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<p>Scanning transmission x-ray microscopes (STXM) focus monochromatic x-rays into an intense sub-30 nm diameter spot. Samples are then positioned at the focal plane and raster scanned through the spot while the transmitted x-rays are acquired to build up images at x-ray photon energies. In addition, x-ray absorption spectroscopy (XAS) can be performed by recording image sequences over a photon energy range of interest. STXMs excel at characterizing thin sections of inhomogeneous soft matter with their combination of high spatial (<30 nm) and photon energy (<0.1 eV) resolution. However, the overarching theme of this thesis is to apply the intense, tightly focused spot of x-rays to induce spatially resolved chemical and physical changes, and directly pattern materials, primarily thin polymer films. The irradiated areas are then investigated using several types of microscopy (scanning transmission x-ray, atomic force, scanning electron) and XAS. The experiments cover three broad areas: i) Nanofabrication; realization of the smallest possible feature sizes, and fabrication schemes unique to focused x-rays with applications including nanofluidics. ii) Radiation chemistry and physics; investigating the mechanisms of radiation-induced processes such as bond formation/loss, morphological change, carbon contamination, and temperature increase. iii) X-ray optics; the spatial distribution of x-rays at a focal plane can be recorded in a thin polymer film and later read out using an atomic force microscope. Applications include feedback for optics fabrication and enhanced image processing, the ultimate goal being increased spatial resolution.</p> / Doctor of Philosophy (PhD)

<p>Magnetotactic bacteria (MTB) are ubiquitous, multi-phylogenetic bacteria that actively synthesize chains of magnetic, membrane bound; single domain magnetite (Fe₃O₄) or greigite (Fe₃S₄) crystals, termed magnetosomes in order to better navigate to their preferred chemical environment using the Earth’s magnetic field. Discovered in 1963, the field is now focused on understanding magnetosome chain formation and associated processes through genetic studies as well as analytical techniques such as Transmission Electron Microscopy (TEM) and Scanning Transmission X-ray Microscopy – X-ray Magnetic Circular Dichroism (STXM-XMCD).</p> <p>This thesis performed studies on <em>Candidatus Magnetovibrio blakemorei</em> strain MV-1 using STXM at the C 1s, O 1s, Ca 2p and Fe 2p edges. STXM-XMCD was used to determine the magnetism of individual magnetosomes and quantitatively determine magnetic properties such as the magnetic moment of individual chains. A sub-population of MV-1 cells was identified as having anomalous magnetic orientations of magnetosome sub-chains when separated spatial gaps. The frequency of this event and the underlying implications to magnetosome formation are discussed.</p> / Master of Science (MSc)

This thesis focuses on the state-of-the-art spectroscopic approaches in studying polymer electrolytes for proton exchange membrane fuel cells. With the aim to optimize architectural and chemical design of hydrogen fuel cells, a variety of perfluorosulfonic acid (PFSA) membranes were explored to establish characteristics that ultimately improve PFSA electrolyte performance. The results of the detailed spectroscopic analyses helped to unveil a structure performance relationship. Solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used to distinguish F and C environments, while scanning transmission X-ray microscopy coupled with X-ray absorption spectroscopy provided complementary chemical structural information with direct access to S and O environments. The combination of these two techniques provided advantages in identifying subtle chemical alterations in PFSAs. Furthermore, a novel ssNMR technique was developed with the purpose of probing local dynamics from the polymer perspective. This ¬¬19F dipolar recoupling ssNMR approach was validated and applied to PFSA membranes by monitoring the normalized double quantum build-up curves as a function of relative humidity (%RH) and temperature, and the polymer side chain showed higher local motion as response to temperature and %RH elevation compared to the backbone. The effective dipolar coupling constant was extracted to represent local dynamics and compared amongst tested PFSAs. A standardized metric, the dynamic order parameter, was also introduced and applied to the materials to quantitatively compare them within the same class. This new method provided an alternative way to extract site-specific local dynamics profile for materials with multiple resonances. Additionally, the combination of in situ fuel cell performance evaluation and ex situ ssNMR characterization created a connection between fundamental chemistry and bulk electrochemical measurements. As the first study to correlate these physicochemical properties to material performances, this work parameterized the structural impact at a molecular level and provided insight into improving polymer electrolyte materials. / Thesis / Doctor of Philosophy (PhD) / Proton