Interactions between hydrophobic surfaces at short separation distances (at the nanometer scale) are very important in a number of industrial applications. For example, in the froth flotation mineral separation process it is the interaction between the hydrophobic particle and the bubble which is paramount in separating the valuable minerals from the gangue. A number of studies, most notably using the atomic force microscope (AFM) and the surface force apparatus (SFA) have found the existence of a long range hydrophobic attractive force between hydrophobic surfaces that cannot be explained by classical colloidal science theories. In many cases, this force is an artefact due to the accumulation of sub-microscopic bubbles, the so called nanobubbles, at the liquid-hydrophobic solid interface. Thus, what was thought to be a hydrophobic force was actually a capillary force resulting from the gaseous bridge formed from the coalescence of nanobubbles, that is, the nanobubble bridging capillary force (NBCF). It is the purpose of this thesis to provide further insight into the accumulation of soluble gases at the liquid-hydrophobic solid interface and the resulting NBCF. Specifically, this thesis studies these phenomena from a fundamental standpoint and additionally relates the findings to froth flotation mineral separation. A systematic method to measure the NBCF by controlling the size of the gaseous capillary bridge was devised in this thesis. Control of the capillary bridge was achieved by utilising the solvent-exchange method to accumulate nanobubbles at the surface, followed by surface scanning of the colloidal probe over the flat surface to harvest nanobubbles. Thus, the NBCF has been controlled to allow for greater success in modelling the interaction, understanding the geometric parameters of the bridge, observing changes in friction force due to nanobubbles and understanding the influence of ethanol on the force. An outcome of this thesis was the development of a capillary force model which describes the NBCF. The model considers a constant volume and constant contact angle assumption for a gaseous capillary bridge of toroidal geometry. The model was very successful in describing the NBCF at long separation distances (>20nm) for both the approach and retract interactions. The close fitting between the experimental data and the model allowed accurate determinations of the advancing and receding contact angles, bridge geometry and volume. The successful implementation of the capillary force model allowed a link between the bridge volume, and the resulting adhesion to the friction force between hydrophobic solid surfaces in water. Additionally, the model allowed the change from an attractive to a repulsive NBCF to be described by a change from a concave to convex bridge geometry. Thus, this thesis has added considerable knowledge to the fundamental aspects of nanobubbles and the NBCF. The final chapters of this thesis utilised the knowledge gained from the fundamental studies to understand the influence of nanobubbles on flotation. In the first study, the influence of NaCl concentration on the morphology of gaseous domains on a graphite surface is discussed in relation to the increased recovery of coal in saline water. In the second study, methanol treatment of a ZnS ore was found to increase the floatability due to slime removal and the artificial formation of nanobubbles.

Neste trabalho, se pretende caracterizar a morfologia de filmes finos poliméricos por meio de técnicas de processamento de imagens, utilizando principalmente a geometria computacional e técnicas de classificação de padrões. Os objetivos principais foram quantificar as grandezas geométricas das estruturas observadas nos filmes finos e descrever padrões de superfície formados nestes filmes. Foram estudadas imagens obtidas por microscopia de força atômica (AFM) de amostras de filmes finos SEBS [poliestireno-poli(etileno-co-butileno)-poliestireno], depositados sobre um substrato de mica por técnicas de imersão. Os filmes finos SEBS são considerados de grande interesse devido à formação de estruturas auto-organizadas na escala nanométrica. A caracterização e a obtenção da morfometria dos filmes são de relevância neste trabalho, pois contribuem para o entendimento da dinâmica de formação destes padrões nas nanoestruturas estudadas. Foram analisadas diferentes morfologias, como forma de gotículas com anéis concêntricos e forma de tiras e pontos regularmente espaçados. Os resultados obtidos permitem caracterizar os padrões observados. / In this work, we intend to characterize the morphology of polymer thin films by techniques of image processing, mainly using computational geometry and pattern classification. The main objectives were to quantify the geometrical structures observed in thin films and describe surface patterns formed in these films. Were studied images obtained by atomic force microscopy (AFM) of SEBS [polystyrene-poly(ethylene-co-butylene)-polystyrene] thin films samples, deposited on a mica substrate by dip-coating technique . SEBS thin film polymers have great interest due to the formation of self-organized structures on the nanometer scale. The characterization and obtaining measurements of the morphology of the thin films are of relevance in this work, because they contribute to the understanding of the formation dynamics of these patterns in nanostructures studied. We analyzed different morphologies, such as droplets form with concentric rings and stripe and regularly spaced points forms. The results allow to characterize the observed patterns.

