VictorJuiz/thesis huggingface dataset:
Algorithm development in computational chemistry
Keywords: Algorithm Development
Algorithm
Theoretical Chemistry
GPGPU
Stochastic
Finite Difference
Electrochemistry
CUDA

This thesis presents algorithm development in computational chemistry, and applies new computer science concepts to voltammetric simulation. To begin, this thesis discusses why algorithm development is necessary, and inherent problems found in commercial simulation solvers. As a result of this discussion, this thesis describes the need for simulators to keep abreast of recent computational developments.
Algorithm development in this thesis is taken through stages.
Chapter 3 applies known theory relating to the stripping voltammetry at a macroelectrode to the diffusional model of a microdisk, using finite difference and alternating direction implicit simulation techniques.
Chapter 4 introduces the concept of parallel computing, and how computational hardware has developed recently to take advantage of out-of-order calculations, by processing them in parallel to reduce simulation time. The novel area of graphics card simulation for highly parallel algorithms is also explained in detail.
Chapter 5 discusses the adaptation of voltammetric finite difference algorithms to a purely parallel format for simulation by explicit solution. Through explicit solution, finite difference algorithms are applied to electrode geometries which necessitate a three-dimensional solution – elliptical electrodes; square, rectangular, and microband electrodes; and dual microdisk electrodes in collector-generator mode.
Chapter 6 introduces 'Random Walk' simulations, whereby individual particles in the simulation are modelled and their trajectories over time are calculated. The random walk technique in this thesis is improved for pure three-dimensional diffusion, and adapted to graphics cards, allowing up to a factor 4000 increase in speed over previous computational methods. This method is adapted to various systems of low concentration confined voltammetry (chapter 6.4) and single molecule detection, ultra low concentration cyclic voltammetry (chapter 6.5), and underpotential deposition of thallium on mobile silver nanoparticles (chapter 6.6).
Overall, this thesis presents, and applies, a series of algorithm development concepts in computational electrochemistry.
Stochastic model predictive control and its application for small satellite attitude control
Keywords: astronautics
small satellite control
model predictive control
probabilistic constraints
stochastic
stochastic tubes

Model predictive control is an attractive control method applicable to a wide range of real-world processes with the ability to handle systems subject to probabilistic constraints and stochastic disturbances. While many methods exist that handle disturbance effects, there are fewer methods that are equipped to handle systems with measurement errors. Additionally, whereas model predictive control is used in a wide range of engineering processes, its use is limited in space applications. This thesis will investigate the use of model predictive control, in a manner that handles stochastic measurement errors, to control the small satellite FalconSAT-5.
This study focused on model predictive control methods that construct a region of tubes in which the state is required to fall in order to meet the probabilistic constraints. Three such methods were studied. The first method used the probabilistic distributions of the disturbances to tighten the constraints so that, even in the presence of disturbances, the constraints would still be met. This method was then expanded to handle both stochastic disturbances and stochastic measurement errors by also including the distribution of the measurement errors as an additional constraint tightening factor. This method was superior to the first method when the system exhibited both disturbances and measurement errors. The third method used state estimation to avoid the errored measurements. When the disturbances have a greater effect on the system response, the method that considers the measurement errors was more effective than the estimation method. However, if the measurement errors have a greater effect, the estimation method was more effective. The model predictive control method was then applied to the FalconSAT-5 dynamic model for all the control modes necessary for satellite operation and the results of these control simulations were compared to the current satellite control scheme of proportional-derivative control.
The simulations showed that, for FalconSAT-5, the model predictive control method that includes the measurement error effects in the constraint definition was superior to the estimation method. This control method was used to simulate control of the satellite in the initial deployment phase, also called the detumble phase, for pointing control, and for control during a slew manoeuvre. This method was found to be superior to the proportional-derivative control in all three control modes in convergence time,control input required, and cost comparison. This study showed that it is possible to develop model predictive control algorithms that handle measurement errors and are applicable to small satellite control. Model predictive control is a viable alternative to classical control for space applications, providing superior performance and better control.
Neutron and x-ray scattering study of magnetic manganites
Keywords: Neutron Scattering
Manganese Oxide
Manganite
Resonant X-ray
Mulitferroic
Magnetoelectric