exchange membrane fuel cells, which help to reduce the reliance on fossil fuels by locally producing only water and heat, have received a significant amount of research attention as an alternative power generator for vehicular and stand-alone energy applications. Perfluorosulfonic acid (PFSA) membranes, the most common commercial polymer electrolyte materials, have been investigated using modern analytical spectroscopies. Solid-state nuclear magnetic resonance (ssNMR) spectroscopy and synchrotron-based scanning transmission X-ray microscopy were used in elucidating material compositions with complementary information. Moreover, an advanced ssNMR method was developed and applied to a variety of PFSAs. Polymer backbones and side chains were separated spectroscopically, and were distinguished based on different local dynamics profiles extracted from the ssNMR experiments. Additionally, bulk material performance evaluations from electrochemical analyses were correlated to PFSA side chain local dynamics profiles. The integrated spectroscopic study illustrated in this thesis provided insight into understanding the structure-performance relationship of PFSA electrolytes.

The demand for electrical energy is steadily increasing. Highly efficient organic solar cells based on mixed, strongly absorbing organic molecules convert sunlight into electricity and, thus, have the potential to contribute to the worlds energy production. The continuous development of new materials during the last decades lead to a swift increase of power conversion efficiencies (PCE) of organic solar cells, recently reaching 12%. Despite these breakthroughs, the usage of highly complex organic molecules blended together to form a self-organised absorber layer results in complicated morphologies that are poorly understood. However, the morphology has a tremendous impact on the photon-to-electron conversion, affecting all processes ranging from light absorption to charge carrier extraction. This dissertation studies the role of phase-separation of the self-organised thin film blend layers utilized in organic solar cells. On the molecular scale, we manipulate the phase-separation, using different molecule combinations ranging from the well-known ZnPc:C 60 blend layers to highly efficient oligothiophene:C60 blend layers. On the macroscopic scale, we shape the morphology by depositing the aforementioned blend layers on differently heated substrates (in-vacuo substrate temperature, Tsub). To characterise the manufactured blend layers, we utilize high resolution microscopy techniques such as photoconductive atomic force microscopy, different electron microscopic techniques, X-ray microscopy etc., and various established and newly developed computational simulations to rationalise the experimental findings. This multi-technique, multi-scale approach fulfils the demands of several scientific articles to analyse a wide range of length scales to understand the underlying optoelectronic processes. Varying the mixing ratio of a ZnPc:C60 blend layer from 2:1 to 6:1 at fixed in vacuo substrate temperature results in a continuous increase of surface roughness, decrease of short-circuit current, and decrease of crystallinity. Additionally performed density functional theory calculations and 3D drift-diffusion simulations explain the observed crystalline ZnPc nanorod formation by the presence of C60 in the bulk volume and the in turn lowered recombination at crystalline ZnPc nanorods. Moving to oligothiophene:C60 blend layers used in highly efficient organic solar cells deposited at elevated substrate temperatures, we find an increase of phase-separation, surface roughness, decrease of oligothiophene-C60 contacts, and reduced disorder upon increasing Tsub from RT (PCE=4.5%) to 80 °C (PCE=6.8%). At Tsub =140 °C, we observe the formation of micrometer-sized aggregates on the surface resulting in inhomogeneous light absorption and charge carrier extraction, which in turn massively lowers the power conversion efficiency to 1.9%. Subtly changing the molecular structure of the oligothiophene molecule by attaching two additional methyl side chains affects the thin film growth, which is also dependent on the substrate type. In conclusion, the utilized highly sensitive characterisation methods are suitable to study the impact of the morphology on the device performance of all kinds of organic electronic devices, as we demonstrate for organic blend layers. At the prototypical ZnPc:C60 blend, we discovered a way to grow ZnPc nanorods from the blend layer. These nanorods are highly crystalline and facilitate a lowered charge carrier recombination which is highly desirable in organic solar cells. The obtained results at oligothiophene: C60 blends clearly demonstrate the universality of the multi-technique approach for an in-depth understanding of the fragile interplay between phase-separation and phase-connectivity in efficient organic solar cells. Overall, we can conclude that both molecular structure and external processing parameters affect the morphology in manifold ways and, thus, need to be considered already at the synthesis of new materials.