Molecules adsorbed on two-dimensional (2D) materials can show interesting physical and chemical properties. This thesis presents scanning probe microscopy (SPM) investigation of emerging 2D materials, molecular nanostructures on 2D substrates at the nanometer scale, and biophysical processes on the biological membrane. Two main techniques of nano-probing are used: scanning tunneling microscopy (STM) and atomic force microscopy (AFM). The study particularly emphasizes on self-assembled molecules on flat 2D materials and quasi-1D wrinkles. First, we report the preparation of novel 1D C60 nanostructures on rippled graphene. Through careful control of the subtle balance between the linear periodic potential of rippled graphene and the C60 surface mobility, we demonstrate that C60 molecules can be arranged into a 1D C60 chain structure of two to three molecules in width. At a higher annealing temperature, the 1D chain structure transitions to a more closely packed, quasi-1D hexagonal stripe structure. The experimental realization of 1D C60 structures on graphene is, to our knowledge, the first in the field. It could pave the way for fabricating new C60/graphene hybrid structures for future applications in electronics, spintronic and quantum information. Second, we report a study on nano-morphology of potential operative donors (e.g., C60) and acceptors (e.g., perylenetetracarboxylic dianhydride, aka. PTCDA) on wrinkled graphene supported by copper foils. We realize sub-monolayer C60 and PTCDA on quasi-1D and quasi-2D real periodic wrinkled graphene, by carefully controlling the deposition parameters of both molecules. Our successful realization of acceptor-donor binary nanostructures on wrinkled graphene could have important implications in future development of organic solar cells. Third, we report an STM and spectroscopy study on atomically thin transition-metal dichalcogenides (TMDCs) material. TMDCs are emerging 2D materials recently due to their intriguing physical properties and potential applications. In particular, our study focuses on molybdenum disulfide (MoS2) mono- to few-layers and pyramid nanostructures synthesized through chemical vapor deposition. On the few-layered MoS2 nanoplatelets grown on gallium nitride (GaN) and pyramid nanostructures on highly oriented pyrolytic graphite (HOPG), we observe an intriguing curved region near the edge terminals. The measured band gap in these curved regions is consistent with the direct band gap in MoS2 monolayers. The curved features near the edge terminals and the associated electronic properties may contribute to understanding catalytic behaviors of MoS2 nanostructures and have potential applications in future electronic devices and catalysts based on MoS2 nanostructures. Finally, we report a liquid-cell AFM study on the endosomal protein sorting process on the biological lipid membrane. The sorting mechanism relies on complex forming between Tom1 and the cargo sorting protein, Toll interacting protein (Tollip). The induced conformational change in Tollip triggers its dissociation from the lipid membrane and commitment to cargo trafficking. This collaborative study aims at characterizing the dynamic interaction between Tollip and the lipid membrane. To study this process we develop the liquid mode of AFM. We successfully demonstrate that Tollip is localized to the lipid membrane via association with PtdIns3P (PI(3)P), a major phospholipid in the cell membrane involved in protein trafficking. / Ph. D. / Two-dimensional (2D) materials are layered materials with thickness of single atom or few atoms. The ultimate thickness leads to novel properties that are useful for a wide range of applications in photovoltaics, electronics and quantum information. In order to explore these properties at the nanometer scale, we used scanning probe techniques, i.e., scanning tunneling microscopy (STM) and atomic force microscopy (AFM), to perform comprehensive investigations on these emerging materials. 2D materials, such as graphene and atomically thin transition-metal dichalcogenides (TMDCs), are promising candidates for building economic, safe and mechanically flexible solar cells with desirable optical and electronic properties, e.g. tunable sunlight absorption. The first part of the thesis focuses on graphene, a single-atom-thick carbon sheet. We deposited key components in organic solar cells, such as perylenetetracarboxylic dianhydride (PTCDA) and C₆₀ molecules, on graphene. On these materials we observed various novel nanostructures, like quasi-1D C₆₀ nanochains. The second part of the thesis focuses on mono- to few-layered MoS₂, which can be used as an active layer in high-efficiency solar cells. Our study has important implications in improving efficiency of organic solar cells in the future. In the final part of the thesis, we extended our subject to the biological lipid membrane, a 2D material critical in biology, and biophysical processes occurring on the membrane. Using a liquid-cell AFM, we investigated the endosomal protein sorting process on the biological membranes. Our study contributes to understanding of the interactions between the adaptor proteins and cell membranes in the protein sorting process that guides proteins to their proper destinations.

