An investigation was carried out into light scattering by Gaussian rough ice crystals. Gaussian rough crystal geometries were generated using roughness parameters derived from mineral dust grains, which have been reported to be suitable proxies for rough ice crystals. Light scattering data for these geometries was computed using the discrete dipole approximation (DDA) method. Phase functions, 2D scattering patterns, degree of linear polarisation patterns and asymmetry parameters were computed for smooth, moderately rough and highly rough crystals with a variety of orientations and size parameters. A sodium fluorosilicate ice analogue crystal with three partially roughened prism facets was created using focused ion beam (FIB) milling and 2D scattering patterns were collected from it using the small ice detector (SID) 3 cloud probe. It was found that roughness reduces features in the phase function compared to scattering by smooth hexagonal prisms, particularly when the roughness features were horizontally much larger than the wavelength. However, the most effective roughness model also takes account of horizontal features whose size is closer to that of the wavelength. Horizontal features smaller than the wavelength have very little effect.

Un des principaux défis du domaine de la biologie structurale est l'obtention d'informations à haute résolution sur les grandes macromolécules biologiques. En raison de leurs tailles et de leurs flexibilités, les techniques traditionnelles de biologie structurales sont souvent impuissantes. Une des techniques prometteuses est la microscopie à force atomique (AFM). Contrairement à la microscopie optique, l'AFM utilise une sonde mécanique de très faible taille (<10 nm) pour obtenir des informations topographiques sur du matériel biologique isolé et déposé sur des surfaces ultras plates. L'objectif du travail de thèse est de développer les outils informatiques pour permettre la modélisation de grandes macromolécules au niveau atomique tout en intégrant des contraintes topologiques obtenues par l'imagerie AFM. À partir d'images AFM de hauteur, à haute résolution, un protocole d'assemblage de domaines protéiques a été mis au point. Il utilise une recherche exhaustive dans l'espace tridimensionnel réel de toutes les orientations possibles des domaines de la macromolécule à modéliser qui respectent les contours imposés par l'image AFM. Un jeu de contraintes de distance entre chacun des domaines permet un premier tri des modèles candidats. Un classement final est attribué à chaque modèle selon un score appelé EFactor, estimateur de la ressemblance entre la surface topographique expérimentale et celle du modèle. Le protocole a été validé sur le système modèle que sont les anticorps. Il a été également utilisé pour reconstruire une particule virale (virus de la mosaïque du tabac) et assembler la structure tétramérique de la protéine membranaire l'aquaporine Z. / A major challenge in the field of structural biology is to obtain high-resolution information on the major biological macromolecules. Because of their size and their flexibility, the traditional techniques of structural biology are often powerless. One of the promising techniques is atomic force microscopy (AFM). Unlike optical microscopy, AFM uses a mechanical probe of very small size (<10 nm) to obtain topographical information on isolated biological material deposited on ultra flat surfaces. The aim of the thesis was to develop tools to enable the modeling of large macromolecules at the atomic level while incorporating topological constraints obtained by AFM imaging. Using high resolution AFM height images, a protocol for assembling protein domains has been developed. It uses an exhaustive search in real three-dimensional space of all possible orientations of the macromolecule's domains respecting the boundaries imposed by the AFM topographical image. A set of distance constraints between each of the domains allows an initial screening of candidate models. A final ranking is assigned to each model according to a score called EFactor, estimator of the similarity between the experimental topography and the model. The protocol was validated on model systems that are antibodies. It was also used to reconstruct a virus particle (tobacco mosaic virus) and assemble the tetrameric structure of the membrane protein aquaporin Z.