Les revêtements de carbone amorphe hydrogéné (a-C:H) avec incorporation de silicium et d’oxygène (a-C:H:Si:O) sont une catégorie de lubrifiants solides, de la famille des Diamond-Like Carbon (DLC), présentant aussi bien de bonnes propriétés mécaniques que tribologiques et une bonne stabilité thermique. Bien qu’il soit établi que le comportement tribologique de ces couches est moins dépendant de l’environnement que celui des couches a-C:H, sans éléments d’addition, l’origine physicochimique de ce comportement reste à élucider. Ce travail de thèse s’inscrit dans le cadre une collaboration internationale entre le Laboratoire de Tribologie et Dynamique des Systèmes de l’Ecole Centrale Lyon et le département de Génie Mécanique et Mécanique Appliquée de l’Université de Pennsylvanie, et a pour objectifs d’apporter des réponses à ces questions ouvertes. Un large éventail de techniques expérimentales complémentaires, notamment la nanoindentation, la microscopie à force atomique (AFM), la microscopie à mesure de force (FFM), la microscopie optique et électronique, le Raman, la spectroscopie de photoélectron X (XPS) et la spectroscopie de structure près du front d’absorption de rayons X (NEXAFS) a été mis en oeuvre pour non seulement établir une carte d’identité mécanique, structurale et chimique du revêtement initial, mais aussi comprendre les modifications structurelles induites par le frottement. Afin de contrôler l’environnement au cours des essais tribologiques, nous avons utilisé d’une part un tribomètre linéaire alternatif, que nous avons équipé d’un système de soufflage de gaz permettant de changer rapidement l’environnent au cours des essais, et d’autre part un tribomètre analytique à environnement contrôlé autorisant des expérimentations tant sous vide poussé qu’à pression élevée de gaz. Ainsi, nous avons pu montrer que le coefficient de frottement augmente avec le taux de vapeur d’eau dans l’environnement et cela est réversible lorsqu’on diminue brusquement l’humidité. En outre, la vapeur d’eau protège la couche de l’usure alors que la présence d’oxygène la favorise. Grace aux observations en microscopie électronique, nous avons pu prouver que le comportement tribologique des couches a- C:H:Si:O, lors d’un frottement contre de l’acier 100Cr6, est essentiellement contrôlé par la formation de jonctions adhésives dans l’interface. Sous vide poussé ou à faible pression de gaz (<1 mbar de vapeur d’eau, <10 mbar d’oxygène ou <50 mbar d’hydrogène), la rupture de ces jonctions adhésives a lieu dans l’acier, résultant en un transfert de matériau de l’acier vers l’a-C:H:Si:O s’accompagnant d’un coefficient de frottement élevé (μ≈1.2). Au delà de ces pressions seuils de gaz, les jonctions adhésives se rompent du côté du a-C:H:Si:O, le transfert de matière s’opérant alors dans la direction opposée, du revêtement vers l’acier. Des analyses NEXAFS ont révélé que ce phénomène s’expliquait par une réaction dissociative entre les éléments du gaz environnant et les liaisons carbone C–C contraintes, favorisée par la sollicitation mécanique en extrême surface de l’a-C:H:Si:O. Ceci résulte en une diminution drastique du coefficient de frottement à des valeurs d’un ordre de grandeur inférieures à celles obtenues dans la configuration précédente. L’ensemble de ces résultats nous a ainsi permis de développer un modèle expérimental expliquant les mécanismes fondamentaux d’interaction entre l’environnement et les lubrifiants solides du type a-C:H:Si:O. / Like Carbon (DLC) coatings that exhibit outstanding mechanical properties, thermal stability and tribological performance. It is well established that the frictional and wear performances of a-C:H:Si:O are less dependent on environment than that of pure hydrogenated amorphous carbon (a-C:H). However the fundamental mechanisms accounting for such excellent tribological behavior of a-C:H:Si:O are still not fully understood. The present work, which is part of a collaboration between the Laboratoire de Tribologie et Dynamique des Systèmes of Ecole Centrale de Lyon and the department of Mechanical Engineering and Applied Mechanics of University of Pennsylvania, consists in using a multi-scale, multidisciplinary and multi-technique experimental approach for understanding the influence of environment on the tribological response of a-C:H:Si:O. A wide rang of complementary techniques, including nanoindentation, Atomic Force Microscopy (AFM), Friction Force Microscopy (FFM), optical and electron microscopy, Raman, X-ray Photoelectron Spectroscopy (XPS) and near edge x-ray absorption fine structure spectroscopy (NEXAFS), have thus been used to