<p>Heteroepitaxial SiGeC layers have attracted immenseattention as a material for high frequency devices duringrecent years. The unique properties of integrating carbon inSiGe are the additional freedom for strain and bandgapengineering as well as allowing more aggressive device designdue to the potential for increased thermal budget duringprocessing. This work presents different issues on epitaxialgrowth, defect density, dopant incorporation and electricalproperties of SiGeC epitaxial layers, intended for variousdevice applications.</p><p>Non-selective and selective epitaxial growth of Si_1-x-yGe_xC_y(0≤x≤30, ≤y≤0.02) layershave been optimized by using high-resolution x-ray reciprocallattice mapping. The incorporation of carbon into the SiGematrix was shown to be strongly sensitive to the growthparameters. As a consequence, a much smaller epitaxial processwindow compared to SiGe epitaxy was obtained. Differentsolutions to decrease the substrate pattern dependency (loadingeffect) of SiGeC growth have also been proposed. The key pointin these methods is based on reduction of surface migration ofthe adsorbed species on the oxide. In non-selective epitaxy,this was achieved by introducing a thin silicon polycrystallineseed layer on the oxide. The thickness of this seed layer had acrucial role on both the global and local loading effect, andon the epitaxial quality. Meanwhile, in selective epitaxy,polycrystalline stripes introduced around the oxide openingsact as migration barriers and reduce the loading effecteffectively. Chemical mechanical polishing (CMP) was performedto remove the polycrystalline stripes on the oxide.</p><p>Incorporation and electrical properties of boron-doped Si_1-x-yGe_xC_ylayers (x=0.23 and 0.28 with y=0 and 0.005) with aboron concentration in the range of 3x10¹⁸-1x10²¹atoms/cm3 have also been investigated. In SiGeClayers, the active boron concentration was obtained from thestrain compensation. It was also found that the boron atomshave a tendency to locate at substitutional sites morepreferentially compared to carbon. These findings led to anestimation of the Hall scattering factor of the SiGeC layers,which showed good agreement with theoretical calculations.</p><p><b>Keywords:</b>Silicon germanium carbon (SiGeC), Epitaxy,Chemical vapor deposition (CVD), Loading effect, Highresolution x-ray diffraction (HRXRD), Hall measurements, Atomicforce microscopy (AFM).</p>

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.

