On deep generative modelling methods for protein-protein interaction

Proteins form the basis for almost all biological processes, identifying the interactions that proteins have with themselves, the environment, and each other are critical to understanding their biological function in an organism, and thus the impact of drugs designed to affect them. Consequently a significant body of research and development focuses on methods to analyse and predict protein structure and interactions. Due to the breadth of possible interactions and the complexity of structures, \textit{in sillico} methods are used to propose models of both interaction and structure that can then be verified experimentally. However the computational complexity of protein interaction means that full physical simulation of these processes requires exceptional computational resources and is often infeasible. Recent advances in deep generative modelling have shown promise in correctly capturing complex conditional distributions. These models derive their basic principles from statistical mechanics and thermodynamic modelling. While the learned functions of these methods are not guaranteed to be physically accurate, they result in a similar sampling process to that suggested by the thermodynamic principles of protein folding and interaction. However, limited research has been applied to extending these models to work over the space of 3D rotation, limiting their applicability to protein models. In this thesis we develop an accelerated sampling strategy for faster sampling of potential docking locations, we then address the rotational diffusion limitation by extending diffusion models to the space of $SO(3)$ and finally present a framework for the use of this rotational diffusion model to rigid docking of proteins

Ghost imaging with engineered quantum states by Hong-Ou-Mandel interference

Traditional ghost imaging experiments exploit position correlations between correlated states of light. These correlations occur directly in spontaneous parametric down-conversion (SPDC), and in such a scenario, the two-photon state used for ghost imaging is symmetric. Here we perform ghost imaging using an anti-symmetric state, engineering the two-photon state symmetry by means of Hong-Ou-Mandel interference. We use both symmetric and anti-symmetric states and show that the ghost imaging setup configuration results in object-image rotations depending on the state selected. Further, the object and imaging arms employ spatial light modulators for the all-digital control of the projections, being able to dynamically change the measuring technique and the spatial properties of the states under study. Finally, we provide a detailed theory that explains the reported observations.Comment: Published version. 19 pages, 5 figure

Natural Resource Management: the Reproduction and Use of Environmental Misinformation in Guinea's Forest?Savanna Transition Zone

Summary An erroneous analysis of environmental change has informed environmental policy in part of Guinea for a century. Using this case study, the relationship between the production of information about environmental problems and external institutions which address them, is examined. To see how certain analyses of change have gained credence and validity, while others ? including local people's own ? have been excluded from investigation, the relative dominance of particular disciplines, of methods and data sets within them, and of deductive theories guiding data interpretation, are considered. Such dominance depends on the sociopolitical and financial structures within which environmental policy institutions have evolved and operate. Resumé La gestion naturelle des resources: la réplacation et le déploiement de fausses informations sur l'environnement dans la zone de transition forêt?savane en Guinée Depuis un siècle déjà, c'est sur une analyse erronnée des changements environnementaux que se fonde la politique environnementale dans une certaine partie de la Guinée. Dans la présente étude de cas, les auteurs offrent un examen du rapport entre la production de l'information concernant les problèmes environnementaux et les institutions externes qui s'y adressent. Pour voir dans quelle manière certaines analyses du changement sont devenues plus vraisemblables et donc plus acceptables alors que d'autres ? y compris celles des autochtones ? auraient été marginalisées de l'étude, les auteurs réfléchissent à la dominance relative des diverses disciplines, des méthodes et des séries de données au sein de celles?ci, et des théories déductrices qui gèrent l'interprétation des données brutes. Cette dominance dépendrait des structures socio?politiques et financières au sein desquelles se sont évoluées les institutions responsables de la politique environnementale, et au sein desquelles elles opèrent toujours. Resumen El manejo de recursos naturales: reproducción y uso de la desinformación ambiental en la zona de transición bosque/sabana de Nueva Guinea Las pautas de acción ambientales en partes de Nueva Guinea han recibido información basada en el análisis erróneo de cambios ambientales por un espacio de un siglo. Usando este caso, se examina en el artículo la relación entre la producción de información sobre los problemas ambientales y las instituciónes externas que se aplican a resolverlos. Se considera la forma en que ciertos análisis de cambio han ganado credibilidad y validez, mientras que otros ? incluyendo algunos de grupos locales ? han sido excluidos de la investigación, del relativo predominio de algunas disciplinas en particular, de métodos y datos contenidos en ellas, y de teorías deductivas que guían la interpretación de datos. Este predominio depende de las estructuras sociopolíticas y financieras dentro de las cuales las institutuciónes ambientales han evolucionado y operado

Feature-based characterisation of laser powder bed fusion surfaces

A novel algorithmic pipeline for the automated identification and dimensional/geometric characterisation of topographic formations of interest (surface features) is proposed, specifically aimed at the investigation of signature features left by laser powder bed fusion of metallic surfaces. Unmelted and partially-melted particles, as well as spatter formations and weld tracks, are automatically identified and extracted from topography datasets obtained via state-of-the-art areal topography measurement instruments, and then characterised in terms of their size and shape properties. Feature -based characterisation approaches, such as the one proposed in this work, allow for development of new solutions for the study of advanced manufacturing processes through the investigation of their surface fingerprint

Nietzsche and moral inquiry: posing the question of the value of our moral values

The continued presence and importance of Christian moral values in our daily lives, coupled with the fact that faith in Christianity is in continual decline, raises the question as to why having lost faith in Christianity, we have also not lost faith in our Christian moral values. This question is also indicative of a more pressing phenomenon: not only have we maintained our faith in Christian values, we fail to see that the widespread collapse of Christianity should affect this faith. To tackle this latter phenomenon, I claim, we have to pose the Nietzschean question of the value of our moral values, so as to see that this value can be a possible object of questioning. In chapter one, I consider different approaches found in the history of moral philosophy that look like potential candidates for this task. I argue that, ultimately, the task requires simultaneously taking our familiarity with Christian moral values as both sui generis and a questionable phenomenon. In chapter two, I articulate in detail the sui generis nature of this familiarity with moral values,in terms of the phenomena of habituation and sedimentation. In chapter three, I consider the possibility of estrangement that is built into our familiarity with moral values, by focusing on the role of cognition. I demonstrate how cognition, in the form of self-consciousness, can disrupt the sedimented, habituated nature of our moral values through a form of ironic disruption. In chapter four, I develop this account by considering the possibility of an appeal to an alternative moral outlook. To do so, I draw upon the structural isomorphism that is present between the process of estrangement and a rite of passage