Enzymes and biochemical mechanisms essential to survival are under extreme selective pressure and are highly conserved through evolutionary time. We applied this evolutionary concept to barnacle cement polymerization, a process critical to barnacle fitness that involves aggregation and cross-linking of proteins. The biochemical mechanisms of cement polymerization remain largely unknown. We hypothesized that this process is biochemically similar to blood clotting, a critical physiological response that is also based on aggregation and cross-linking of proteins. Like key elements of vertebrate and invertebrate blood clotting, barnacle cement polymerization was shown to involve proteolytic activation of enzymes and structural precursors, transglutaminase cross-linking and assembly of fibrous proteins. Proteolytic activation of structural proteins maximizes the potential for bonding interactions with other proteins and with the surface. Transglutaminase cross-linking reinforces cement integrity. Remarkably, epitopes and sequences homologous to bovine trypsin and human transglutaminase were identified in barnacle cement with tandem mass spectrometry and/or western blotting. Akin to blood clotting, the peptides generated during proteolytic activation functioned as signal molecules, linking a molecular level event (protein aggregation) to a behavioral response (barnacle larval settlement). Our results draw attention to a highly conserved protein polymerization mechanism and shed light on a long-standing biochemical puzzle. We suggest that barnacle cement polymerization is a specialized form of wound healing. The polymerization mechanism common between barnacle cement and blood may be a theme for many marine animal glues. / Dissertation

Degenerative disorders of the rotator cuff tendons account for nearly 75% of all shoulder pain, causing considerable pain and morbidity. Given the strong correlation between age and tendinopathy, and unprecedented population aging, these disorders will become increasingly prevalent. Improved understanding of tendon degeneration will guide the development of future diagnostic and treatments, and is therefore urgently needed. However, the aetiology and pathology of rotator cuff tendinopathy remain unclear. The complicated mechanical environment of the rotator cuff is hypothesised to influence the susceptibility of the tendons to degeneration and tearing. Studies have reported biological adaptations in torn cuff tendons indicative of increased compressive loading within the tendon. The material adaptations of healthy and degenerative cuff tendons are largely unreported but will provide further insight into the role of the mechanical environment in rotator cuff aetiology and pathology. This thesis examined the material adaptations of healthy and diseased tendons to explore the role of mechanical loading in rotator cuff pathology. The material adaptations of healthy animal tendons, and healthy and delaminated human cadaveric rotator cuff tendons, in response to different loading environments were characterised. The effects of age, tears, steroid injection and subacromial decompression surgery on the structural adaptations of human cuff tendons were also studied, as was the effect of tendon cell proliferation on the mechanical properties and degradation behaviour of collagen scaffolds. Loading environment significantly affected the structural adaptations of healthy tendons. Regions exposed to compressive and shear strains exhibited thinner fibres, shorter crimp lengths and thinner, less aligned fibrils compared with regions exposed to tensile strains alone. In healthy rotator cuff tendons, the inhomogeneous loading environment produced topographically inhomogeneous structural adaptations. The tendons of a delaminated rotator cuff exhibited less topographical variation in properties and thinner, less aligned fibrils compared with healthy cuff tendons. Torn cuff tendons exhibited thinner fibrils and shorter crimp lengths compared with control samples. These adaptations were identifiable early in the disease progression, and neither steroid injection nor subacromial decompression surgery significantly influenced these adaptations at seven weeks post‐treatment. Significant correlations between decreasing dimensions and increasing tear size were found when age was included as a confounding factor, reflecting the importance of age and tear size in determining the material properties of tendons. Tendon cell proliferation influenced the mechanical properties and degradation behaviour of the collagen scaffolds, emphasising the integral role of cells in the functional adaptation of biological materials. These results demonstrate the effect of mechanical environment on the material adaptations of tendons. They also indicate the importance of the complicated mechanical environment experienced by the rotator cuff tendons in predisposing the tendons to degeneration and tearing. The observed material adaptations of degenerative and torn tendons suggest that rotator cuff pathology is associated with increased levels of compressive and/or shear strains within the tendon. These changes begin early in the disease progression and neither steroid injection nor sub‐acromial decompression surgery are capable of reversing the changes in the timeframe investigated. These findings highlight the urgent clinical need for pre‐rupture diagnostic techniques for the detection of early pathological changes in the rotator cuff. They also emphasize the requirement for new intervention strategies that restore the healthy mechanical environment and reverse early pathological adaptations in order to prevent catastrophic failure of the tendons.

