Il est indispensable pour comprendre la diagenèse, i.e., la formation des roches sédimentaires, le durcissement des matériaux de construction hydrauliques comme le ciment ou le plâtre, ou la biominéralisation, d'identifier les mécanismes élémentaires de la cristallisation minérale. Le taux de réaction macroscopique des minéraux est généralement déduit de mesures de chimie des solutions. A côté de ces mesures macroscopiques, l'étude de la réactivité des minéraux inclut maintenant l'analyse des mécanismes atomiques a l'origine des réactions chimiques. Cela a été rendu possible depuis deux décennies par l'apparition d'outils capables d'observer des surfaces avec une résolution nanométrique, tels que la microscopie à force atomique et l'interférométrie à balayage vertical. Le gypse et la calcite font partie des minéraux dits mous. Ce sont des minéraux extrêmement répandus, que l'on peut trouver autant dans la nature sous forme de roches sédimentaires que dans le monde industriel. Le gypse (CaSO4,2H2O) est une évaporite dont les applications incluent la fabrication des plaques de plâtre, l'ajout au ciment Portland comme retardateur, l'élaboration du plâtre de Paris et l'amendement des sols. La sélénite ou l'albâtre sont des variétés de gypse utilisés comme matériaux pour l'ornement, mais leur faible dureté limite leur durabilité. La calcite, forme la plus stable de CaCO3, est un des principaux biominéraux, et un des constituants majeurs des roches des réservoirs carbonates, stockant naturellement de l'eau, du pétrole ou du gaz naturel. Quand les organismes biologiques font croitre leur coquille, ils contrôlent la morphologie, la taille, l'orientation et même la phase des cristaux de carbonates de calcium qui la constituent. Cela conduit à des biomatériaux présentant des propriétés physiques et chimiques qui diffèrent significativement de ceux de la calcite inorganique. Une connaissance plus approfondie des mécanismes sous-jacents à la réactivité de surface de la calcite et de l'effet des impuretés sur celle-ci permettra de nous rapprocher de la possibilité de synthétiser des minéraux biomimétiques, aux propriétés comparables à celles de la calcite biogénique. Dans ce contexte, ma thèse s'est développée dans trois directions. Dans la première, j'ai étudié l'influence d'une contrainte mécanique sur les mécanismes de dissolution. Mon objectif dans cette partie a été de tacher de déduire le taux de dissolution macroscopique à partir de la cinétique des mécanismes atomiques. La seconde partie de la thèse, la plus conséquente, a consisté à étudier l'influence d'une contrainte mécanique sur la croissance de la calcite, et à sonder le rôle d'un additif organique lors de cette croissance sous contrainte. Dans la troisième partie, je me suis penchée sur la dissolution de cristaux de calcite à l'aide de mesures topographiques quantitatives sur des aires relativement étendues de la surface des cristaux, dans une large gamme de pH. J'ai en particulier étudié l'influence d'un additif organique sur la dissolution et la cinétique de réaction à grande échelle. Les taux de dissolution macroscopique et microscopique, c'est-à-dire déduits de la dynamique d'évènements moléculaires (croissance de piqure d'attaque, migration de marche atomique), ne sont presque jamais en accord, même qualitativement, et l'élaboration d'une théorie générale liant la cinétique du phénomène aux deux échelles est encore en cours. Je présente ici des taux de dissolution microscopique du gypse, mesures par microscopie par force atomique (AFM), en accord quantitatif avec les taux de dissolution macroscopiques. Cet accord inédit a été obtenu en prenant soin de neutraliser le biais induit par le fait que la pointe AFM applique une force sur la surface qu'elle sonde, et en identifiant avec soin les mécanismes moléculaires majeurs à l'œuvre lors de la dissolution...[etc] / Identifying reaction mechanisms of minerals is fundamental to understand diagenesis, i.e, sedimentary rock formation, construction material, like cement or gypsum, hardening, and biomineralization. The macroscopic reaction rates of minerals are generally deduced from solution chemistry measurements. Beside the measurement of macroscopic reaction rates, the study of the reactivity of minerals includes now the investigation of the atomic mechanisms involved in the reactions. This has been made possible for two decades by the use of tools resolving nanometric objects, such as vertical scanning interferometry (VSI) and atomic force microscopy (AFM). Gypsum and calcite are among soft minerals. They are extremely widespread mineral that can be found naturally in sedimentary rocks. They are also used in many industrial fields. Gypsum (CaSO4,2H2O) is an evaporate mineral. Gypsum uses include: manufacture of wallboards, plaster of Paris, soil conditioning, and hardening retarder in Portland cement. Varieties of gypsum known as "satin spar" and "alabaster" are used for a variety of ornamental purposes; however, their low hardness limits their durability. Calcite, the most stable crystalline form of CaCO3, is moreover important as a bio-mineral and a major constituent of host rock in carbonate reservoirs, which host drinking water and natural oil and gas. When biological