京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第20361号 / 工博第4298号 / 新制||工||1666(附属図書館) / 京都大学大学院工学研究科マイクロエンジニアリング専攻 / (主査)教授 安達 泰治, 教授 小寺 秀俊, 教授 田畑 修 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

no / Low frequency (0.1¿2 Hz) dynamic mechanical analysis on individual type I collagen fibrils has been carried out using atomic force microscopy (AFM). Both the elastic (static) and viscous (dynamic) responses are correlated to the characteristic axial banding, gap and overlap regions. The elastic modulus (¿5 GPa) on the overlap region, where the density of tropocollagen is highest, is 160% that of the gap region. The amount of dissipation on each region is frequency dependent, with the gap region dissipating most energy at the lowest frequencies (0.1 Hz) and crossing over with the overlap region at ¿0.75 Hz. This may reflect an ability of collagen fibrils to absorb energy over a range of frequencies using more than one mechanism, which is suggested as an evolutionary driver for the mechanical role of type I collagen in connective tissues and organs. / BBSRC

Reservoir characterization is an essential step in the oil/gas exploration process and is of great significance in the evaluation of oil/gas resources. To evaluate the production potential of the Lower Huron shale in the central Appalachian Basin, matrix permeability, Raman spectroscopy, Fourier Transform infrared spectroscopy (FTIR), and atomic force microscopy (AFM) were used in this study. According to the experimental results, matrix permeability is relatively high for a shale gas formation, suggesting great production potential of shale gas resources in this region. Additionally, four shale samples with varying thermal maturity were characterized by the complementary Raman and FTIR spectroscopy, and curve-fitting results successfully demonstrated the change of chemical structures with the evolution of thermal maturity. Raman spectroscopy results show that the curve fitted G band position and the band separation between the G band and D1 band tend to increase with the rise of thermal maturity level. Results of FTIR spectroscopy show that the aromaticity level and the condensation extent of aromatic rings show an increasing tendency with the increase of maturation level. Moreover, mechanical properties of these four shale samples were characterized by AFM. Results show that Young's modulus is in the range of 8.20 GPa - 12.94 GPa, which is in the normal range compared with the results from other shale formations. Additionally, scanned results show an increasing tendency for Young's modulus of the organic components with the rise of thermal maturity level in these shale samples. The potential reason for this phenomenon was also explored, specifically, the growth of aromatic groups and the decrease of the CH2/CH3 ratio may be possible reasons for the rise of Young's modulus of organic components in these shale samples. This work is meaningful for the evaluation of shale gas resources, especially emerging plays, in the central Appalachian Basin, and it also provides a valuable database for relevant research on shale matrix permeability, Raman, FTIR and AFM. / Master of Science / Reservoir characterization is important in evaluating the production potential of unconventional resources. The purpose of this work is to characterize key reservoir properties of shale samples from the central Appalachian Basin to provide support for improved shale gas production in this region. This work includes the analysis of matrix permeability testing, Raman and Fourier Transform infrared spectroscopy (FTIR) characterization, and atomic force microscopy (AFM) mapping. Matrix permeability testing results show that the matrix permeability of these six samples is relatively high for a shale gas formation, suggesting great production potential of shale gas resources in this region. Additionally, four shale samples with different thermal maturity were scanned using Raman and FTIR spectroscopy, and mineral components of these same four samples were also identified by the FTIR analysis. Processed Raman data show that two important measures, the G band position and the difference between the G band position and D1 band position, tend to increase with the rise of thermal maturity. FTIR results show that the aromaticity rings would likely be compressed due to the increased number of aromaticity rings. Also, AFM provides a high-resolution map for the Young's modulus, a measure of material stiffness, of these four samples. The modulus value is in the normal range compared with scans from other shale formations. In addition, the modulus value tends to increase with the increase of thermal maturity level. The increase of aromatic rings and the decrease of the CH2/CH3 ratio can be regarded as potential reasons for the change of modulus value. This work has potential to improve the production design of shale gas resources, especially emerging plays, in the central Appalachian Basin and can be regarded as a valuable reference for other similar research.

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.

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.

<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.

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.