La physique mésoscopique est actuellement dominée par des mesures de transport permettant d'extraire les propriétés électroniques globales des systèmes étudiés. La spectroscopie tunnel permet d'avoir un accès direct à la densité d'états locale (LDOS). Nous pouvons donc sonder les évolutions spatiale des propriétés électroniques notamment à l'interface entre 2 matériaux possédant des propriétés différentes. Au cours de cette thèse, nous avons développé un microscope à sonde locale qui combine microscopie à force atomique (AFM) et microscopie à effet tunnel (STM) et qui fonctionne à 100mK. L'AFM permet de localiser un nanocircuit unique sur un substrat isolant grâce à un Length Extension Resonator (LER). Nous pouvons ensuite mesurer la spectroscopie tunnel locale du nanocircuit conducteur. La résolution énergétique obtenue avec ce système est de 70µeV. Nous avons montré la faisabilité expérimentale d'une telle étude en mesurant l'effet de proximité sur un îlot de cuivre (métal normal) connecté par deux électrodes supraconductrices en aluminium à l'équilibre, hors-équilibre et sous champ magnétique. Nous avons également mesuré la LDOS du graphène sur Ir(111) qui présente des propriétés proches du graphène intrinsèque avec un dopage de type p de l'ordre de 0.34eV. Nous avons observé que ce dopage fluctue spatialement avec la présence de poches de charges avec une taille typique de l'ordre de 9nm. Ces observations sont similaires à des résultats déjà reportés sur des systèmes graphène sur SiO2. Cependant, le profil des poches que nous avons mesuré montre une forte corrélation avec la topographie due à une modulation du potentiel électrostatique induit par le métal sous le graphène. Une analyse plus fine a permis également de réveler la présence d'interférences de quasiparticules se traduisant par une inhomogénéité de la DOS. La taille typique des structures est de l'ordre de la longueur d'onde de Fermi avec une dépendance linéaire avec l'énergie selon E=ħvFk avec vF = 8.3±0.7x10^5m/s proche de la vitesse de Fermi théorique de 1x10^6m/s. Cela met évidence la présence de diffusion intravallée et prouve le caractère de fermions de Dirac sans masse des particules du graphène sur Ir(111). / Mesoscopic physic is currently dominated by transport measurements that extract overall electronic properties of the studied sytstems. Tunneling spectroscopy gives access to the local density of states (LDOS). Hence, we can probe the spatial evolution of the electronic properties especially at the interface between two materials with different properties. During this thesis, we built-up a scanning probe microscope at 100mK that combine both atomic force microscopy (AFM) and scanning tunneling microscopy (STM). AFM helps to locate a single nanocircuit on insulating substrate thanks to a Length Extension Resonator (LER). We can then measure the tunneling spectroscopy on the conductive nanocircuit. The energy resolution of the system is of 70µeV. We show the experimental proof of such a system by measuring the proximity effect in copper island (normal island) connected by two superconducting leads in aluminum at equilibrium, out of equilibrium and with a magnetic field. We also measured the LDOS of graphene on Ir(111) that displays electronic properties close to the one of intrinsic graphene with p-doping of about 0.34eV. We observe spatial inhomogeneities of this doping forming charge puddles with a typical size af about 9nm. Those observations are close to previous results reported on graphene on SiO2. However, the profile of the measured puddles shows a strong correlation with the topography due to the modulation of the electrostatic potential induced by the metal below the graphene. A closer look to the DOS shows quasiparticles interferences forming DOS inhomogeneities. The typical size of the DOS structures is of the order of the Fermi wavelength with a linear dependence with energy as E=ħvFk with vF = 8.3±0.7x10^5m/s which is close to the theoretical Fermi velocity of 1x10^6m/s. This point out the presence intravalley scattering and demonstrate the fact that particles in graphene on Ir(111) are Dirac fermions without mass.

