Improving digital image correlation in the TopoSEM Software Package

Dissertação de mestrado integrado em Informatics EngineeringTopoSEM is a software package with the aim of reconstructing a 3D surface topography of a microscopic sample from a set of 2D Scanning Electron Microscopy (SEM) images. TopoSEM is also able to produce a stability report on the calibration of the SEM hardware based solely on output images. One of the key steps in both of these workflows is the use of a Digital Image Correlation (DIC) algorithm, a no-contact imaging technique, to measure full-field displacements of an input image. A novel DIC implementation fine-tuned for 3D reconstructions was originally developed in MATLAB to satisfy the feature requirement of this project. However, near real-time usability of the TopoSEM is paramount for its users, and the main barrier towards this goal is the under-performing DIC implementation. This dissertation work ported the original MATLAB implementation of TopoSEM to sequential C++ and its performance was further optimised: (i) to improve memory accesses, (ii) to explore the available vector exten sions in each core of current multiprocessor chips processors to perform computationally intensive operations on vectors and matrices of single and double-precision floating point values, and (iii) to additionally improve the execution performance through parallelization on multi-core devices, by using multiple threads with a front wave propagation scheduler. The initial MATLAB implementation took 3279.4 seconds to compute the full-field displacement of a 2576 pixels by 2086 pixels image on a quad-core laptop. With all added improvements, the new parallel C++ version on the same laptop lowered the execution time to 1.52 seconds, achieving an overall speedup of 2158.TopoSEM é um programa cujo objetivo é reconstruir em 3D a topografia de uma amostra capturada por um mi croscópio electrónico de varrimento. Esta ferramenta é também capaz de gerar um relatório sobre a estabilidade da calibração do microscópio com base apenas em imagens capturadas. Um dos passos chave para ambas as funcionalidades trata-se da utilização de um algoritmo de Correlação Digital de Imagens (DIC), uma técnica de visão por computador que não envolve contacto direto com a amostra e que permite medir deslocamentos e deformações entre imagens. Criou-se uma nova implementação de DIC em MATLAB especialmente formulada para reconstrução 3D. No entanto, a capacidade de utilizar o TopoSEM em quase tempo real é fundamental para os seus utilizadores e a principal barreira para tal são os elevados tempos de execução da implementação em MATLAB. Esta dissertação portou o código de MATLAB para código sequencial em C++ e a sua performance foi melho rada: (i) para otimizar acessos a memória, (ii) para explorar extensões de vetorização disponíveis em hardware moderno para otimizar operações sobre vetores e matrizes, e (iii) para através de paralelização em dispositivos multi-core melhorar ainda mais a performance utilizando para isso vários fios de execução com um escalonador de propagação em onda. A implementação inicial em MATLAB demorava 3279.4 segundos para computar uma imagem com resolução de 2576 pixels por 2086 pixels num portátil quad-core. Com todas as melhorias de performance, a nova imple mentação paralela em C++ reduziu o tempo de execução para 1.52 segundos para as mesmas imagens no mesmo computador, atingindo um speedup de 2158

Towards convection-resolving, global atmospheric simulations with the Model for Prediction Across Scales (MPAS) v3.1: an extreme scaling experiment

The Model for Prediction Across Scales (MPAS) is a novel set of Earth system simulation components and consists of an atmospheric model, an ocean model and a land-ice model. Its distinct features are the use of unstructured Voronoi meshes and C-grid discretisation to address shortcomings of global models on regular grids and the use of limited area models nested in a forcing data set, with respect to parallel scalability, numerical accuracy and physical consistency. This concept allows one to include the feedback of regional land use information on weather and climate at local and global scales in a consistent way, which is impossible to achieve with traditional limited area modelling approaches. Here, we present an in-depth evaluation of MPAS with regards to technical aspects of performing model runs and scalability for three medium-size meshes on four different high-performance computing (HPC) sites with different architectures and compilers.We uncover model limitations and identify new aspects for the model optimisation that are introduced by the use of unstructured Voronoi meshes.We further demonstrate the model performance of MPAS in terms of ist capability to reproduce the dynamics of the West African monsoon (WAM) and its associated precipitation in a pilot study. Constrained by available computational resources, we compare 11-month runs for two meshes with observations and a reference simulation from the Weather Research and Forecasting (WRF) model. We show that MPAS can reproduce the atmospheric dynamics on global and local scales in this experiment, but identify a precipitation excess for the West African region. Finally, we conduct extreme scaling tests on a global 3 km mesh with more than 65 million horizontal grid cells on up to half a million cores. We discuss necessary modifications of the model code to improve its parallel performance in general and specific to the HPC environment. We confirm good scaling (70% parallel efficiency or better) of the MPAS model and provide numbers on the computational requirements for experiments with the 3 km mesh. In doing so, we show that global, convection-resolving atmospheric simulations with MPAS are within reach of current and next generations of high-end computing facilities