This thesis presents three investigations of the magnetic and electronic proper- ties of manganese oxide materials. The investigations are performed using a variety of neutron scattering and x-ray scattering techniques.
The electronic ground-state of Pr(Sr0.1 Ca0.9)2 Mn2O7 an antiferromagnet with CE-type ordering, is determined using neutron spectroscopy, as opposed to the more usual approach of using diffraction. The Zener polaron model of the elec- tronic ground state of the CE-type magnetic phase is shown to be unsuitable for this material. The ground-state is shown to agree well with the electronic ground state proposed by Goodenough in the 1950’s, but without significant Mn3&plus;/Mn4&plus; disproportionation.
The distribution of the magnetisation density within the unit cell of the CE-type antiferromagnet La0.5Sr1.5MnO4 is determined from a polarised neutron diffraction experiment by analysing the results with the maximum entropy method. The majority of the magnetisation density is found to be located at the Mn site. The investigation shows tentative evidence of a small magnetic moment on the in-plane O site. However, a larger moment is observed at both the La/Sr site and the out-of-plane O site.
The magnetic structure of the magnetoelectric multiferroic DyMn2O5 is inves- tigated using resonant magnetic x-ray scattering. The magnetic structure is shown to be similar to other members of the RMn2O5 series of multiferroics, but with the key difference that the magnetic moments are closely aligned parallel with the crystallographic b-axis, in contrast to the usual observation of the moments being close to parallel with the a-axis. This study also shows evidence that the electrical polarisation has a significant contribution from the valence electrons of the O ions, agreeing with previous work.
Reactions of [FeFe]-hydrogenase with carbon monoxide and formaldehyde
Keywords: hydrogen
protein film electrochemistry
Hydrogenase
inhibition
carbon monoxide

The use of H2 as an energy carrier has in recent years been identified as a promising future solution to the current energy crisis. Hydrogenases are metalloenzymes found in many microorganisms and are used to catalyse the reversible inter-conversion of protons and H2. These enzymes and their synthetic analogues have been recognised as a way to facilitate the use of H2 as a fuel. A major challenge to the future use of these catalysts is their reactions with small molecule inhibitors, such as oxygen and carbon monoxide. Detailed understanding of the structure and catalytic mechanism of these highly efficient catalysts is vital for the design of bio-inspired functional analogues for use in technological applications.
In this thesis electrochemical studies of three [FeFe]-hydrogenases are presented, performed using the technique of protein film electrochemistry. The strong potential dependence of the reaction of these hydrogenases with carbon monoxide and formaldehyde is characterised and rationalised. These studies provide compelling evidence for the formation of a previously ambiguous super-reduced state of [FeFe]-hydrogenase at low potential. This state is shown to be active and stable, and it is proposed that this state is involved in catalytic H2 production.
This super-reduced state is shown to have a high affinity for the reversible binding of formaldehyde, but a very low affinity for both carbon monoxide and oxygen. Activation of carbon monoxide inhibited [FeFe]-hydrogenase can be very rapidly induced by the application of a sufficiently reducing potential. These enzymes, considered to be oxygen sensitive, are shown to be extremely tolerant to irreversible oxygen damage at very reducing potentials where the super-reduced state is formed.
Cancer metabolic pathways regulated by hypoxia
Keywords: microRNA
hypoxia
Cancer metabolism
glycogen

Metabolic reprogramming in cancer cells provides energy and important metabolites required to sustain tumour proliferation. Hypoxia represents a hostile environment that can encourage these transformations and other adaptive responses that contribute to poor prognosis and resistance to radiation and chemotherapy. Hypoxic signatures associated with worse prognosis were previously derived in different cancer types, and led to the selection of two candidates with potential metabolic implications, namely the mir210-putuative target iron-sulfur scaffold protein ISCU and glycogen phosphorylase (PYGL). Firstly, it was verified that the hypoxia-induced miR-210 targets ISCU. Iron-sulfur clusters represent cofactors for key enzymes involved in Krebs cycle and electron transport chain. Downregulation of ISCU was associated with the induction of reactive oxygen species (ROS) and reduced mitochondrial complex I and aconitase activity, caused a shift to glycolysis in normoxia and enhanced cell survival. This indicates that the induction of a single microRNA, miR-210, can mediate a new mechanism of adaptation to hypoxia, by regulating mitochondrial function via iron-sulfur cluster metabolism and free radical generation. Secondly, it was found that changes in PYGL expression reflect a characteristic upregulation of glycogen metabolism in hypoxia in both tumour xenografts and in cancer cell lines. More specifically, hypoxia stimulates glycogen accumulation and its utilisation, as well as the concurrent upregulation of several glycogen-metabolizing enzymes such as glycogen synthase (GYS1) and PYGL. PYGL depletion led to glycogen accumulation in hypoxic cells, increased intracellular levels of ROS, and a reduction in proliferation due to a p53-dependent induction of senescence. Furthermore, depletion of PYGL was associated with markedly impaired tumorigenesis in vivo. Finally, metabolic analyses indicated that glycogen degradation by PYGL is important for the optimal functioning of the pentose phosphate pathway. Collectively, this study shows the contribution of two important pathways to the metabolic adaptations induced by hypoxia.
Education, Islamophobia, and security : narrative accounts of Pakistani and British Pakistani women in English universities
Keywords: Diaspora
Islamophobia
Islam
British Muslims
Women
Security
Pakistani
University Activism