organisms grow their shells, they control the crystal morphology, size, orientation and even the crystal phase of precipitated calcium carbonate. This results in materials with physical and chemical properties that differ significantly from those of inorganically precipitated calcite. Gaining more insight into the surface reactivity of calcite and the effect of surface impurities will bring us one step closer to being able to synthesize biomimetic material, which mimic the properties of biogenic calcite. In this thesis, I had three main focus points. In the first part I studied the effect of stress on the dissolution mechanisms. I investigated to deduce the dissolution rate from the atomic kinetics. The second and the most extensive was the study of the influence of stress on the calcite growth and probing the role of an organic additive on the dynamics of calcite growth while applying stress. In the third part I emphasised on quantitative topographic measurements of dissolving calcite crystal over a relatively large and fixed view at vast range of pH. I considered the influence of an organic additive on the dissolution and surface reaction kinetics at this larger scale. Both macroscopic and microscopic dissolution rates can also be deduced from the dynamics of molecular events (etch pit growth, atomic step migration), but they hardly ever agree, even qualitatively, and the elaboration of a general theory linking the kinetics at the two scales is still in progress. I presented here microscopic dissolution rates of gypsum, measured by atomic force microscopy (AFM), in quantitative agreement with macroscopic rates. This agreement has been obtained in taking care to neutralize the bias induced by the force applied by the AFM tip on the surface, and to identify clearly the driving molecular mechanism. The force applied by the AFM tip on the surface has been seen to increase the solubility of the mineral, thereby introducing a bias, so I have always worked with a constant and low applied force. This result shows that the determination, among the topographic changes during the dissolution of a mineral, of the dominant one, and the measurement of its dynamics, may permit deducing from AFM experiments a reliable macroscopic dissolution rate. The transformation of loose grains into a cohesive solid requires the crystallites to grow eventually constrained by the surrounding grains. Whereas never measured, this confinement and the associated stress is expected to influence noticeably the growth, and the final properties of the material… [etc]

L’étude avancée de systèmes polymères complexes (mélanges compatibilisés, nanocomposites, copolymères à bloc, etc) est cruciale pour le développement de nouvelles solutions d'ingénierie. Afin d'élucider les relations mise en œuvre-structure-propriétés de ces systèmes, la co-localisation d’informations chimique, physique et morphologique devient essentielle pour obtenir des réponses fiables. La caractérisation de la surface et de l’intérieur des matériaux est également d'une importance primordiale, en particulier pour les matériaux polymères minces (<100 μm) tels que les membranes, qui peuvent présenter des profils de propriétés contrastés entre les surfaces et le coeur. Ces profils de propriétés peuvent être induits par le procédé de mise en œuvre, la chimie du matériau ou son vieillissement. Pour cela, le matériau doit être correctement ouvert sans modification structurelle, chimique ou morphologique. Par conséquent, l'objectif principal de cette thèse a été de développer une méthodologie expérimentale de caractérisation alliant la co-localisation des informations morphologiques, nanomécaniques et chimiques obtenues par le couplage de la Microscopie de Force Atomique (AFM) et la Microspectroscopie Confocale Raman et d’une technique de préparation des coupes transversales par cryo-ultramicrotomie.La stratégie développée a été appliquée à trois systèmes polymères différents: 1) des mélanges polyamide 6 (PA6) / acrylonitrile-butadiène-styrène (ABS), compatibilisés avec un styrène-acrylonitrile greffé anhydride maléique (SAN-MA); 2) de membranes hybrides constituées d’une matrice polymère de type polyétheréthercétone sulfoné (sPEEK) et d’une phase inorganique chimiquement active préparée par chimie Sol-Gel (SG); 3) des copolymères à bloc de type PS-PEO-PS utilisés comme électrolytes pour les batteries lithium. L’étude morphologique du mélange PA/ABS a montré que l'addition d’un copolymère SAN-MA améliore significativement la dispersion de la phase ABS dans la matrice PA et, en fonction du protocole appliqué, modifie la morphologie du mélange et la structure cristalline de la phase PA (teneur/distribution des phases -). Les modifications morphologiques observées ont ensuite été corrélées aux propriétés rhéologiques des mélanges. L’étude des membranes hybrides sPEEK/SG avait pour objectif de comprendre l’impact des étapes clés d’élaboration de ces membranes sur la morphologie des mélanges, la distribution de la phase SG dans la matrice sPEEK et sa densité de réticulation et le précurseur utilisé: (3-mercaptopropyl)-methyldimethoxysilane (SHDi) et (3-mercaptopropyl)-triméthoxysilane (SHTriM). L'efficacité des traitements thermiques appliqués aux différentes