A oxidação anódica local utilizando o Microscópio de Força Atômica (AFM - Atomic Force Microscopy) foi investigada aplicando-se uma tensão negativa entre sonda de nitreto de silício e superfícies de Si. Todas as amostras foram limpas em uma solução de 1 NH4OH (30%): 1H2O2 (38%): 4H2O(DI) a 80ºC conhecida na literatura como SC1 (Standard Cleaning 1) ou, alternativamente, uma imersão em solução diluída de ácido hidrofluorídrico seguido de SC1 ou fervura em álcool isopropílico. As nano-oxidações consistiram de padrões quadrados localizados de óxido com área de 0,25 µm² e foram obtidos através do crescimento de linhas paralelas com espaço e comprimento interlinear constante (<2 nm) e várias varreduras dos quadrados em uma mesma área. Das análises de AFM, foram obtidos perfis transversais e 3D, os quais foram empregados na obtenção da espessura do óxido como função da tensão aplicada, número de varreduras e intervalo de tempo após a limpeza SC1. Foi observado que a espessura aumenta com a tensão negativa aplicada e com o número de varreduras. Também foram realizadas simulações para levantar as distribuições de tensão e de campo elétrico no sistema sonda-ar-silício ou sonda-ar-óxido-silício(substrato). Observou-se uma oxidação local assistida por um alto campo elétrico capaz de induzir difusão iônica local finita na extremidade da sonda. Foi simulado também o efeito das diferentes terminações de sonda do AFM, circular ou pontiaguda, no campo elétrico e na queda de tensão. Foram também realizadas oxidações com sondas recobertas com ouro em superfícies de Si precedidas de imersão simples em solução de ácido hidrofluorídrico seguido ou não do procedimento de limpeza SC1. Por fim, análises de absorção por infravermelho (FTIR) foram realizadas em superfícies de Si oxidadas por AFM para analisar a estrutura dos óxidos anódicos obtidos. A oxidação anódica utilizando sondas de nitreto de silício ocorre apenas após pré-limpeza terminada com SC1, sendo catalisada pelos altos campos elétricos (_ 106 V/cm), tendo como elementos reagentes, as espécies H2O adsorvidas e o óxido nativo hidrolisado na superfície após a etapa de limpeza SC1. / Local anodic oxidation of silicon using Atomic Force Microscopy (AFM) was investigated by applying a negative voltage between silicon nitride tip and Si surfaces. All samples were cleaned with an ammonium-based solution known in literature as standard cleaning 1 (SC1) or a dip in a diluted hydrofluoric acid solution followed by SC1 or, also, boiling in isopropyl alcohol. Localized squares patterns of oxide, 0.25 µm² in area, were formed by growing parallel lines with constant interlinear spacing and length and several scans in the same area. From AFM analysis with non-biased tip, it was obtained 3D and section profiles, which were used to obtain the oxide thickness as a function of the applied voltage, number of scans and interval of time after SC1 cleaning. It was noteworthy that thickness increases with the applied negative voltage and with the number of scans. Simulations were performed in order to model voltage and electric field distributions of the system tip-air-silicon or tip-air-oxide-silicon(substrate) indicating a local oxidation assisted by high electrical field and local ionic diffusion of species. It was simulated the effect of tip termination, circular or sharpen, on the electric field and voltage distributions. In addition, oxidations were performed using Au coated tips onto Si surfaces previously dipped in diluted hydrofluoric acid solution followed or not by SC1 cleaning process. Finally, infrared absorption analysis (FTIR) were performed in order to analise the structure of the obtained anodic oxides. The anodic oxidation using silicon nitride tips has occurred only after SC1 precleaning step, being catalized by high electric field (_ 106 V/cm), having as reagents, the adsorbed water species and hydrolized native oxide on the surface after the SC1 cleaning step.

