) chaperone to retinoblastoma but also associated to the tumor necrosis factor receptor. HSPs are primarily up regulated in cancer. Work in our lab noted a down regulation of TRAP1 in some non-small cell lung cancers compared to normal lung. The first aim of this project was to evaluate the effect of the loss of TRAP1 on cell proliferation using a spheroid model. The presence of TRAP1 in spheroids promoted cell proliferation and a faster onset of hypoxia. This suggests an oncogenic role for TRAP1 since rapid hypoxia development equates to poor prognosis.
Micro array analysis showed that TRAP1’s loss was associated with increased transcrpition of the Junctional Mediating and Regulatory protein (JMY). JMY possesses an oncogenic property due to its ability to facilitate cell motility. Additionally it has tumor suppressor activity in promoting p53 activation. The second aim of this project was to produce an anti-JMY antibody and use it to characterize JMY and additionally verify the association between TRAP1 and JMY.
JMY was found to be widely expressed in normal tissues and in many types of tumors. In neoplastic tissues, comparing primary versus metastatic tumors, JMY was found to have significantly higher expression in the metastatic compared with the primary tumors. A pilot study showed that nuclear co-expression of JMY and P53 was associated with shorter overall survival suggesting that a possible tumorigenesis mechanism could be via a deregulation/mutation of JMY/p53 or both.
Finally, using 3 dimensional constructions, I demonstrated the distinct morphological difference between an angiogenic tumor and a non-angiogenic tumor. Additionally, I showed a characteristic cytoplasmic p53 sequestration in the non-angiogenic phenotype that is absent in the angiogenic phenotype. This could be the mechanism that the non-angiogenic tumor uses to adapt to hypoxia. This would imply that there is a potential for cancers to escape therapy by switching between these 2 phenotypes.
Finite temperature dynamical structure factors of low dimensional strongly correlated systems
Keywords: transverse field Ising
quantum field theory
cumulant expansion
Heisenberg ladder

We determine the dynamical structure factors of two gapped correlated electron systems, namely the Ising model in a strong transverse field and the two-leg spin-1/2 Heisenberg ladder in the limit of strong rung coupling. We consider the low-temperature limit, employing a variety of analytical and numerical techniques. The coherent modes of single-particle excitations, which are delta functions at zero temperature, are shown to broaden asymmetrically in energy with increasing temperature. Firstly, we apply a low-temperature “resummation” inspired by the Dyson equation to a linked-cluster expansion of the two-leg Heisenberg ladder. We include matrix elements to second order in the interaction between states containing up to two particles. A low-frequency response similar to the “Villain mode” is also observed. Next, we apply a cumulant expansion technique to the transverse field Ising model. We resolve the issue of negative spectral weight caused by double pole in the leading self-energy diagram by including a resummation of terms obtained from the six-point function, demonstrating that the perturbation series in 2n-spin correlation functions can be extended to higher orders. The result generalises to higher dimensions and the analytic calculation is compared to a numerical Pade approximant. We outline the extension of this method to the strong coupling ladder. Finally, we compare the previous results to numerical data obtained by full diagonalisation of finite chains and numerical evaluation of the Pfaffian, a method specific to the transverse field Ising chain. The latter method is used for a phenomenological study of the asymmetric broadening as well as an evaluation of fitting functions for the broadened lineshapes.
Functional differentiation along the dorso-ventral axis of the hippocampus
Keywords: electrophysiology
spatial memory
Hippocampus
learning