Towards convection-resolving, global atmospheric simulations with the Model for Prediction Across Scales (MPAS): an extreme scaling experiment

The Model for Prediction Across Scales (MPAS) is a novel set of earth-system simulation components and consists of an atmospheric model, an ocean model and a land-ice model. Its distinct features are the use of unstructured Voronoi meshes and C-grid discretisation to address shortcomings of global models on regular grids and of limited area models nested in a forcing data set, with respect to parallel scalability, numerical accuracy and physical consistency. This makes MPAS a promising tool for conducting climate-related impact studies of, for example, land use changes in a consistent approach. Here, we present an in-depth evaluation of MPAS with regards to technical aspects of performing model runs and scalability for three medium-size meshes on four different High Performance Computing sites with different architectures and compilers. We uncover model limitations and identify new aspects for the model optimisation that are introduced by the use of unstructured Voronoi meshes. We further demonstrate the model performance of MPAS in terms of its capability to reproduce the dynamics of the West African Monsoon and its associated precipitation. Comparing 11 month runs for two meshes with observations and a Weather Research & Forecasting tool (WRF) reference model, we show that MPAS can reproduce the atmospheric dynamics on global and local scales, but that further optimisation is required to address a precipitation excess for this region. Finally, we conduct extreme scaling tests on a global 3 km mesh with more than 65 million horizontal grid cells on up to half a million cores. We discuss necessary modifications of the model code to improve its parallel performance in general and specific to the HPC environment. We confirm good scaling (70 % parallel efficiency or better) of the MPAS model and provide numbers on the computational requirements for experiments with the 3 km mesh. In doing so, we show that global, convection-resolving atmospheric simulations with MPAS are within reach of current and next generations of high-end computing facilities

Survey, characterisation and condition assessment of Palustriella dominated springs 'H7220 Petrifying springs with tufa formation (Cratoneurion)' in Gloucestershire, England

Twenty-two Gloucestershire sites were surveyed between 18th and 29th January 2017. Gloucestershire, due to its geology, often steep topography, very high levels of saturated calcium carbonate associated with springs of the Stroud Valley area in particular and large areas of woodland, has a large potential for the H7220 petrifying spring habitat. Fifteen sites (68%) are identified as having the European Annex 1 habitat H7220, Petrifying springs with tufa formation (Cratoneuron) while 7 sites had tufa formation without H7220. The total estimated area for H7220 habitat surveyed within Gloucestershire is 2 ha ranging in size from just 0.0001 ha (Sedbury Cliff) to 0.76 ha (Alder Carr) with the greatest length being some 600 m (Dowdeswell). The H7720 feature has been assessed as being in favourable condition for all of the 15 sites where it has been shown to occur although shading (planted conifers) and water quality (Nitrogen) have been highlighted as having potential for negative impact. No plants of conservation concern were recorded as directly associated with H7220 vegetation although the following were recorded more generally from sites: the aquatic moss Fissidens rivularis (Slade Brook), 6 Red data Book England (Near Threatened) flowering plants; 8 flowering plants generally considered to be ancient woodland indicators. Spring and seepages (particularly when calcareous and/or wooded) are of great importance for invertebrates (crane flies, soldier flies and some specialized snails and water beetles). These habitats are widespread in the UK (and include the H7720 habitat) but their associated invertebrate fauna is poorly known. Observations suggest that Palustriella commutata starts growth on firm substrates, mainly stones or living roots, as opposed to deadwood or rotting organic matter and is associated with slower flows and often more gently sloping sites. Restoration of H7720 is considered for two sites and restoration techniques discussed

Portmerion, Proportion and Perspective

The holiday village of Portmerion was created by Bertram Clough Williams-Ellis (1883 1978) over a period of fifty-one years, starting in 1926. It was grade II listed in 1971. However, Portmerion has become a part of western popular culture rather than of mainstream architectural history. Its use as the setting for the cult 1967 television series “The Prisoner” ensures continued worldwide interest and a constant stream of visitors. Williams Ellis’ design methods were empirical, initial designs being adjusted by eye on site in close collaboration with trusted builders. This paper analyses the development of Portmerion as a gesamtkunstwerk; considering the experience of movement through the village as a dynamic composition of shifting vistas, focussing the visitor on a series of constructed views. Through this analysis, Portmerion is revealed as both a manifestation of the architecture of pleasure and an exercise in the pleasure of architecture