étapes du processus de fabrication des membranes SHDi a été démontrée. Pour les membranes basées sur le précurseur SHTriM, il a été démontré que la phase SG présente un système hiérarchiquement organisé, avec des domaines sphériques composés de particules élémentaires plus petites. L’inclusion d'une phase SG à l'intérieur de la membrane sPEEK ne perturbe pas la nanoséparation hydrophobe/hydrophile de la matrice, mais limite son gonflement. Enfin, une 'analyse morphologique a été réalisée sur une série de copolymères à bloc utilisés comme électrolytes polymères dans les batteries lithium. Le contraste nanomécanique des différentes phases a permis de mesurer les distances inter-domaine entre les phases PS et PEO par AFM et une bonne corrélation a été obtenu avec des résultats de diffusion de rayons X aux petits angles (SAXS). Il a été démontré que les propriétés nanomécaniques de surface du matériau évoluent avec son hydratation (humidité relative de la pièce).Dans chacune des trois études présentées dans cette thèse, la stratégie de co-localisation et a fourni des informations précieuses inaccessibles autrement. Cela ne fut possible qu'après une mise en œuvre spécifique de la cryo-ultramicrotomie pour la coupe de membranes fines et d’échantillons sensibles à l'eau. / The comprehension of the intrinsic characteristics and interactions found in complex polymeric systems is important and challenging for the development of new engineering solutions. In order to elucidate the process-structure-properties interplays, the co-localization of different information becomes essential, to obtain reliable answers. The characterization of both the surface and the bulk of materials is also of prime importance, especially for thin polymeric materials (<100 µm) such as membranes, which can present contrasted properties profiles throughout their thickness. To do so, the material must be properly opened with no structural, chemical and morphological modifications. Therefore, the main objective of this thesis was to develop an experimental methodology of characterization allying the co-localization of morphological, nanomechanical and chemical information using a special setup combining Atomic Force Microscopy and Confocal Raman Microspectroscopy to study cross-sections of cryo-ultramicrotomed samples.We applied the developed strategy to three different polymer systems: 1) blends of Polyamide 6 (PA6) and Acrylonitrile-Butadiene-Styrene (ABS), compatibilized with a Styrene-Acrylonitrile grafted with Maleic Anhydride (SAN-MA); 2) hybrid membranes of sulfonated polyether-etherketone (sPEEK) with active networks prepared by Sol-Gel (SG) chemistry; 3) block copolymers based on PS-PEO-PS used as polymer electrolyte membranes. The first study was focused on the impact of the compatibilizer and the mixing protocols on the morphology of an immiscible PA6/ABS blend. Co-localized AFM/Raman established that the addition of the SAN-MA copolymer, at different steps of the blending, favors the formation of the PA6 γ polymorph with amounts and distribution depending on the blending protocols. The different resulting morphologies were found to impact the blends’ rheological properties. The second study focused on the fabrication of hybrid sPEEK/SG membranes for Fuel Cell based on two different SG precursors. The main goal of this study was to qualify the impact of each step of fabrication on the membranes’ physical, nanomechanical and chemical properties, as well as their stability over time. Quantitative nano-mechanical (AFM) and chemical analysis (Raman) of the SG phase revealed its evolution throughout the fabrication process, confirming the efficiency of the applied thermal treatments. For membranes based on (3-mercaptopropyl)-trimethoxysilane SG precursor, it has been shown that the SG phase presents a hierarchically organized system, composed of elementary particles which aggregate into the round shape domains. The presence of SG phase inside the membrane (AFM/Raman) conserves the hydrophobic/hydrophilic nanophase separation of the host sPEEK, but the increasing SG uptake limits the swelling of the host membrane, which can affect its proton conductivity. Finally, the third study was focused on the morphological analysis of a series of triblock copolymers, used as polymer electrolytes in batteries. Their nanomechanical heterogeneities allowed the measurement of the inter-domain distances between the PS and PEO phases directly from the AFM images which were correlated to Small Angle X-Ray Scattering (SAXS) measurements. It has been shown that the material’s surface nanomechanical properties evolve from the dry state to the equilibrium with the room relative humidity.To summarize, the development of the characterization methodology allying co-localized AFM/Raman with multiple complementary techniques allowed for the study of different complex polymeric systems for a variety of applications. In each of the three studies of this thesis, the co-localization and multi-technique strategy provided precious information that could not be accessed by other means. This could only be possible by the adaptation of cryo-ultramicrotomy for sample preparation, especially for thin polymer membranes and water sensitive samples.

