Structure of a seeded palladium nanoparticle and its dynamics during the hydride phase transformation

Palladium absorbs large volumetric quantities of hydrogen at room temperature and ambient pressure, making the palladium hydride system a promising candidate for hydrogen storage. Here, we use Bragg coherent diffraction imaging to map the strain associated with defects in three dimensions before and during the hydride phase transformation of an individual octahedral palladium nanoparticle, synthesized using a seed-mediated approach. The displacement distribution imaging unveils the location of the seed nanoparticle in the final nanocrystal. By comparing our experimental results with a finite-element model, we verify that the seed nanoparticle causes a characteristic displacement distribution of the larger nanocrystal. During the hydrogen exposure, the hydride phase is predominantly formed on one tip of the octahedra, where there is a high number of lower coordinated Pd atoms. Our experimental and theoretical results provide an unambiguous method for future structure optimization of seed-mediated nanoparticle growth and in the design of palladium-based hydrogen storage systems

Design and Topology Optimisation of Tissue Scaffolds

Tissue restoration by tissue scaffolding is an emerging technique with many potential applications. While it is well-known that the structural properties of tissue scaffolds play a critical role in cell regrowth, it is usually unclear how optimal tissue regeneration can be achieved. This thesis hereby presents a computational investigation of tissue scaffold design and optimisation. This study proposes an isosurface-based characterisation and optimisation technique for the design of microscopic architecture, and a porosity-based approach for the design of macroscopic structure. The goal of this study is to physically define the optimal tissue scaffold construct, and to establish any link between cell viability and scaffold architecture. Single-objective and multi-objective topology optimisation was conducted at both microscopic and macroscopic scales to determine the ideal scaffold design. A high quality isosurface modelling technique was formulated and automated to define the microstructure in stereolithography format. Periodic structures with maximised permeability, and theoretically maximum diffusivity and bulk modulus were found using a modified level set method. Microstructures with specific effective diffusivity were also created by means of inverse homogenisation. Cell viability simulation was subsequently conducted to show that the optimised microstructures offered a more viable environment than those with random microstructure. The cell proliferation outcome in terms of cell number and survival rate was also improved through the optimisation of the macroscopic porosity profile. Additionally artificial vascular systems were created and optimised to enhance diffusive nutrient transport. The formation of vasculature in the optimisation process suggests that natural vascular systems acquire their fractal shapes through self-optimisation

Design and Topology Optimisation of Tissue Scaffolds

Tissue restoration by tissue scaffolding is an emerging technique with many potential applications. While it is well-known that the structural properties of tissue scaffolds play a critical role in cell regrowth, it is usually unclear how optimal tissue regeneration can be achieved. This thesis hereby presents a computational investigation of tissue scaffold design and optimisation. This study proposes an isosurface-based characterisation and optimisation technique for the design of microscopic architecture, and a porosity-based approach for the design of macroscopic structure. The goal of this study is to physically define the optimal tissue scaffold construct, and to establish any link between cell viability and scaffold architecture. Single-objective and multi-objective topology optimisation was conducted at both microscopic and macroscopic scales to determine the ideal scaffold design. A high quality isosurface modelling technique was formulated and automated to define the microstructure in stereolithography format. Periodic structures with maximised permeability, and theoretically maximum diffusivity and bulk modulus were found using a modified level set method. Microstructures with specific effective diffusivity were also created by means of inverse homogenisation. Cell viability simulation was subsequently conducted to show that the optimised microstructures offered a more viable environment than those with random microstructure. The cell proliferation outcome in terms of cell number and survival rate was also improved through the optimisation of the macroscopic porosity profile. Additionally artificial vascular systems were created and optimised to enhance diffusive nutrient transport. The formation of vasculature in the optimisation process suggests that natural vascular systems acquire their fractal shapes through self-optimisation

Computational processing and analysis of ear images

Tese de mestrado. Engenharia Biomédica. Faculdade de Engenharia. Universidade do Porto. 201