Les mégacaryocytes sont des cellules de la moelle osseuse, à l’origine de la production des plaquettes sanguines. Quand elles arrivent à maturité, elles grossissent et émettent des prolongements de cytoplasme à travers la paroi des vaisseaux irriguant la moelle. Dans la circulation sanguine, ces prolongements, soumis aux forces de l’écoulement, s’allongent et se rompent pour former des plaquettes. Des techniques microfluidiques capables de produire des plaquettes in vitro existent et sont une alternative prometteuse au don. Mais le rendement reste à améliorer. Pour cela, il est nécessaire de mieux comprendre la fragmentation des mégacaryocytes en plaquettes. Ce travail de doctorat s’inscrit dans ce contexte et sera développé en deux axes principaux dans ce manuscrit. Dans une première partie nous développons une méthode pour trier des cellules en fonction de leur déformabilité, afin de savoir si les propriétés mécaniques d’un mégacaryocyte sont liées à leur stade de maturité. La méthode a d’abord été mise au point avec des microcapsules. Leurs propriétés mécaniques sont déterminées par analyse inverse à partir de la mesure de leur forme en écoulement dans des constrictions droites. Puis le dispositif utilisé a été miniaturisé pour s’adapter à la taille des cellules. Pour la caractérisation de leurs propriétés mécaniques, deux outils ont été utilisés: l’analyse inverse et la microscopie à force atomique sans pointe. Une deuxième partie porte sur l’étude de l’élongation et de la rupture de mégacaryocytes soumis écoulement. Nous avons quantifié les variations spatiotemporelles du taux d’élongation et développé un protocole d’ablation laser pour étudier les mécanismes de rupture de cellules en élongation. / When they mature in the bone marrow, the precursors of platelets, called megakaryocytes, grow and extend protrusions able to join blood circulation. There these protrusions elongate and break into platelets. Microfluidic techniques for in vitro platelet production represent a promising alternative to donation. In order to enhance platelet production and match the needs of clinical applications such as transfusion, we need to better understand the fragmentation of megakaryocytes into platelets. Our contribution will be described in this manuscript in two main axes. First, in order to know if mechanical properties of megakaryocytes can indicate their maturity stage, we develop a cell sorting method based on deformability. The method is first validated with microcapsules. Their mechanical properties are determined by inverse analysis from their shape under flow in straight microchannels. Then the device is downscaled. The characterization of cell mechanical properties are performed using inverse analysis and tipless atomic force microscopy. Second, we study megakaryocyte elongation and rupture in a microfluidic device. We quantify the spatial and temporal variations of the elongation rate and develop a laser ablation protocol to trigger and study the rupture of elongating cells.

Les foldamères sont des architectures moléculaires synthétiques repliées, inspirées par les structures et les fonctions des biopolymères naturels. Le repliement est un processus sélectionné par la nature pour contrôler la conformation de sa machinerie moléculaire afin de réaliser des tâches chimiques ou mécaniques. Durant les dix dernières années de recherche sur les foldamères, des oligomères synthétiques, capables d'adopter des conformations repliées bien définies et prévisibles, comme des hélices, ont été proposés. Les progrès récents ont montré que la synthèse chimique par étapes et le design moléculaire basé sur un squelette oligoamide aromatique permettaient de produire des architectures moléculaires repliées de manière hélicoïdale. La forme du squelette et sa rigidité, des préférences conformationnelles locales, des interactions spécifiques entre monomères éloignés dans une séquence, ainsi que l'action de paramètres externes comme le solvant, ou la présence d'ions peuvent être combinés pour induire une tendance au repliement. Ces architectures sont remarquables car elles peuvent donner lieu à des motifs de repliement qui n'ont pas d'équivalent dans les structures des biopolymères naturels. Par exemple, des hélices dont le diamètre varie le long de la séquence, ou des hélices possédant un centre d'inversion du pas, des hélices en chevrons,... ont été rapportées. Alors que les structures de ces molécules hélicoïdales ont été abondamment caractérisées à l'état solide par cristallographie des rayons X, leur comportement en solution, et surtout le comportement dynamique, est très peu connu. Leurs propriétés mécano-chimiques sont quant à elles inconnues à ce jour. L'objectif du projet est de synthétiser différentes molécules synthétiques hélicoïdales de type oligoamide aromatique et d'obtenir une description détaillée de leur conformation dynamique en solution, ainsi que de leurs propriétés mécano-chimiques, par spectroscopie de force sur molécule unique basée sur l'AFM. / Foldamers are artificial folded molecular architectures inspired by the structures and functions of natural biopolymers. Folding is the process selected by nature to control the conformation of its molecular machinery to carry out chemical functions and mechanical tasks, such as en-zyme catalysis, duplication in nucleic acids, force generation,... During the last decade of research on foldamers, synthetic oligomers able to adopt well- defined and predictable folded conformations, such as helices, have been proposed. Recent progress has shown that stepwise chemical synthesis and molecular design based on aromatic oligoamide backbones enable to produce large helically folded molecular architectures. The shape and stiffness of the backbone, local conformational preferences, specific interactions between distant monomers in sequences, as well as the action of external parameters such as the solvent or the presence of ions, can be combine to induce folding tendency. A remarkable aspect of these architectures is that they can give rise to folded patterns that have no in natural counterparts biopolymer structures. For instance, helices whose diameter varies along the se-quence, helices possessing a handedness inversion centre, herringbone helices have been reported. While the structures of these helical molecules have been well characterized in the solid state by X-ray crystallography, much less is known about their dynamic behavior in solution. Their mechanochemical properties are unknown. The objective of the project is to synthesize various helical nanorchitectures based on an oli-goamide aromatic backbone and to obtain a detailed picture of their dynamical conformation in solution, as well as, their mechanochemical properties, by AFM-based single molecule force spectroscopy.