fully characterize the structure, composition and mechanics of the studied material, as deposited as well as after tribological testing. Control of the environment has been achieved first thanks to an open air linear reciprocating tribometer that we equipped with a gas blowing system, thus allowing a quick change of the sliding environment, and a environment-controlled analytical tribometer operating from high vacuum to elevated pressures of desired gases. We were able to evidence the strong influence of the amount of water vapor in the environment on the friction behavior of a- C:H:Si:O, with a reversible behavior when abruptly changing the environment. Contrary to water vapor, oxygen promotes the wear of a-C:H:Si:O. SEM observations revealed that while sliding a-C:H:Si:O against 52100 steel, the frictional response is controlled by the build-up and the release of adhesive junctions within the interface. Under high vacuum and below a threshold pressure of water vapor (1 mbar), oxygen (10 mbar) and hydrogen (50 mbar), adhesive junctions are released in the steel, resulting in a transfer of material from steel to a-C:H:Si:O and in a high coefficient of friction (μ≈1.2). However, as the gas pressure is increased above the threshold, the adhesive junctions break on the a-C:H:Si:O side, leading to a material transfer in the opposite direction, from the a-C:H:Si:O to the steel. NEXAFS spectroscopy revealed that a dissociative reaction occurs between the gaseous species and the strained C–C atoms in the near surface region ofa-C:H:Si:O, thus resulting in a drastic decrease of the steady state coefficient of friction by at least an order of magnitude. In light of these observations, an analytical model has been proposed to describe the fundamental interaction mechanisms between the environment and the a-C:H:Si:O/steel tribopairs.

The demand for electrical energy is steadily increasing. Highly efficient organic solar cells based on mixed, strongly absorbing organic molecules convert sunlight into electricity and, thus, have the potential to contribute to the worlds energy production. The continuous development of new materials during the last decades lead to a swift increase of power conversion efficiencies (PCE) of organic solar cells, recently reaching 12%. Despite these breakthroughs, the usage of highly complex organic molecules blended together to form a self-organised absorber layer results in complicated morphologies that are poorly understood. However, the morphology has a tremendous impact on the photon-to-electron conversion, affecting all processes ranging from light absorption to charge carrier extraction. This dissertation studies the role of phase-separation of the self-organised thin film blend layers utilized in organic solar cells. On the molecular scale, we manipulate the phase-separation, using different molecule combinations ranging from the well-known ZnPc:C 60 blend layers to highly efficient oligothiophene:C60 blend layers. On the macroscopic scale, we shape the morphology by depositing the aforementioned blend layers on differently heated substrates (in-vacuo substrate temperature, Tsub). To characterise the manufactured blend layers, we utilize high resolution microscopy techniques such as photoconductive atomic force microscopy, different electron microscopic techniques, X-ray microscopy etc., and various established and newly developed computational simulations to rationalise the experimental findings. This multi-technique, multi-scale approach fulfils the demands of several scientific articles to analyse a wide range of length scales to understand the underlying optoelectronic processes. Varying the mixing ratio of a ZnPc:C60 blend layer from 2:1 to 6:1 at fixed in vacuo substrate temperature results in a continuous increase of surface roughness, decrease of short-circuit current, and decrease of crystallinity. Additionally performed density functional theory calculations and 3D drift-diffusion simulations explain the observed crystalline ZnPc nanorod formation by the presence of C60 in the bulk volume and the in turn lowered recombination at crystalline ZnPc nanorods. Moving to oligothiophene:C60 blend layers used in highly efficient organic solar cells deposited at elevated substrate temperatures, we find an increase of phase-separation, surface roughness, decrease of oligothiophene-C60 contacts, and reduced disorder upon increasing Tsub from RT (PCE=4.5%) to 80 °C (PCE=6.8%). At Tsub =140 °C, we observe the formation of micrometer-sized aggregates on the surface resulting in inhomogeneous light absorption and charge carrier extraction, which