La formation de minéraux carbonatés magnésiens par carbonatation de silicates de magnésium constitue une option pérenne et sûre de séquestration du dioxyde de carbone, dont les estimations les plus optimistes indiquent qu'elle pourrait participer significativement à l'effort global de réduction des émissions de CO2 d'origine anthropique. À ce jour cependant, ces réactions chimiques se heurtent à de fortes limitations cinétiques, dont l'origine réside dans la faible réactivité des phases minérales en présence. Alors que de nombreuses études se sont intéressées à la phase de dissolution des silicates magnésiens, souvent considérée comme l'étape limitante du processus, ce travail de thèse prend le parti d'étudier expérimentalement les mécanismes et les vitesses de formation des minéraux carbonatés magnésiens qui constituent le produit final des réactions de carbonatation. Dans une première partie, nous nous intéressons à l'influence sur la cinétique de précipitation de la magnésite (MgCO3) de ligands organiques connus pour accélérer la vitesse de dissolution des silicates magnésiens : oxalate, citrate et EDTA. Sur la base d'expériences menées en réacteur à circulation entre 100 et 150°C, nous montrons que ces ligands diminuent significativement la vitesse de précipitation de la magnésite en raison (1) de la complexation des cations Mg2+ en solution, estimée grâce à une base de données thermodynamiques établie à partir d'une revue critique de la littérature, et (2) de l'adsorption des ligands au niveau d'un nombre limité de sites à la surface du minéral, avec pour conséquence une diminution de la constante cinétique de précipitation. Cette inhibition de la cristallisation de la magnésite est maximale dans le cas du citrate. L'utilisation de la microscopie à force atomique en conditions hydrothermales nous a permis de sonder l'origine de l'inhibition observée. Elle nous indique en particulier que le citrate et l'oxalate agissent sur le processus de croissance cristalline à la surface de la magnésite, modifiant la forme des îlots de croissance ainsi que la fréquence de génération des marches cristallines par le processus de croissance en spirale. Nous montrons que ces deux ligands agissent au niveau de sites surfaciques différents, probablement fonction de leurs structures et de leurs propriétés chimiques. Nous proposons que l'inhibition plus forte exercée par le citrate sur le processus de croissance de la magnésite provienne d'une interaction préférentielle du ligand avec les marches cristallines aigües, qui limitent le processus de croissance en spirale de par leur faible vitesse d'avancement. La description de ces phénomènes à l'aide d'une loi cinétique empirique permet d'effectuer une modélisation numérique simple de la carbonatation de la forstérite (Mg2SiO4) en présence de ligands à 120°C, qui suggère que les ligands organiques étudiés ont une influence défavorable sur le processus global de carbonatation de ce minéral .La troisième et dernière partie de ce travail s'intéresse à la solubilité et à la cinétique de précipitation d'un carbonate de magnésium hydraté, l'hydromagnésite, entre 25 et 75°C. Les résultats obtenus indiquent que la vitesse de croissance de l'hydromagnésite excède largement celle de la magnésite à affinité chimique comparable, tandis que l'énergie d'activation du processus est beaucoup plus faible que celle de la magnésite. Ces données cinétiques originales confirment que la déshydratation des ions Mg2+ est l'étape limitante de la précipitation de la magnésite en solution aqueuse. Toutefois, du fait de sa solubilité plus forte, l'hydromagnésite n'est susceptible de se former plus rapidement que la magnésite qu'à pH alcalin et basse température. Elle ne peut à ce titre constituer un palliatif à la faible vitesse de précipitation de la magnésite lors de la carbonatation des silicates magnésiens / Forming magnesium carbonate minerals through carbonation of magnesium silicates has been proposed as a safe and durable way to store carbon dioxide, with a possibly high potential to offset anthropogenic CO2 emissions. To date however, chemical reactions involved in this process are facing strong kinetic limitations, which originate in the low reactivity of both Mg-silicates and Mg-carbonates. Numerous studies have focused on the dissolution of Mg-silicates, under the questionable hypothesis that this step limits the whole process. This thesis work focuses instead on the mechanisms and rates of formation of magnesium carbonates, which are the final products of carbonation reactions. The first part of the work is dedicated to studying the influence on magnesite precipitation kinetics of three organic ligands