La présence de matière biologique (biofilms) dans les sites de stockage géologique profond, d'éléments toxiques ou encore de l'eau potable des aquifères est maintenant clairement démontrée. Cette biomasse est à l'origine de processus physiques et chimiques qui modifient considérablement la durabilité et la pérennité des sites concernés. Ces processus, principalement de type oxydo-réductif, sont encore mal compris. Ceci est principalement dû aux méthodes d'investigation, principalement macroscopiques, loin de l'échelle micrométrique caractéristique des bactéries. Seules des études, basées sur des méthodes d'investigation locale, peuvent apporter les informations requises. Ainsi, nous avons développé un dispositif expérimental basé sur l'utilisation combinée de la microscopie optique (en transmission), la microscopie à force atomique (AFM) et la microscopie AFM en mode électrique et électrochimique (EC_AFM) afin d'obtenir des informations simultanées sur la topographie de l'échantillon et sur les processus électrochimiques à l'échelle des bactéries. La première étape sensible consistait à utiliser l'AFM sur des échantillons biologiques en milieu liquide: nous présentons ici les résultats de l'imagerie AFM en milieu liquide de plusieurs types de bactéries dans leurs conditions physiologiques naturelles (conditions in vivo). Aucun protocole d'immobilisation, ni chimique ni mécanique, n'a été nécessaire; et pour la première fois, les mouvements de reptation de cyanobactéries Nostoc ont été étudiés par l'AFM. Les études AFM ont permis d'acquérir des données topographiques mais aussi mécaniques : nous avons pu ainsi mesurer le module d'Young, la pression de turgescence de différentes souches bactériennes (Anabaenopsis circularis, Rhodococcus wratislaviensis). Cette étude complète, a révélé que l'imagerie AFM est donc possible sur des espèces vivantes en mouvement. Ces résultats ouvrent une grande fenêtre sur de nouvelles études d'intérêts tels que la formation de biofilms et les propriétés dynamiques de bactéries dans des conditions physiologiques réelles. La deuxième étape délicate était de combiner l'AFM aux mesures optiques et électriques. Nous avons développé un nouveau dispositif expérimental permettant (i) le suivi de l'évolution de la croissance bactérienne par la mesure des propriétés optiques comme la densité optique DO (pour le développement bactérien en volume – milieu planctonique) , ou l'analyse de l'image du substrat par comptage du nombre de bactéries sur la surface de l'échantillon (biofilm), et (ii) les mesures électriques et électrochimiques. L'ensemble de ces résultats sera prochainement appliqué au développement de nouveaux outils de surveillance d'une biodépollution de terrain contaminé par les hydrocarbures, par le suivi in situ et en temps réel de l'activité de bactéries dépolluantes (ECOTECH_BIOPHY ANR). / The presence of biological matter (biofilms) in deep geological sites for storage of, for instance, toxic elements or groundwater in aquifers was clearly proved. That biomass triggers physical and chemical processes which greatly modify the durability and the sustainability of the sites. These processes, mainly from oxidative/reductive reactions, are poorly understood. This is mainly due to the fact that former studies were done at the macroscopic level far away from the micrometric scale where relevant processes induced by bacteria take place. Investigations at microscopic level are needed. Thus, we developed an experimental set-up based on the combined use of optical microscopy (transmission), atomic force microscopy (AFM) and electrical and electro-chemical AFM microscopy (EC_AFM) in order to get simultaneous information on topographic and electro-chemical processes.The first highly sensitive step was to use AFM with biological samples in liquid environment: we present here a study about AFM imaging of living, moving or self-immobilized bacteria, in their