A microscopia de fluorescência é uma das técnicas mais poderosas disponíveis atualmente, uma vez que proporciona uma combinação excepcional de alta sensibilidade na detecção, alta especificidade, além de ser consideravelmente não invasiva. Avanços recentes permitiram a detecção em resolução de subdifração, o que eleva sua potencialidade de investigação de um maior número de sistemas e, consequentemente, de avanço científico. O estudo de novas sondas fluorescentes é de fundamental importância para a aplicação em métodos avançados de microscopia óptica. Na primeira vertente da pesquisa, Capítulo 2, foi realizado o estudo fotofísico de uma série de compostos bisarilados derivados do anidrido maleico e de maleimidas sintetizados pela reação de Heck-Matsuda. Visando o aprimoramento do design dessas moléculas, foi realizada a ciclização fotoquímica de tais compostos, resultando em moléculas com anéis condensados, nomeados como derivados de fenantreno, as quais proporcionaram maior estabilidade fotoquímica. A dinâmica do estado excitado remete ao efeito push-pull, em que há um deslocamento de carga notável, mas não completo. Para os compostos com a substituição 4-hidroxifenil foi observado um processo de deslocamento de carga combinado com uma transferência de próton no estado excitado assistida por solvente. Ademais, o estudo dos compostos derivados de fenantreno em microscopia confocal demonstrou que as propriedades locais do solvente afetam a dinâmica de relaxação de fluorescência em diferentes meios condensados e que os mesmos são passíveis de serem aplicados a técnicas avançadas de microscopia de fluorescência. A segunda vertente desta tese, Capítulo 3, explora um sistema biológico em nível de uma única molécula. Especificamente, este capítulo concerne à investigação de uma metodologia ótima para a marcação fluorescente de DNA em sequência específica, através de microscopia de fluorescência com super-resolução. As reações foram conduzidas utilizando uma metodologia de marcação de duas etapas, de acordo com o princípio mTAG. Na primeira etapa, grupamentos contendo alquino terminal, azida ou amina primária são transferidos do cofator análogo ao S-adenosil-L-metionina para o DNA através de uma enzima metiltransferase. Foi utilizada a enzima M.TaqI, a qual tem como alvo a sequência 5\'- TGCA -3\' para modificação. Na segunda etapa é realizado o acoplamento do fluoróforo aos sítios funcionais do plasmídeo (pUC19) através de reações químicas bioortogonais, tais como reação click catalisada por cobre (CuAAC), reação click na ausência de cobre (SPAAC) e acoplamento do grupo amina primária com NHS-éster. Também foi desenvolvida uma metodologia direta de uma etapa, na qual o fluoróforo é diretamente transferido do cofator análogo para o DNA em uma única etapa reacional. Para acompanhar o desempenho das reações foi desenvolvido um ensaio single-molecule para a contagem do número de moléculas de corante ligadas a plasmídeos individuais. A topologia dos plasmídeos após a marcação foi investigada por imagens de AFM em alta resolução. A combinação de ambas as análises demonstrou que a reação SPAAC assim como a reação direta de uma etapa promoveram uma marcação fluorescente quase completa e a técnica de AFM confirmou que o acoplamento de fluoróforos não induziu danos à estrutura dos plasmídeos, os quais preservaram sua morfologia nativa, superenrolada. Além disso, os plasmídeos marcados foram aplicados com sucesso a procedimentos de transfecção em células de mamíferos, indicando que o DNA reteve sua capacidade de codificar informação genética, mesmo na presença de fluoróforos ligados. / Fluorescence microscopy is one of the most powerful techniques currently available, since it provides the unique combination of a high sensitivity in detection, a high specificity, and a considerable non-invasiveness. Recent developments have allowed the detection at a sub-diffraction resolution, which elevates its potentiality to investigate several systems and hence to go further in science. The study of new fluorescent probes is crucial for the application in advanced methods in optical microscopy. In the first extent of this research, Chapter 2, a photophysical study of maleic anhydride and maleimide derivatives, synthesized by the Heck-Matsuda reaction, was performed. Aiming at the improvement of the design of these molecules, a photochemical cyclization was carried out, resulting in molecules with condensed rings, termed as phenanthrene derivatives, which promoted more photochemical stability. The excited state dynamics rely on the push-pull