in turn massively lowers the power conversion efficiency to 1.9%. Subtly changing the molecular structure of the oligothiophene molecule by attaching two additional methyl side chains affects the thin film growth, which is also dependent on the substrate type. In conclusion, the utilized highly sensitive characterisation methods are suitable to study the impact of the morphology on the device performance of all kinds of organic electronic devices, as we demonstrate for organic blend layers. At the prototypical ZnPc:C60 blend, we discovered a way to grow ZnPc nanorods from the blend layer. These nanorods are highly crystalline and facilitate a lowered charge carrier recombination which is highly desirable in organic solar cells. The obtained results at oligothiophene: C60 blends clearly demonstrate the universality of the multi-technique approach for an in-depth understanding of the fragile interplay between phase-separation and phase-connectivity in efficient organic solar cells. Overall, we can conclude that both molecular structure and external processing parameters affect the morphology in manifold ways and, thus, need to be considered already at the synthesis of new materials.

Das Hauptanliegen dieser Arbeit war es valide chemische Verfahren für die Optimierung der Gesamtleistung von Glykan-Microarrays bereitzustellen. Dafür erfolgte eine gründliche Untersuchung jedes einzelnen Prozessschritts innerhalb der Arrayproduktion durch Anwendung komplementärer Methoden der chemischen Oberflächenanalytik. Mit Hilfe von fortgeschrittenen Verfahren der Elektronen-Spektroskopie für die chemische Anlayse (ESCA/XPS) wurden valide quantitative Daten bei der chemischen Charakterisierung der Oberflächen erhalten die mit den häufig eingesetzten qualitativen bzw. indirekten Verfahren (z.B. Kontaktwinkel Goniometrie und Fluoreszenz-Spektroskopie) so nicht erhalten werden können. Die robuste Anbindung von Glykanen auf der Substratoberfläche ist Voraussetzung für eine reproduzierbare Anwendung in der Diagnostik aber auch für die Entwicklung valider quantitativer Charakterisierungsmethoden zur Bewertung der Effizienz der Immobilisierungsreaktionen. Ein Schwerpunkt der Arbeit lag in der Charakterisierung und Optimierung der Glykananbindung an amin-reaktive Oberflächen. Hierzu wurden z.B. spezielle Glykane mit Fluorlabel auf epoxid-funktionalisierten Siliziumoberflächen immobilisiert. Eine Quantifizierung der angebundenen Glykane ist zum Beispiel über die Bestimmung der CF3-Gruppe im hochaufgelösten C1s XPS Spektrum möglich. Die Interaktionen Sonde-Analyt wurden modellhaft mit immobilisierten Glykanen und dem Lektin Concanavalin A mit Verfahren der chemischen Oberflächenanalytik untersucht. Neben der chemischen Charakterisierung frisch präparierter Glykansonden wurde auch das Alterungsverhalten der Glykan-Microarrays untersucht. / The objective of this research is to sidestep many of the initial and current problems of glycan microarray based devices by using new analytical approaches to control molecular engineering. For this purpose, a thorough investigation of each individual step in the array production is carried out by applying complementary methods of surface chemical analysis. New fluorophore-free protocols based on methods of surface analysis as XPS will be developed and validated to enable glycan microarray performance optimization. The advantage of these methods is the direct quantitative access to chemical bonds at high lateral resolution. In contrast to the frequently used qualitative or indirect methods (e.g. contact angle goniometry and fluorescence spectroscopy), valid quantitative data are obtained. The robust binding of glycans on the substrate surface, is a prerequisite for a reproducible application in the diagnostics but also for the development of valid quantitative characterization methods for the evaluation of the efficiency of the immobilization reactions. One focus of the work was the characterization and optimization of the glycan binding to popular amine-reactive surfaces. For this purpose, specific glycans with fluorine-label were immobilized on epoxide-functionalized silicon surfaces. A quantification of the attached glycan molecules is possible, for example, by determining the amount of CF3 groups using the high-resolution C1s XPS spectrum. The interactions between model probe (glycan molecules) and model analyte (lectin concanavalin A) were investigated using powerful methods surface chemical analysis. In addition to the chemical characterization of freshly prepared glycan probes, the aging behavior of the glycan microarrays was also investigated.