THE SPATIO-TEMPORAL BEHAVIOR OF BASIC MULTICELLULAR UNITS IN A PTH-INDUCED CORTICAL BONE REMODELING RABBIT MODEL

The adult skeleton is continuously renewed by the bone remodeling process, which is carried out by coupled and balanced activities, localized in time and space, via cellular groupings known as basic multicellular units (BMUs). In cortical bone, a BMU is depicted as a cutting cone of osteoclasts in the front resorbing bone, followed by a reversal phase, and then a closing cone lined by osteoblasts behind forming new bone. Any imbalance in this sequence of events can lead to bone diseases such as osteoporosis. Although it is well known that many factors affect BMU activity and contribute to osteoporosis, little is known about BMU dynamic spatio-temporal regulation. The rate of BMU progression, their longitudinal erosion rate (LER) is a key example of where knowledge is lacking. LER has only been inferred by 2D (histological) double-labeling techniques based on remodeling in a steady state where the cutting cone advance is equal to that of the closing cone. If these spatio-temporal relationships are valid and constant, increasing the bone formation rate, as observed with recombinant parathyroid hormone (PTH), an anabolic treatment for osteoporosis, would concomitantly elevate LER. The present study utilizes a new methodology to explore whether the increased cortical remodeling activity induced by PTH, including accelerated bone formation, leads to an elevated LER. BMU progression was manipulated via different dosing regimens: PTH and PTH withdrawal (PTHW). It was hypothesized that LER would be higher during active dosing. After 14 days of PTH dosing, rabbit distal right tibiae were imaged in vivo by synchrotron-based phase-contrast micro-CT. For the following 14 days, the PTH group received the same treatment while the PTHW group was administered saline. At 28 days, the rabbits were then euthanized, and the tibiae were imaged ex vivo by micro-CT. The in vivo and ex vivo right limb data sets were then registered, and LER was measured as the distance traversed by BMU cutting cones divided by 14 days. A total of 638 BMUs were assessed. Counter to the hypothesis, LER was lower in the PTH (34.61 µm/day) compared with the PTHW (39.37 µm/day; p < 0.01) group. Slower BMU progression suggests that PTH has an important role in enhancing coupling both by increasing bone formation and slowing the advance of bone resorption within BMUs. This novel insight into BMU dynamics indicates that further investigation into LER modulation is warranted, with potential implications for combatting remodeling-related disease, improving treatment, and potentially reducing drug side effects

Three dimensional numerical simulations of non-linear MHD instabilities in the solar corona

The aim of this thesis has been to carry out 3D MHD simulations to investigate nonlinear MHD instabilities and the behaviour of solar coronal loops. The simulations have been carried out on a parallel computer using a new shock-capturing Lagrangian-remap code, LareSd. As part of the PhD this code has been extended to include resistivity allowing the study of the non-linear resistive evolution of the instability. In particular the kink instability in line-tied coronal loops has been studied. This was suggested as a possible explanation of compact loop flares, sudden brightenings of a coronal loop due to a release of energy which does not destroy the loop. For the kink instability to explain such flares it must drive reconnection. This requires high current densities, i.e. current sheets. The results presented in this thesis suggest that the formation of current sheets during the non-linear evolution of the kink instability is more complicated than was previously believed. Indeed, if the loop is allowed to evolve slowly until the instability is triggered than the current appears to saturate at a finite value. This suggests that the kink instability cannot explain a compact loop flare. LareSd has also been used to model space observations from NASA’s SoHO (a joint NASA/ESA satellite) and TRACE satellites. These observations showed a group of rotating sunspots and their overlying system of loops. The simulations will allow further investigations of this behaviour to be carried out

Development of a 3D Laser Imaging System and its Application in Studies of Turbulent Flame Structure

The necessity for increasing the efficiency of combustion engines whilst simultaneously reducing the emissions of various pollutants is widely accepted. With reference specifically to premixed spark ignition (SI) engines, the turbulence/flame interaction is of particular relevance as it not only determines the maximum possible burning rate in such an engine, but also if flames are likely to extinguish (quench). The present study describes a three-dimensional laser imaging technique which has been developed to study turbulent premixed flames in a fan-stirred combustion bomb. This has, for the first time, allowed the full 3D structure of flames developing at engine-like conditions to be analysed without the assumptions required in previous works using 2D flame imaging techniques. Methane/air mixtures at a starting temperature and pressure of 298K and 0.1 MPa respectively and an equivalence ratio with respect to stoichiometry of 0.6 were centrally ignited using a laser ignition system at various root-mean-square (RMS) turbulence velocities, where for each explosion, a 3D image of the growing flame was captured at various instants in time. The flame images were quantitatively characterised to yield flame surface area, burned gas volume, reaction progress variable and flame surface density. From the flame surface areas and burned gas volumes, turbulent burning velocities were directly measured from surface area ratios and compared with correlations of turbulent burning velocities made previously at Leeds using 2D flame imaging techniques. This tested the assumption that flame structure observed with 2D imaging techniques gave a good representation of the overall 3D flame structure. An excellent agreement was found between the datasets, indicating that such assumptions were valid under the conditions employed in the present work. The surface area ratio data obtained in the present work were also compared with the predictions of direct numerical simulation (DNS) studies conducted at Cambridge University, where it was found that the experimentally derived results typically exhibited slightly higher flame surface area ratios. This was attributed to the combustion chamber geometry in the DNS study and differences in mixture properties between the two studies, with more work at similar starting conditions required to elucidate the exact cause of the differences. Reaction progress variable was calculated for the 2D laser sheet images obtained in the present work and their 3D counterparts. Although a good agreement was seen where the central laser sheet image in a 3D reconstruction was analysed, disparities were observed when laser sheet images at a fixed position in the combustion bomb was used at high root mean square turbulence velocities. This indicates that the use of fixed position laser sheet imaging techniques, such as particle image velocimetry, are of limited use for highly turbulent flame analysis