effect, in which a notable, but not complete, charge shift takes place. For the compounds with a 4-hydroxyl substituent, a charge shift combined with an excited state solvent-assisted proton transfer was observed. Additionally, the confocal microscopy study of the phenanthrene derivatives showed that the local properties of the solvent modulate the fluorescence relaxation dynamics in condensed media and hence such dyes can be potential candidates for use in advanced fluorescence microscopy techniques. The second extent of this thesis, Chapter 3, explores a biological system at the single-molecule level. Specifically, this chapter concerns to an investigation of an optimal sequence-specific DNA fluorescent labelling, using super-resolution fluorescence microscopy. The reactions were performed using a two-step methodology, according to the mTAG approach. In the first step, moieties containing a terminal alkyne, azide, or primary amine group are transferred from an S-adenosyl-L-methionine analogue cofactor to the DNA by a methyltransferase enzyme. Herein, the enzyme M.TaqI was used, which targets the 5\'- TCGA -3\' sequence for modification. In the second step, a fluorophore is coupled to the functional sites of the plasmid (pUC19) using bio orthogonal reactions, such as the click reaction catalysed by copper (CuAAC), the copper-free click reaction (SPAAC), and the amino-to-NHS-ester coupling reaction. A direct one-step approach in which the fluorophore is directly transferred to the DNA from the analogue cofactor in a single reaction step, was also developed. A single-molecule assay was developed for counting the number of fluorophores associated with the individual plasmids. The topology of the plasmids after labelling was also investigated by high-resolution AFM imaging. Combining both analysis, the SPAAC as well as the direct one-step reactions were found to promote near-complete labelling and the AFM showed that the fluorophore coupling did not damage the structure of the plasmids and that their native, supercoiled, morphology was preserved. Moreover, labelled plasmids were successfully applied for transfection into mammalian cells, implying that the DNA retained its ability to encode genetic information, even while carrying bound fluorophores.

L’objet de cette thèse est l’étude de la croissance de silicène sur des substrats d’argent,ainsi que l’étude de sa réactivité vis-à-vis de l’oxygène. La croissance a été réalisée sous ultra-vide et contrôlée par spectroscopie d’électrons Auger (AES) et par diffraction d’électrons lents (LEED). Les structures obtenues et leurs réactivités à l’oxygène ont été étudiées par microscopie à champ proche (STM et nc-AFM) et par spectroscopie de photoémission résolue en angle (ARPES). Nous avons étudié la structure interne des nano-rubans de silicène auto-assemblés sur un substrat d’Ag(110). Sur Ag(111) nous obtenons un feuillet de silicène qui présente différentes structures en fonction de la température du substrat. L’étude de la réactivité des rubans et des feuillets a montré que le silicène formé sur substrat d’argent est relativement stable vis-à-vis de l’oxygène ce qui ouvre des perspectives de fonctionnalisation du silicène. La dernière partie de cette thèse concerne la synthèse de feuillets de silicium par voie chimique. Nous avons mis au point une nouvelle méthode prometteuse de synthèse chimique qui nous a permis de synthétiser des feuillets de silicium de structure graphitique. / The objective of this thesis is the study of the growth of silicene on silver substrates as well as its reactivity towards the oxygen. The growth was performed under ultra-high vacuum and controlled by Auger electrons spectroscopy (AES) and low energy electrons diffraction (LEED). The obtained structures and their relativities towards the oxygen were studied by near field microscopy (STM and nc-AFM) and by angle resolved electrons photoemission spectroscopy (ARPES). We have studied the internal structure of the selfassembled silicene nanoribbons on Ag(110) substrate. On Ag(111), we have obtained a silicene sheet presenting different structures versus the temperature of the substrate. The reactivity of silicene nanoribbons and sheets grown on silver show that silicene is relatively stable towards the oxygen which opens a new perspectives of functionalization of the silicene. The last part of this thesis concerns the synthesis of silicone sheets by chemical process. We have develpped a new promising process of chemical synthesis which allowed us to synthesize silicon sheets with graphitic structure.