The hippocampus plays an important role in the processing of spatial memory. During exploration, theta oscillations (4-12 Hz) are prominent in the hippocampus, whereas during sleep and rest irregular sharp wave/ripple (SWR) events occur spontaneously in the hippocampus and may support memory consolidation. To date, the ventral sub-region of the rodents hippocampus, has received less attention relative to the more accessible dorsal part. It has been suggested that spatial information decreases along the septo-temporal axis in favour of coding salient features and coordinated oscillatory activity might enable the binding of spatial and nonspatial information. The first goal of my research was to investigate how the spatial representation by dorsal and ventral neurons is organised by theta oscillations in the hippocampal network. The second goal was to investigate the role of the ventral hippocampus in spatial learning. Finally, the third goal examined to what extent the firing relationships established during spatial learning are replayed during subsequent sleep in the ventral CA1.
I recorded the network activity of dorsal and ventral CA1 in rats performing a spatial memory task on the cheese board maze (Dupret et al., 2010). By using parallel multi-channel extracellular recordings in the dorsal and ventral portions of the hippocampus in behaving rats, I found that dorsal and ventral CA1 were theta coupled at particular times of the spatial learning. High coherence periods across the two regions were characterized by a strong speed-modulation of ventral theta oscillations, which was absent in other conditions. During sleep, it was found that SWR-related activity was presented in the ventral hippocampus as well, when the coordinated population activity established in spatial learning was reactivated within the two sub-regions. By contrast, reactivation across the two regions was observed outside the SWRs epochs. Overall, the data suggests that the ventral hippocampus might be involved in the processing of salient features of the environment such as rewards. On a temporal scale, this non-spatial information might be integrated to the spatial information provided by the dorsal hippocampus during theta oscillation. During sleep/rest periods, the coordinated communication of learned information might underlie the consolidation of memory traces.
Elucidating the pathway of centrosome formation
Keywords: centriole
centrosome
activation
drosophila
oocyte

Centrosomes are cellular organelles present in most animal cells, and are formed of two main components: the centrioles and the pericentriolar material (PCM). Centrosomes perform a variety of functions: they are the main microtubule organising centre in the cell, and are important localisation hubs for kinases involved in regulating the cell cycle. Hundreds of proteins are thought to localise to centrosomes, but work in the last decade has narrowed down this list to a handful of proteins that are thought to be essential for centrosome structure and function in Drosophila. Asl, Ana2, DSas-4, DSas-6 and Sak have been identified as essential components for centriole duplication, while Cnn and DSpd-2 are thought to be important in establishing the PCM. However, the relative position of these 7 components in the pathway of centrosome assembly in Drosophila embryos remains elusive, as a genetics analysis of this process is hampered by the absence of centrioles in most mutant embryos for these proteins.
In this thesis I elucidate the pathway of centrosome assembly in Drosophila by using SAPs (DSas-6/Ana2 particles that form in Drosophila unfertilised eggs upon moderate expression of DSas-6 and Ana2) as proxy models of centrosomes. I show SAPs are very similar to centrosomes in composition and dynamics but unlike centrosomes are able to form even in the absence of some of the essential centriolar components. SAP analysis in the absence of each of the main centrosome components reveals that: Sak is not required for the recruitment of downstream components; DSas-4 is necessary for Ana2 and DSas-6 to interact; Asl is the most upstream component of the PCM recruitment pathway, followed by DSpd-2; it is likely that there is an additional PCM recruitment pathway. I then take advantage of some of these results to examine how centrosome formation is potentiated after egg activation. My work allows me to propose an improved description of the pathway of centrosome formation in Drosophila.
The development of a fast intra-train beam-based feedback system capable of operating on the bunch trains of the International Linear Collider
Keywords: FPGA
accelerator
BPM
beam
linear collider
feedback

This thesis will describe the latest work from the Feedback On Nanosecond Timescales project, commonly known as FONT. The goal of the FONT project is the development of a beamline feedback system to be installed at the interaction point (IP) of a future linear collider in order to maximize the luminosity that can be achieved. The prototype FONT feedback system is beam-based, meaning that the correction is determined from direct measurement of the position of the beam, and intra-train, meaning that the correction is applied within the duration of the current bunch train.
The FONT system, consisting of three stripline beam position monitors, a digital processor unit built around a Field Programmable Gate Array (FPGA) and a pair of electromagnetic kickers, is described. Recent improvements to the position measurement process are detailed and the performance of the feedback system is presented.
The modification of the firmware to operate on a machine with a large number of bunch trains, such as the International Linear Collider, is described and the design is verified through the use of a laboratory test bench developed to simulate such a machine. The FONT5 digital board is proved capable of operating on a train resembling the specification for the International Linear Collider: 2820 bunches separated in time by 308 ns.
Investigating maintenance and discard patterns for Middle to Late Magdalenian antler projectile points : inter-site and inter-regional comparisons
Keywords: Osseous technology; Magdalenian; Upper Palaeolithic; projectile technology