This thesis explores the experiences, encounters, responses and reactions to Islamophobia through a narrative study of forty female Pakistani and British students with a Pakistani heritage in universities across England. In exploring Islamophobia as a ‘racialised’ phenomenon, the participant narratives locate the experiences and encounters of Islamophobia within their ‘intersubjective’ realities, across various ‘communities’ of ‘discourse.’ These realities are informed by the wider socio-political milieu of a war against Al Qa’ida and its affiliates that ‘securitizes’ the Muslim and Pakistani identity(s) particularly in Britain. The university is also implicated in the counter terrorism agenda of the state, depicted as a ‘vulnerable’ space for radicalizing students. However, females in this discussion are predominantly absent within the academic and public narratives. Therefore, this research will explore the experience of Islamophobia, the way it is perceived by the British/Pakistani/Muslim/female student, and the way students respond and react to it within the university.
The research employs a narrative method of inquiry. The narrative analysis is informed by a Bakhtinian notion of ‘dialogics’ to explore the multiplicity of ‘meanings’ that emerge through individual accounts of Islamophobia located within their public and private realms. In exploring these narratives the thesis illustrates how ‘degrees of religiosity’ influences encounters and experiences of Islamophobia, and highlights responses and reactions of students to such experiences, that include individual and group activism to challenge Islamophobia and the insecure meta-narrative about Muslims and terrorism. The research further focuses on both the religious identity of the Muslim student, and their problematic ethnic identity, Pakistani demonstrating how in a securitized socio-political milieu Muslim students are further vulnerable to experiences of Islamophobia, in the form of Pakophobia, where both their religious and ethnic identities are held suspect.
These narratives have implications for the emerging understanding of Islamophobia as a ‘racialised’ phenomenon. They further have implications for universities that are encouraged to participate in the government’s counter-terrorism agenda. The narratives by locating the research within the particularities of a wider socio-political milieu that ‘racialises’ and ‘securitizes’ Muslims raises critical questions about the nature of discrimination in a post 9/11, 7/7 era that may have repercussions for other Muslim minority groups.
Mobility in context: exploring the impact of environmental stress on mobility decisions in northern Ethiopia
Keywords: migration
drought
urbanisation
Ethiopia
climate change

This thesis examines the relationship between environmental stress and human mobility with a view to understanding the impacts of climate change on human migration. Using a conjuncture of political ecology and migration theory, it firstly explores the literature on 'environmental refugees' identifying a distinction between general agreement on the existence of a relationship between environmental stress and migration, and debate over the appropriateness of the 'environmental refugee' as a suitable means for representing that relationship. Secondly this conjuncture is used to examine accounts from farmers and migrants in northern Ethiopia, with a focus on understanding how environmental and non-environmental factors interact to shape mobility decisions in a context of environmental stresses, thought analogous to those predicted to accompany future climate change.
The principal finding of the study is that although environmental stress matters in mobility decisions, it does so due to the context of non-environmental factors in which it occurs, not in spite of them. With this in mind the work provides a framework of additive, vulnerability, enabling and barrier effects as a means for elaborating our understanding of how environmental and non-environmental factors interact to determine mobility strategies in a context of environmental stress.
Focussing on the role of non-environmental factors, the work reveals that while biophysical features operate at a macro-scale to shape mobility decisions, these decisions are determined by non-environmental features operating at a micro-scale. The research then traces differences in the existence of these micro-scale, non-environmental, factors across two field sites, finding that their origins lie in both historical and contemporary forces of regional and global political economy. As such, the work concludes that understanding the relationship between climate change and human migration will require a contextualisation of that relationship within this broader framework.
Prime boost vaccination with viral vectors targeting apical membrane antigen1
Keywords: immunology
infectious disease
malaria vaccines