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.

Neste trabalho foi estudado o desenvolvimento de uma superfície modelo de silício monocristalino, SiO2/Si, modificada com organossilanos derivados de N-heterocíclicos que permitisse a imobilização de um complexo de coordenação, FeTIM. Estas superfícies modificadas poderão ser empregadas em estudos de reatividade frente a analitos de interesse, como o NO. Sob esse aspecto, a síntese desses novos silanos, contendo N-heterocíclicos, e o desenvolvimento de uma metodologia de formação dos filmes finos automontados, sobre a superfície de SiO2/Si, tornou-se de grande relevância na aplicabilidade deste trabalho. Para a obtenção dessas superfícies, fez-se necessária a compreensão dos parâmetros de formação dos filmes de silanos. Os parâmetros estudados foram os efeitos do tempo de adsorção, da concentração da solução dos silanos, da polaridade do solvente e do tamanho da cadeia alquílica do silano no processo de formação dos filmes. Deste modo, foi possível inferir sobre as alterações na morfologia e na estrutura química dos filmes formados, através de medidas de Espectroscopia de Fotoelétrons excitados por Raios-X (XPS), Microscopia de Força Atômica (AFM) e Microscopia Eletrônica de Varredura (MEV). A imobilização do complexo de FeTIM sobre a superfície organomodificada foi comprovada pela variação da linha de fotoemissão do Fe 2p nas medidas de XPS. / This work describes the study of model surfaces on oxidized silicon wafer, SiO2/Si, modified with N-heterocycles rings, that allows the grafting of a macrocycle iron complex, FeTIM, that could be used in reactivity studies, with biologically relevant molecules, as nitrogen monoxide (NO). On this way, the synthesis of these silanes and a new methodology of the formation of self-assembled monolayers had become a relevant question on this work applicability. These thin films contain silanes bearing nitrogenated Lewis bases on silicon surfaces. In order to obtain these modified surfaces, it was necessary a comprehensive study of the adsorption parameters of the thin films. The parameters studied were the effect of: adsorption time, the solution concentration, the role of the solvents polarity and the chain length alkylsilanes in the film formation. Then, it was possible to infer about the film\'s morphology differences and chemical structures by the XPS, AFM and MEV measurements. X-ray photoemission lines of Fe 2p were used to probe the iron chemical environment in the chemically adsorbed macrocycles complexes.

In der Arbeit wird das Reibungsverhalten an Polymerbürsten im nanoskopischen und makroskopischen Kontakt beschrieben. Besonderes Augenmerk liegt auf den durch Reibung hervorgerufenen Deformationen.

Single-molecule force spectroscopy (SMFS) is a unique approach to study the mechanical unfolding of proteins. SMFS unfolding experiments yield insight into how interactions stabilize a protein and guide its unfolding and refolding pathways. In contrast to various water-soluble proteins whose unfolding and refolding patterns have been characterized, only α-helical membrane proteins have been probed by SMFS. It was shown that α-helical membrane proteins unfold via many intermediates; this differs from the two-state unfolding process usually observed in water-soluble proteins. In membrane proteins, upon mechanically pulling the peptide end of the protein, single and grouped α-helices and polypeptide loops unfold in steps until the entire protein is unfolded. Whether the α-helices and loops unfold individually or cooperatively to form an unfolding intermediate depends on the interactions established within the membrane protein and the membrane. Each unfolding event relates to an unfolding intermediate with the sequence of these intermediates defining the unfolding pathway of the protein. β-barrel-forming membrane proteins are the second major group of membrane proteins and have not yet been studied by SMFS. To fill this void this study was designed to characterize interactions, unfolding, and refolding of the β-barrel forming outermembrane protein G (OmpG).Folding of transmembrane proteins, despite the important part these proteins play in every biological process in a cell, is studied in only a few examples. Of those only a handful were β-stranded membrane proteins (Tamm et al., 2004; Kleinschmidt et al., 2006). Current models describe that transmembrane β-barrels fold into the lipid membrane via two major steps. First the unfolded polypeptide interacts with the lipid surface where it then folds and inserts into the membrane (Kleinschmidt et al., 2006; Huysmans et al., 2010). Conventionally, thermal or chemical denaturation is used to study folding of membrane proteins. In most cases membrane proteins were solubilized in detergent or exposed to urea to be studied, conditions that are not compatible with In vivo conditions. This suggests that the folding pathways described so far may not be a realistic representation of such pathways in nature. SMFS represents a unique approach to study the unfolding and refolding of membrane proteins into the lipid membrane (Kedrov et al., 2006; Kessler et al., 2006). Using SMFS makes it possible to study unfolding and refolding of membrane proteins in their nativephysiological environment with controlled pH, electrolyte, temperature, and most importantly in the absence of any chemical denaturant or detergent. In this thesis, SMFS was utilized to unfold and refold OmpG in E coli lipid extract. Bulk unfolding experiments suggested that OmpG unfolds and folds reversibly and much faster than α-helical proteins (Conlan et al., 2000). The folding process is thought to be a coupled two-state membrane partition-folding reaction. To the contrary, the mechanical unfolding of OmpG consisted of many sequential unfolding intermediates. Our SMFS refolding experiments showed that a partially unfolded OmpG molecule also refolds via several sequential steps. The predominant refolding steps are defined by individual β-hairpins that could later assemble the transmembrane β-barrel of OmpG. In conclusion, the most probable unfolding and refolding pathways of OmpG as a membrane β-barrel protein go through the β-hairpins as the structural segments or unfolding-refolding intermediates and the process is a multi step one rather than the simple two state process. We also used SMFS to study the physical interactions that switch the functional state and gating of OmpG. The structural changes that gate OmpG have been previously described by X-ray crystallography (Yildiz et al., 2006). They showed when the pH changes from neutral to acidic the flexible extracellular loop L6 folds into the pore and closes the OmpG pore. Here, SMFS was used to structurally localize and quantify the interactions that are associated with the pH-dependent closure. At an acidic pH, a pH-dependent interaction at loop L6 was detected. This interaction changed the unfolding of loop L6 and β-strands 11 and 12, which connect loop L6. All other interactions detected within OmpG were found to be unaffected by changes in pH. These results provide a quantitative and mechanistic explanation of how pHdependent interactions change the folding of a peptide loop to gate the transmembrane pore. It has also been shown how the stability of OmpG is optimized so that pH changes modify only those interactions necessary to gate the transmembrane pore and there are no global changes in protein conformation or mechanical properties. In the next step of interactions study, dynamic SMFS (DFS) was applied to quantify the parameters characterizing the energy barriers in energy landscape for unfolding of the OmpG. Some of these parameters are: free energy of activation and distance of the transition state from the folded state. The pH-dependent functional switching of OmpG directs the protein along different regions at the unfolding energy landscape. The two functional states of OmpG sequential folding take the same unfolding pathway as β-hairpins I–IV. After the initial unfolding events, the unfolding pathways diverge. In the open state, the unfolding of β-hairpin V in one step precedes the unfolding of β-hairpin VI. In the closed state, β-hairpin V and β-strand S11 with a part of extracellular loop L6 unfold cooperatively, and subsequently β-strand S12 unfolds with the remaining loop L6. These two unfolding pathways in the open and closed states join again in the last unfolding step of β-hairpin VII. Also, the conformational change from the open to the closed state witnesses a difference in Xu and κ in the energy landscape that translates to rigidified extracellular loop L6 at the gating area. Thus, a change in the conformational state of OmpG not only bifurcates its unfolding pathways but also tunes its mechanical properties for optimum function.

This dissertation focuses on quantitative subsurface and mechanical properties imaging potential of AFM probes. Extensive modeling of AFM probes are presented for thorough understanding of capabilities and limitations of current techniques, these models are verified by various experiments, and different methods are developed by utilizing force-sensing integrated read-out active tip (FIRAT), which is an active AFM probe with broad bandwidth. For quantitative subsurface imaging, a 3-D FEA model of AFM tip-sample contact is developed and this model can simulate AFM tip scan on nanoscale-sized buried structures. FIRAT probe, which is active and broadband, is utilized for interaction forces imaging during intermittent contact mode and mechanical characterization capability of this probe is investigated. It is shown that probe dynamics, stiffness, stiffness ambiguity, assumed contact mechanics, and noise are important parameters for the accuracy of mechanical properties imaging. An active tip control mechanism is introduced to limit contact forces during intermittent contact mode. In addition to these, a combined ultrasonic AFM and interaction forces imaging method is developed and modeled to solve the reduced elasticity measurement sensitivity on composite materials. This method is capable of imaging a broader range of elasticity on combination samples such as metal nanoparticles in polymers at nanoscale.