known to accelerate Mg-silicates dissolution rates : oxalate, citrate and EDTA. With help of mixed-flow reactor experiments performed between 100 and 150°C, we show that these ligands significantly reduce magnesite growth rates, through two combined mechanisms: (1) complexation of Mg2+ cations in aqueous solution, which was rigorously estimated from a thermodynamic database established through a critical review of the literature, and (2) adsorption of ligands to a limited number of surface sites, leading to a decrease of the precipitation rate constant. The observed growth inhibition is maximal with citrate. We then used hydrothermal atomic force microscopy to probe the origin of the documented growth inhibition. Our observations show that citrate and oxalate interact with the crystal growth process on magnesite surface, modifying the shape of growth hillocks as well as the step generation frequency through spiral growth. We also show that the ligands adsorb preferentially on different kink-sites, which is probably related to their different structures and chemical properties. We propose that the stronger magnesite growth inhibition caused by citrate is related to a preferential interaction of the ligand with acute steps on the magnesite surface, which limit the spiral growth process through their low advancement rate. The description of these processes with an empirical rate law allows performing simple numerical simulations of forsterite carbonatation at 120°C in the presence of the ligands. We thus demonstrate that the use of the investigated ligands would clearly be detrimental to the carbonation of forsterite. The third and last part of this work deals with hydromagnesite solubility and growth kinetics between 25 and 75°C. The obtained results show that hydromagnesite growth rates largely exceed magnesite rates at comparable chemical affinity, while the activation energy of the process is much smaller than for magnesite. This original kinetic dataset thus confirms the long-standing hypothesis that Mg2+ dehydration is the rate-limiting step for Mg-carbonate precipitation from aqueous solution. However, due to its higher solubility, hydromagnesite may grow more quickly than magnesite only at low temperature and alkaline pH. Thus, it may not provide a solution to the sluggish precipitation kinetics of magnesite during Mg-silicates carbonation

The thesis focuses on the development of instruments used for surfaces and nanostructures characterization. Individual techniques of scanning probe microscopy provide different information of the sample surface. The resolution of scanning probe microscopy, providing 3D topography information, reaches subnanometer values or even an atomic level. Therefore, the scanning probe microscopy is one of the most employed method in the field of nanotechnology. The thesis describes the details of development of two scanning probe microscopes intended for measurement under ultra high vacuum conditions. As for the first one, many changes were proposed leading to its better variability, extended functionality and increased user comfort. The second microscope is being design with the aim of its combination with other analytic techniques, especially with scanning electron microscopy. An integral part of scanning probe microscopes is a precise positioning system for navigation of the probe to the selected site. Therefore, the thesis also deals with the development of linear piezoceramic actuators used not only in the ultra high vacuum compatible microscopes but also as a general purpose nanomanipulators.

Die eingereichte Dissertation beschäftigt sich mit der messtechnischen Erfassung sowie der Modellierung von Haftkräften zwischen rauen Oberflächen. Dabei wurden durch Variation von Flüssigkeiten sowie dem Nutzen beschichteter Oberflächen verschiedene Benetzungseigenschaften eingestellt und untersucht. Zusätzlich wurden neben dem Kontaktwinkel der untersuchten Systeme die freien Ober- und Grenzflächenenergien bestimmt und mit den Kräften korreliert. Es zeigte sich, dass Haftkräfte auf rauen Oberflächen stets über mehrere Größenordnungen verteilt vorliegen. Die Beschreibung der ermittelten Verteilungen ist dabei entweder durch statistischer Funktionen oder zumindest teils auch durch eine im Rahmen der Arbeit entwickelten Modellierung möglich. Weiterhin zeigte sich, dass eine Unterteilung in verschiedene Haftmechanismen (durch Kapillarbrücken oder van der Waals- sowie polare Wechselwirkungen) vorgenommen werden kann. Kapillarbrücken bilden dabei die größten Kräfte aus. Sie entstehen auf Grund nanoskaliger Blasen (Nanobubbles), welche vor allem auf schlecht benetzenden Oberflächen existieren.