The nature and timing of Late Quaternary glaciation in southernmost South America

The timing and extent of former ice sheet fluctuations can demonstrate leads and lags during periods of climatic change and the forcing factors responsible, but this requires robust glacial chronologies. Patagonia, in southern South America, offers a well preserved record of glacial geomorphology over a large latitudinal range that is affected by key climatic systems in the Southern Hemisphere, but establishing the timing of ice advances has proven problematic. This thesis targets five southernmost ice lobes that extended from the former Patagonian Ice Sheet during the Quaternary; from north to south: the Río Gallegos, Skyring, Otway, Magellan and Bahía Inútil – San Sebastián (BI-SSb) ice lobes. The region is chosen because there is ambiguity over the age of glacial limits, which have been hypothesised to relate to different glacial cycles over hundreds of thousands of years but yield cosmogenic nuclide exposure data dominantly < 50 ka. This contradiction is the focus of the thesis: was the sequence of glacial limits deposited over multiple glacial cycles, or during the last glacial cycle? A new geomorphological map is used to reconstruct glacial limits and to help target new dating. Cosmogenic nuclide depth-profiles through glacial outwash are used to date glacial limits whilst accounting for post-depositional processes. These reveal that limits of the BI-SSb lobe hypothesized to date from MIS 12 (ca. 450 ka) and 10 (ca. 350 ka) were actually deposited during the last glacial cycle, with the best-dated profile giving an MIS 3 age of ca. 30 ka, indicating an extensive advance prior to the global Last Glacial Maximum (gLGM). A glacial reconstruction indicates that this may not have been unique to the BI-SSb lobe, and a compilation of published dates reveals that similar advances during the last glacial cycle indicate related forcing factors operating across Patagonia and New Zealand

The development of thiosulfonates as cysteine protease inhibitors

Cysteine proteases are ubiquitous throughout nature as proteolytic machinery that are responsible for key physiological processes. Unregulated, uncontrolled or undesired proteolysis is often a key process in many disease states. As such, specific inhibitors of cysteine proteases offer a unique therapeutic target for chemotherapeutic intervention. This is particularly true in many diseases caused by parasitic infections, such as Malaria, Schistosomiasis and Chagas disease, as the parasitic lifecycle is often highly dependent upon cysteine proteases. The majority of attempts at conferring specificity of covalent inhibitors have been derived from classical structure activity relationship (SAR) studies. Such studies place emphasis on the primary non-covalent interaction with little optimisation of the electrophillic trap, which forms the covalent bond, being attempted. In this work a new class of electrophillic traps, the thiosulfonates, will be developed as cysteine protease inhibitors. This aims to take advantage of the differing chemistry observed for cysteine proteases, with a sulfur centred nucleophile, rather than the oxygen centred nucleophile which is present in all other protease classes. When combined with classical SAR this two pronged attack should greatly increase inhibitor specificity and reduce off target effects, adding to the chemical toolkit available to medicinal chemists. Throughout this work the synthesis, reactivity profiles and biological evaluation of thiosulfonates as cysteine protease inhibitors will be explored. Computational modelling studies will be incorporated, highlighting the synergy between classical SAR and electrophilic trap optimisation. This will culminate in the application of thiosulfonates towards schistosomiasis, the second biggest neglected tropical disease after malaria