Proteine spielen auf der zellulären Ebene eines Organismus eine fundamentale Rolle. Sie sind quasi die „Maschinen“ der Zelle. Ihre Bedeutung wird nicht zuletzt in ihrem Namen deutlich, welcher 1838 erstmals von J. Berzelius verwendet wurde und „das Erste“, „das Wichtigste“ bedeutet. Proteine sind aus Aminosäuren aufgebaute Moleküle. Unter physiologischen Bedingungen besitzen sie eine definierte dreidimensionale Gestalt, welche für ihre biologische Funktion bestimmend ist. Es wird heutzutage davon ausgegangen, dass diese dreidimensionale, stabile Struktur von Proteinen eindeutig durch die Abfolge der einzelnen Aminosäuren, der Sequenz, bestimmt ist. Diese Abfolge ist für jedes Protein in der Desoxyribonukleinsäure (DNS) gespeichert. Es ist allerdings eines der größten ungelösten Probleme der letzten Jahrzehnte, wie die Beziehung zwischen Sequenz und 3D-Struktur tatsächlich aussieht. Die Beantwortung dieser Fragestellung erfordert interdisziplinäre Ansätze aus Biologie, Informatik und Physik. In dieser Arbeit werden mit Hilfe von Methoden der theoretischen (Bio-) Physik einige der damit verbundenen Aspekte untersucht. Das Hauptaugenmerk liegt dabei auf Wechselwirkungen der einzelnen Aminosäuren eines Proteins untereinander, wofür in dieser Arbeit ein entsprechendes Energiemodell entwickelt wurde. Es werden Grundzustände sowie Energielandschaften untersucht und mit experimentellen Daten verglichen. Die Stärke der Wechselwirkung einzelner Aminosäuren erlaubt zusätzlich Aussagen über die Stabilität von Proteinen bezüglich mechanischer Kräfte. Die vorliegende Arbeit unterteilt sich wie folgt: Kapitel 2 dient der Einleitung und stellt Proteine und ihre Funktionen dar. Kapitel 3 stellt die Modellierung der Proteinstrukturen in zwei verschiedenen Modellen vor, welche in dieser Arbeit entwickelt wurden, um 3D-Strukturen von Proteinen zu beschreiben. Anschließend wird in Kapitel 4 ein Algorithmus zum Auffinden des exakten Energieminimums dargestellt. Kapitel 5 beschäftigt sich mit der Frage, wie eine geeignete diskrete Energiefunktion aus experimentellen Daten gewonnen werden kann. In Kapitel 6 werden erste Ergebnisse dieses Modells dargestellt. Der Frage, ob der experimentell bestimmte Zustand dem energetischen Grundzustand eines Proteins entspricht, wird in Kapitel 7 nachgegangen. Die beiden Kapitel 8 und 9 zeigen die Anwendung des Modells an zwei Proteinen, dem Tryptophan cage protein als dem kleinsten, stabilen Protein und Kinesin, einem Motorprotein, für welches 2007 aufschlussreiche Experimente zur mechanischen Stabilität durchgeführt wurden. Kapitel 10 bis 12 widmen sich Membranproteinen. Dabei beschäftigt sich Kapitel 10 mit der Vorhersage von stabilen Bereichen (sog. Entfaltungsbarrieren) unter externer Krafteinwirkung. Zu Beginn wird eine kurze Einleitung zu Membranproteinen gegeben. Im folgenden Kapitel 11 wird die Entfaltung mit Hilfe des Modells und Monte-Carlo-Techniken simuliert. Mit dem an Membranproteine angepassten Wechselwirkungsmodell ist es möglich, den Einfluss von Mutationen auch ohne explizite strukturelle Informationen vorherzusagen. Dieses Thema wird in Kapitel 12 diskutiert. Die Beziehung zwischen Primär- und Tertiärstruktur eines Proteins wird in Kapitel 13 behandelt. Es wird ein Ansatz skizziert, welcher in der Lage ist, Strukturbeziehungen zwischen Proteinen zu detektieren, die mit herkömmlichen Methoden der Bioinformatik nicht gefunden werden können. Die letzten beiden Kapitel schließlich geben eine Zusammenfassung bzw. einen Ausblick auf künftige Entwicklungen und Anwendungen des Modells.