Projectile points manufactured from antler, bone, ivory, and horn were a significant component of the Pleistocene hunter-gatherer’s weapons toolkit. While this situation appears to have been particularly the case for Upper Palaeolithic Europe where thousands of implements from Aurignacian to Azilian contexts have been recovered, elements of osseous technologies are increasingly being identified in Africa, Asia, Australia and North America. Projectile weaponry tipped with osseous raw materials therefore constitute a major dataset for the investigation of technological, subsistence, and social aspects of various and numerous Pleistocene populations.
Having once been described as ‘impossible to evaluate’, investigation of maintenance and discard patterns for osseous projectile point assemblages has been severely neglected in the archaeological literature. As previous work has generally been restricted to qualitative descriptions of single artefacts exhibiting clear signs of rejuvenation or recycling, our knowledge of ‘the keeping’ of these toolkits is therefore extraordinarily limited.
This thesis addresses this imbalance through beginning to build a robust methodology for investigating the maintenance, recycling, and discard of osseous projectile weaponry. More than 4,000 whole and fragmentary barbed and unbarbed osseous projectile points recovered from 25 Middle to Late Magdalenian sites located throughout France and southern Germany were examined, and through employing a multi-faceted approach incorporating metric analyses, statistics, use wear analysis, and the examination of contemporaneous depictions of weaponry, inter-site and inter-regional differences in maintenance and discard patterns were successfully identified.
These results are discussed from a regional perspective in order to articulate these new data into interpretations of wider Magdalenian economic and social organisation.
English diplomatic agents 1603-1688
Keywords: diplomacy
diplomats
English diplomacy
Stuart diplomacy
English diplomats

The general historiography of Stuart diplomacy has, by and large, argued that those who were tasked with carrying out foreign policy were ineffective, amateurish and, in some cases, incompetent. This harsh view is in need of reassessment in the light of a number of incidents, which suggest that much effective foreign policy and general diplomatic work was carried out by lower-ranking diplomats, who were titled agents. These agents have attracted little historical comment or study. This thesis sets out to redress this by considering the agents employed from 1603 to 1688, when the title disappeared due to rank inflation, duties transferred to consuls, and other factors.
The texts of the period on the perfect ambassador leave clear omissions in descriptions of diplomatic work, which therefore suggests a role for another type of diplomat, the agent.
The initial chapter looks at background and education and offers a portrait of an average agent as typically a well-educated member of the lower gentry. The terms under which agents served are compared with other professional groups of comparable social rank and those in other government positions. Agents’ work in information gathering, including where and from what sources they obtained material and how it was transmitted, is investigated. The existence of an efficient international network is uncovered. Agents’ role in negotiations, unconstrained by protocol, allowed them a greater degree of freedom than ambassadors. This and the element of deniability are key to understanding their importance to Stuart diplomacy. The task of protecting merchants’ rights is demonstrated by a case study in France which shows all the usual stages involved in resolving a dispute. Involvement in buying naval supplies and cultural transfer are also discussed in chapters concerned with agents’ practical activities. Finally, the careers pursued after their agencies are outlined, showing how some, such as Cottington, used their skills and knowledge to their advantage. Having demonstrated the differences amongst, and the utility of, agents it is possible to suggest that some of the criticism of Stuart diplomacy comes from a misunderstanding of the use of both agents and ambassadors, and how, when and why each could be employed for a specific task.