genuine physiological liquid medium and in true in vivo conditions. No external immobilization protocol, neither chemical nor mechanical was needed. For the first time, the native gliding movements of Gram negative Nostoc cyanobacteria upon the surface were studied by AFM. AFM height and mechanical stiffness data were simultaneously acquired. From these, mechanical parameters, inner turgor pressure and Young modulus, were derived for different bacterial species (Anabaenopsis circularis, Rhodococcus wratislaviensis). Our study revealed that AFM imaging is thus possible on moving living species. These results open a large window on new studies of both dynamical phenomena of practical and fundamental interests such as the formation of biofilms and dynamic properties of bacteria in real physiological conditions.The second delicate step was to combine AFM and optical measurements with electrical ones. We mounted a new experimental set-up coupling real-time (i) monitoring of optical properties as the optical density (OD) evolution related to bulk bacterial growth in liquid or as the counting of number of bacteria adhering on the surface of the sample as well and (ii) electrical and electrochemical measurements. Furthermore, these results will shortly be applied to the optimized monitoring of the in-situ activity of bacteria consuming oil pollutants, following this way, in real-time, the bioremediation of an oil-contaminated soil (ANR ECOTECH_BIOPHY program).

Carbon nanotubes (CNTs) have gathered a lot of interest because of their extraordinary mechanical, electrical and thermal properties and have potential applications in a wide variety of areas such as material-reinforcement and nano-electronics. The properties of nanotubes are dependent on their diameter and methods for determining this using atomic force microscopy (AFM) in tapping mode assume that the measured height of the tubes represent the real diameter. Based on early, faulty calculations, the forces in tapping mode were assumed to be much lower than in contact mode, however it was later shown that forces in tapping mode can at point of impact rival the forces present in contact mode. This means that there is a potential risk of tube deformation during tapping mode measurements, resulting in incorrectly determined diameters. This work studies CNTs deposited on a silicon-substrate to analyze the effect of three common AFM settings (tapping frequency, free oscillation amplitude and setpoint) to determine their effect on measured CNT diameters and recommendations for choosing settings are given. / Kolnanorör har skapat mycket intresse på grund av sina extraordinära mekaniska, elektriska och termiska egenskaper och har lovande tillämpningar inom en mängd olika områden så som materialförstärkning och nanoelektronik. Kolnanorörens egenskaper påverkas kraftigt av deras diameter och de metoder som använder sig av atomkraftsmikroskopi(AFM) för att mäta diametern hos rören antar att den höjd-data man får fram är ett bra mått på den verkliga diametern hos rören. Baserat på tidiga, felaktiga beräkningar, antog man att kraften i ’tapping mode’ skulle vara mycket lägre än i ’contact mode’ vilket skulle leda till att man inte deformerar ytan man undersöker. Senare forskning visade att kraften mellan spets och prov kan vara lika stor eller rentutav större i tapping mode än i contact mode under det ögonblick då spetsen slår ner i provytan. Det medför att det finns en potentiell risk för att man deformerar kolnanorören när man mäter på dom vilket skulle resultera i att man får felaktiga värden på deras diametrar. Under det här projektet har kolnanorör som placerats på ett kisel-substrat undersökts för att analysera hur tre vanliga inställningar hos AFMet påverkar de erhållna värdena för diametern hos kolnanorören. De tre inställningarna som testats är svängnings-frekvensen, svängnings-amplituden i luft och börvärdet hos svängnings-amplituden.