Doctor of Philosophy / Department of Chemistry / Duy H. Hua / The objectives of this research project were to (i) synthesize different bicyclic and tricyclic pyrone and pyridinone compounds; (ii) study the mechanism of action of these compounds in solution as anti-Aβ (amyloid β) agents using different biophysical techniques; and (iii) study the biological activity of pyrone compounds for the counteraction of Aβ toxicity using MC65 cells, a human neuroblastoma cell line and 5X- familial Alzheimer’s disease (5X FAD, a transgenic mice with five different mutations) mice. A series of tricyclic pyrone and pyridinone compounds were investigated. The tricyclic pyrones and pyridinones were synthesized utilizing a condensation reaction between cyclohexenecarboxaldehye (25) and 4-hydroxy-6-methyl-2-pyone (24) or 4-hydroxy-6-methyl-2-pyridinone (51), respectively. A tricylic pyrone molecule CP2 (2, code name) was synthesized and has an adenine base unit attached to the pyrone core. For structure activity relationship (SAR) studies, the adenine group of CP2 was replaced with other DNA base units (thymine, cytosine and guanine) and various heterocyclic moieties. Since nitrogen containing compounds often exhibit increased bioactivity and brain-penetrating abilities, oxygen atom (O5’) was displaced with a nitrogen atom in the middle ring of the tricyclic pyrone. A condensation reaction of pyrone 51 and 25 was carried out to give the linear pyranoquinoline (52) and the L-shaped pyranoisoquinoline (53). The neurotoxicity of amyloid-β protein (Aβ) is widely regarded as one of the fundamental causes of neurodegeneration in Alzheimer’s disease (AD). Recent studies suggest that soluble Aβ oligomers rather then protofibrils and fibrils may be the primary toxic species. Different biophysical techniques including atomic force microscopy (AFM), circular dichroism (CD), surface plasmon resonance (SPR) spectroscopy, and protein quantification assays were used to study the mechanism of aggregation of Alzheimer Aβ peptide in solution. In search of potentially bioactive compounds for AD therapies, MC65 cell line was used as a screening model. Different tricyclic pyrone and pyridinone compounds protect MC65 cells from death. We studied the efficacy of CP2 in vivo by treatment of 5X FAD mice, a robust Aβ42-producing animal model of AD, with a 2-week course of CP2, which resulted in 40% and 50% decreases in non-fibrillar and fibrillar Aβ species respectively.

Doctor of Philosophy / Department of Physics / Bruce M. Law / Three diverse first author surfaces science experiments conducted by Sean P. McBride 1-3 will be discussed in detail and supplemented by secondary co-author projects by Sean P. McBride, 4-7 all of which rely heavily on the use of an atomic force microscope (AFM). First, the slip length parameter, b of liquids is investigated using colloidal probe AFM. The slip length describes how easily a fluid flows over an interface. The slip length, with its exact origin unknown and dependencies not overwhelming decided upon by the scientific community, remains a controversial topic. Colloidal probe AFM uses a spherical probe attached to a standard AFM imaging tip driven through a liquid. With the force on this colloidal AFM probe known, and using the simplest homologous series of test liquids, many of the suspected causes and dependencies of the slip length demonstrated in the literature can be suppressed or eliminated. This leaves the measurable trends in the slip length attributed only to the systematically varying physical properties of the different liquids. When conducting these experiments, it was realized that the spring constant, k, of the system depends upon the cantilever geometry of the experiment and therefore should be measured in-situ. This means that the k calibration needs to be performed in the same viscous liquid in which the slip experiments are performed. Current in-situ calibrations in viscous fluids are very limited, thus a new in-situ k calibration method was developed for use in viscous fluids. This new method is based upon the residuals, namely, the difference between experimental force-distance data and Vinogradova slip theory. Next, the AFM’s ability to acquire accurate sub nanometer height profiles of structures on interfaces was used to develop a novel experimental technique to measure the line tension parameter, τ, of isolated nanoparticles at the three phase interface in a solid-liquid-vapor system. The τ parameter is a result of excess energy caused by the imbalance of the complex intermolecular forces experienced at the three phase contact line. Many differences in the sign and magnitude of the τ parameter exist in the current literature, resulting in τ being a controversial topic.