Développement d’un cathéter multimodal visant l’étude de la plaque d’athérosclérose

Résumé L’objectif de cette thèse est de concevoir et valider un système d’imagerie par cathéter visant l’étude de la plaque d’athérosclérose. L’innovation repose dans l’intégration de plusieurs modalités d’imagerie dans un seul appareil. En effet, le système combine des techniques d’imagerie anatomique et moléculaire. Ceci permet d’obtenir de l’information riche et diversifiée en temps réel à propos de la plaque d’athérosclérose. Le système conçu permet d’effectuer simultanément l’imagerie ultrasonore intravasculaire (IVUS), l’imagerie photoacoustique intravasculaire (IVPA), ainsi que l’imagerie de fluorescence intravasculaire (NIRF). L’élastographie intravasculaire (IVE) est également possible en post-traitement. L’hypothèse de travail est que la combinaison de l’ensemble de ces techniques d’imagerie permet une étude plus détaillée que l’utilisation d’une seule modalité. L’IVUS est une technique d’imagerie morphologique largement utilisée en recherche clinique qui permet d’obtenir en temps réel des séries de coupes transversales des artères à haute résolution. La paroi artérielle peut être étudiée afin d’identifier certains types de plaque. L’IVUS est la composante principale du système d’imagerie par cathéter conçu dans le cadre de ce projet. Bien que cette technique d’imagerie permette de visualiser l’anatomie générale de l’artère, elle permet difficilement de caractériser les composantes principales d’une plaque vulnérable. Afin de complémenter l’IVUS, des techniques d’imagerie moléculaire, l’IVPA et la NIRF, ont été incorporées au système. Le but est d’étudier le développement de la plaque à un stade d’évolution plus précoce, alors qu’il y a inflammation de la paroi artérielle, mais une accumulation insuffisante de dépôts lipidiques pour être visibles en IVUS. L’imagerie moléculaire a le potentiel de mieux caractériser les plaques vulnérables, qui sont plus susceptibles de subir des complications, telle une thrombose. Une des applications potentielles est l’étude de l’effet de nouveaux médicaments, qui ne se traduit pas nécessairement par un changement anatomique perceptible en IVUS, mais plutôt par un changement au niveau moléculaire. L’IVE permet d’obtenir de l’information quantitative à propos des propriétés élastiques de la paroi artérielle. Elle vise à complémenter l’IVUS en fournissant des propriétés mécaniques de l’artère et en évaluant la vulnérabilité de la plaque d’athérosclérose. La première contribution de ce travail contient une description détaillée du système d’imagerie par cathéter qui a été conçu. Une preuve de concept est ensuite présentée en exposant des résultats sur fantômes exprimant un contraste dans toutes les modalités d’imagerie intégrées au système : l’IVUS, l’IVPA, la NIRF et l’IVE.La deuxième contribution pousse la validation du système plus loin en évaluant le potentiel de détection de la plaque d’athérosclérose in vivo chez le lapin. La combinaison de l’IVUS et de la NIRF, avec injection d’un biomarqueur, soit le vert d’indocyanine (ICG), a permis la détection de certaines plaques et a été comparée avec des techniques d’imagerie ex vivo. La performance ainsi que la reproductibilité des mesures ont été évaluées. La troisième contribution est reliée à la colocalisation des images en IVUS et en NIRF obtenues chez le lapin avec des images ex vivo volumétriques à très haute résolution. Les images ex vivo sont comparées à celles obtenues avec le cathéter, afin de mieux apprécier les capacités et les limites du système d’imagerie in vivo conçu.----------Abstract The aim of this thesis is to design and validate a catheter imaging system for the study of the atherosclerotic plaque. The innovation resides in the integration of multiple imaging modalities in a single device. Indeed, the system combines anatomical and molecular imaging techniques. This allows obtaining rich and diversified information in real time about the atherosclerotic plaque.The designed system allows simultaneously performing intravascular ultrasound imaging (IVUS), intravascular photoacoustic imaging (IVPA) and intravascular fluorescence (NIRF). Intravascular elastography (IVE) is also possible in post-processing. The hypothesis of this work is that the combination of all these imaging techniques allows a more detailed study than the usage of a single modality.IVUS is a morphological imaging technique widely used in preclinical research that allows obtaining in real time series of cross sections of arteries at a high resolution. The artery wall can be studied to identify certain types of plaque. IVUS is the main component of the catheter imaging system designed in this project. While this imaging technique allows visualizing the general anatomy of the artery, it is not well suited for characterizing the main components of a vulnerable plaque. To complement IVUS, molecular imaging techniques, IVPA and NIRF, were incorporated to the system. The goal is to study the development of the plaque at an earlier evolution stage when there is inflammation in the artery wall, but an insufficient accumulation of lipids to be visible in IVUS. Molecular imaging has the potential to better characterize vulnerable plaques, which are more prone to complications, such as thrombosis. One of the potential applications is the study of the effect of new drugs, that doesn’t always translate by an anatomical change perceptible in IVUS, but rather a change at the molecular level. IVE allows obtaining quantitative information about elastic properties of the artery wall. It aims at complementing IVUS by providing mechanical properties of the artery and by evaluating the vulnerability of atherosclerotic plaque. The first contribution to this work contains a detailed description of the designed catheter imaging system. A proof of concept is then presented by exposing results on phantoms with contrasts in all the imaging modalities integrated to the system: IVUS, IVPA, NIRF and IVE. The second contribution further validates the system by evaluating the detection potential of atherosclerotic plaque in vivo on rabbits. The IVUS and NIRF combination, with the injection of a biomarker, indocyanine green (ICG), allowed the detection of certain plaques and was compared to ex vivo imaging techniques. The performance and the reproducibility of the measures were evaluated. The third contribution is related to the colocalisation of IVUS and NIRF images obtained in rabbits with volumetric ex vivo images at a very high resolution. Ex vivo images are compared to the ones obtained with the catheter, in order to better appreciate the capabilities and the limitations of the designed in vivo imaging system