Apical membrane antigen 1 (AMA1) is a leading candidate vaccine antigen against blood stage malaria and several clinical trials using mostly protein-in-adjuvant vaccines have shown limited success. This thesis describes the development of recombinant adenoviral (AdHu5) and poxviral (MVA) vectors encoding AMA1 from Plasmodium chabaudi murine parasites. In this murine malaria model, AdHu5 and MVA encoding AMA1 when used in a heterologous prime boost regime showed excellent immunogenicity, both humoral and cellular. The vaccination regime was protective against blood stage challenge and both antibodies and CD4+ T cells found to be important for vaccine induced blood stage protection. In parallel to this novel P. falciparum vaccines encoding AMA1 were also developed and administered in a similar prime boost regime to mice and rabbits. The vaccination regime induced cellular immune response and high titre antibodies against AMA1 and these antibodies showed growth inhibitory activity against the homologous parasite strain. In an effort to overcome the issue of antigenic polymorphism and to circumvent pre-existing immunity to human adenovirus, biallelic simian and human adenoviral vectors and MVA encoding AMA1 vaccines were also developed and administered to mice and macaques. These vectors also induced high titre antibodies and the serum from macaques was found to have growth inhibitory activity. These vaccine candidates are now being taken forward to Phase I/II clinical trials in Oxford. This work also described the attempt to improve MVA as a antibody inducing vector to allow better antibody mediated immunity to blood stage malaria.
Classicism, Christianity and Ciceronian academic scepticism from Locke to Hume, c.1660-c.1760 
Keywords: Locke
history
seventeenth century
secular ethics
Mandeville
classical reception
Christian ethics
eighteenth century
intellectual life
Cicero
Hume
Religious thought
Shaftesbury
political science
philosophy
Middleton

This study explores the rediscovery and development of a tradition of Ciceronian academic scepticism in British philosophy between c.1660-c.1760. It considers this tradition alongside two others, recently recovered by scholars, which were recognised by contemporaries to offer opposing visions of man, God and the origins of society: the Augustinian-Epicurean, and the neo-Stoic. It presents John Locke, Conyers Middleton and David Hume as the leading figures in the revival of the tradition of academic scepticism. It considers their works in relation to those of Anthony Ashley Cooper, third earl of Shaftesbury, and Bernard Mandeville, whose writings refashioned respectively the neo-Stoic and Augustinian-Epicurean traditions in influential ways. These five individuals explicitly identified themselves with these late Hellenistic philosophical traditions, and sought to contest and redefine conventional estimations of their meaning and significance. This thesis recovers this debate, which illuminates our understanding of the development of the ‘science of man’ in Britain.
Cicero was a central figure in Locke’s attempt to explain, against Hobbes, the origins of society and moral consensus independent of political authority. Locke was a theorist of societies, religious and civil. He provided a naturalistic explanation of moral motivation and sociability which, drawing heavily from Cicero, emphasised the importance of men’s concern for the opinions of others. Locke set this within a Christian divine teleology. It was Locke’s theologically-grounded treatment of moral obligation, and his attack on Stoic moral philosophy, that led to Shaftesbury’s attempt to vindicate Stoicism. This was met by Mandeville’s profoundly Epicurean response. The consequences of the neo-Epicurean and neo-Stoic traditions for Christianity were explored by Middleton, who argued that only academic scepticism was consistent with Christian belief. Hume explored the relationship between morality and religion with continual reference to Cicero. He did so, in contrast to Locke or Middleton, to banish entirely moral theology from philosophy.
Disturbance, recovery and resilience in tropical forests: a focus on the coastal peat swamp forests of Malaysian Borneo
Keywords: climate change
Southeast Asia
fire
Sarawak
peat swamp forest
fossil pollen
biodiversity conservation
Malaysia
peatland
disturbance dynamics
vegetation change
long-term ecology
resilience
sustainable management
tropical forest

Tropical forests have existed for up to one hundred million years, and today provide many ecosystem services vital for human well-being. They also harbour great biodiversity, which, in addition to its intrinsic value, plays a key role in the functioning of these ecosystems. Despite their local to global significance, there are still many knowledge gaps concerning the dynamic processes that govern the functioning of tropical forests. Rapid rates of deforestation and landscape conversion, predominantly for logging and industrial agriculture, are limiting the time and opportunity available to collect the information needed to fill these gaps. This research aims to shed light on the long-term ecological functioning of tropical forests, specifically investigating the history of disturbance in these ecosystems and the response of forest vegetation to past perturbations. The carbon-rich tropical peat swamp forests found along the coast of Sarawak, Malaysian Borneo, are a central focus of this study. For these forests in particular, a large deficit of knowledge surrounding their history and unique ecological functioning is coupled with some of the highest conversion rates of all tropical forest ecosystems across the world. In this thesis, palaeoecological data has been used to reconstruct temporal variability in forest vegetation coincident with external perturbations in order to identify changes in the resilience of these ecosystems through time, via indicators such as slowing rates of recovery and reduced regeneration of forest vegetation. Results suggest that tropical forest ecosystems have, for the most part, shown resilience to natural disturbances in the past, ranging from instantaneous localised tree-fall to longer-term regional climatic change; but that recent anthropogenic disturbances, of novel forms and greater intensities, are jeopardizing the potential for forest recovery and thus compromising ecosystem resilience. These findings enhance our understanding of the ecology of tropical peat swamp forests, and tropical forests more broadly. They also provide a context for contemporary tropical forest management, allowing for predictions on future responses to disturbance and enabling more ecologically sustainable landscape planning.