Simulation intrusive dynamique d'imagerie à effet tunnel

La microscopie à effet tunnel (STM) est une technique d’imagerie très utilisée en nanoscience qui permet d’étudier les états électroniques et la morphologie d’un substrat en exploitant la nature quantique des électrons traversant une barrière de potentiel. Cette méthode, en plus de donner lieu à l’observation d’objets à l’échelle atomique, permet aussi de les manipuler et d’induire des réactions chimiques. Le problème inverse en STM consiste à déterminer la structure atomique d’un échantillon à partir des images expérimentales. La complexité des phénomènes physiques rendent parfois difficile l’interprétation des images obtenues. Des outils permettant de calculer des images STM à partir d’un modèle moléculaire sont donc nécessaires pour comprendre la source des contrastes observés en imagerie expérimentale. Dans sa forme la plus simple, le calcul d’images STM peut être réalisé en utilisant les théories Bardeen ou de Tersoff-Hamann (TH). Ces approches consistent à utiliser la structure électronique des électrodes isolées pour calculer rapidement, par une méthode perturbative, le courant tunnel de manière semi-quantitative. Dans l’état actuel du domaine, cette méthode est utilisée pour obtenir rapidement des images STM calculées. Certaines approches permettent aussi de considérer une modification physique ou chimique (intrusion) de manière interactive, mais dans un cadre statique sans tenir compte de la réorganisation atomique pouvant survenir à la suite de cette modification. L’objectif de ce projet de recherche consiste donc à utiliser la théorie TH pour développer un outil d’imagerie STM qui considère la relaxation moléculaire survenant à la suite d’une intrusion de manière interactive. Pour concrétiser cet objectif, quatre stratégies sont employées. Nous utilisons la théorie de la superposition atomique et de la délocalisation électronique (ASED)à laquelle un terme de van der Waals est ajouté pour calculer l’énergie totale et la structure électronique des systèmes. Pour considérer la relaxation moléculaire, l’algorithme d’optimisation non-linéaire de Broyden-Fletcher-Goldfarb-Shanno (BFGS) est utilisé pour optimiser la géométrie de nos systèmes. La structure électronique des molécules relaxées est par la suite utilisée pour calculer, pixel par pixel, le courant tunnel en utilisant principalement le formalisme de Tersoff-Hamann (TH). Finalement, afin de tirer profit des architectures informatiques modernes, les étapes du calcul de la structure électronique et de l’image STM sont réalisées en parallélisant les problèmes. En particulier, un algorithme hybride utilisant des processeurs graphiques (GPU) permet d’accélérer drastiquement le calcul de l’image.----------Abstract Scanning Tunneling Microscopy (STM) is an imaging technique widely used in nanoscience that allows to study the electronic states and the morphology of a substrate by exploiting the quantum nature of electrons passing through a potential barrier. While this method allows the observation of objects on the atomic scale, it can be used to manipulate them and induce chemical reactions. The inverse problem in STM consists in determining the atomic structure of a sample from the experimental images. Sometimes, the complexity of physical phenomena makes it difficult to interpret the images obtained. Therefore, simulation tools that compute STM images from a molecular model are necessary to understand the source of the contrasts observed in the experimental images. In its simplest form, the calculation of STM images can be performed using the Bardeen or Tersoff-Hamann (TH) theories. These approaches consist in using the electronic structures of the isolated electrodes to calculate the tunneling current in a semi-quantitative manner by a perturbative method. In the current state of the field, this method is used to quickly obtain computed STM images. Some approaches also allows the consideration of a physical or chemical modification (intrusion) interactively, but in a static framework without taking into account the atomic reorganization that can occur as a result of this modification. The objective of this research project is therefore to use the TH theory to develop an STM imaging tool that considers molecular relaxation occurring as a result of an intrusion in an interactive way. To achieve this goal, four strategies are used. To calculate the total energy and electronic structure of the systems while considering weak intermolecular interactions, we use the Atomic Superposition and Electron Delocalization Molecular Theory (ASED) to which a van der Waals term is added. Moreover, the Broyden-Fletcher-Goldfarb-Shanno (BFGS) nonlinear optimization algorithm is used to optimize the geometry of our systems to consider molecular relaxation. The electronic structure of the relaxed molecules is then reused to calculate the tunnel current pixel by pixel using mainly the Tersoff-Hamann formalism (TH). Finally, in order to take advantage of modern computer architectures, the steps of calculating the electronic structure and the STM image are carried out in a parallel way. In particular, a hybrid algorithm using graphical processors (GPU) makes it possible to accelerate drastically the calculation of the image

Resisting Postmodern Architecture

Since its first appearance in 1981, critical regionalism has enjoyed a celebrated worldwide reception. The 1990s increased its pertinence as an architectural theory that defends the cultural identity of a place resisting the homogenising onslaught of globalisation. Today, its main principles (such as acknowledging the climate, history, materials, culture and topography of a specific place) are integrated in architects’ education across the globe. But at the same time, the richer cross-cultural history of critical regionalism has been reduced to schematic juxtapositions of ‘the global’ with ‘the local’. Retrieving both the globalising branches and the overlooked cross-cultural roots of critical regionalism, Resisting Postmodern Architecture resituates critical regionalism within the wider framework of debates around postmodern architecture, the diverse contexts from which it emerged, and the cultural media complex that conditioned its reception. In so doing, it explores the intersection of three areas of growing historical and theoretical interest: postmodernism, critical regionalism and globalisation. Based on more than 50 interviews and previously unpublished archival material from six countries, the book transgresses existing barriers to integrate sources in other languages into anglophone architectural scholarship. In so doing, it shows how the ‘periphery’ was not just a passive recipient, but also an active generator of architectural theory and practice. Stylianos Giamarelos challenges long-held ‘central’ notions of supposedly ‘international’ discourses of the recent past, and outlines critical regionalism as an unfinished project apposite for the 21st century on the fronts of architectural theory, history and historiography