The Historical and Archaeological Analysis of the Swords of La Belle

ABSTRACT This research involves the conservation, historical and archaeological analysis of a cache of swords recovered from the 17th-century French shipwreck La Belle. The central premise of my research model is the incorporation of the theories and methodologies of several convergent disciplines; concentrating on the material and cultural aspect of these weapons, and the technical processes involved with their conservation. The integration of the conservation process and research results with the archaeological evidence, both objects and context, can lead to new methods of archaeological inquiry. The details of materials composition and structure, sequence of processing, properties, performance, or use should define the way modern material culture research is conducted. This research approach seeks to answer such relevant questions as what is the past and current history of the sword types recovered from La Belle? What materials, technology or skilled craft aided in the production of these swords and their individual components? What was the practical and symbolic function of these edged weapons? Subsequently, the data lead to interpretations of the finds and their broader meaning within the context of the shipwreck itself. I am convinced that the research presented in this dissertation will help to facilitate a wider dialogue about swords and other edged weapons among weapons historians and archaeologists. The conservator is dedicated to maintaining the long-term preservation of cultural artifacts through examination, documentation, treatment, and preventive care and research. Conservation is an interdisciplinary field involving knowledge and skills acquired from a number of diverse disciplines in the arts and sciences. As a result, conservators must have a working knowledge of materials technology, chemistry, biology, physics, art history, and archaeology. The results of the case studies discussed in chapter six, though limited in scope, proved most promising, indicating that there are always viable alternatives to the methods and materials used by artifact conservation and preservation. The collaboration between conservators and experts in other related fields, such as conservation science, computer science, radiography, digital imaging, and rapid-prototyping technology is critical to the successful practice of artifact conservation and interpretation

A volumetric technique for fossil body mass estimation applied to Australopithecus afarensis

Fossil body mass estimation is a well established practice within the field of physical anthropology. Previous studies have relied upon traditional allometric approaches, in which the relationship between one/several skeletal dimensions and body mass in a range of modern taxa is used in a predictive capacity. The lack of relatively complete skeletons has thus far limited the potential application of alternative mass estimation techniques, such as volumetric reconstruction, to fossil hominins. Yet across vertebrate paleontology more broadly, novel volumetric approaches are resulting in predicted values for fossil body mass very different to those estimated by traditional allometry. Here we present a new digital reconstruction of Australopithecus afarensis (A.L. 288-1; ‘Lucy’) and a convex hull-based volumetric estimate of body mass. The technique relies upon identifying a predictable relationship between the ‘shrink-wrapped’ volume of the skeleton and known body mass in a range of modern taxa, and subsequent application to an articulated model of the fossil taxa of interest. Our calibration dataset comprises whole body computed tomography (CT) scans of 15 species of modern primate. The resulting predictive model is characterized by a high correlation coefficient (r2 = 0.988) and a percentage standard error of 20%, and performs well when applied to modern individuals of known body mass. Application of the convex hull technique to A. afarensis results in a relatively low body mass estimate of 20.4 kg (95% prediction interval 13.5–30.9 kg). A sensitivity analysis on the articulation of the chest region highlights the sensitivity of our approach to the reconstruction of the trunk, and the incomplete nature of the preserved ribcage may explain the low values for predicted body mass here. We suggest that the heaviest of previous estimates would require the thorax to be expanded to an unlikely extent, yet this can only be properly tested when more complete fossils are available