The donor-acceptor couple CuPc/C60 has been the subject of recent studies in organic solar cells due to its combined abilities in light absorption (CuPc) and charge transport (C60). By better understanding the electronic and geometric nature of the system it is possible to shed light on how the molecules act under different conditions. In this study the geometric properties for three different configurations have been studied by means of Density Functional Theory (DFT). By comparing the molecular structure of pristine CuPc with the structure of CuPc in the presence of C60, a slight elongation of the bonds is observed when the fullerene is present. This is especially true for the Cu-N bonds. By further including van der Waals interactions, no change in bond lengths is observed. This, in turn, suggests that, most likely, the interaction between the two molecules is relatively weak and the C60 will not have a major influence on the electronic structure of CuPc. The N1s X-ray Photoelectron Spectroscopy (XPS) and Near Edge X-ray Absorption Fine Structure (NEXAFS) calculations confirm these conclusions, as only very small changes in peak positions are observed when comparing pristine CuPc with CuPc/C60. / Tack vare sina egenskaper inom absorption och laddningsöverföring har CuPc och fullerenen C60 varit föremål för omfattande studier bland forskare inom organiska solceller. Genom att få större förståelse för den geometriska såväl som den elektroniska konfigurationen inom och mellan paret kan man förutse hur dessa kommer att bete sig i olika sammansättningar. I denna studie har de geometriska förutsättningarna studerats där olika konfigurationer beräknats genom täthetsfunktionalteori (DFT). Genom att mäta bindningslängderna mellan koppar, kol och de olika typer av kväve i CuPc i de olika systemen, kan det inses att bindningarna förlängs då C60 läggs till. Då van der Waals-interaktioner inkluderades observerades ingen större förändring i bindingslängderna i jämförelse med fallet utan van der Waals-interaktioner. Detta tyder på att växelverkan mellan de två molekylerna är relativt svag och att C60-fullerenen ej har någon större påverkan på elektronkonfigurationen i CuPc. Beräkningarna av N1s X-ray Photoelectron Spectroscopy (XPS) och Near Edge X-ray Absorption Fine Structure (NEXAFS) stödjer denna slutsats då endast små skiftningar i topparna observerades vid jämförelse mellan rent CuPc och CuPc/C60.

Two-dimensional layered materials, namely monolayer hexagonal boron nitride and graphene were grown by CVD on various transition metals. The physical and chemical properties of these systems were characterized systematically using synchrotron-based spectroscopic techniques, scanning tunneling microscopy and low energy electron diffraction. It is learned that the overlayer–substrate interaction is caused by the overlayer π–substrate d band hybridization. The physical properties of these overlayers depend on the strength of interaction and the degree of lattice matching at the interface. The strength of interaction between the boron nitride and graphene overlayers and the transition metal substrates is increasing from Pt(111)–Ir(111)–Rh(111)–Ru(0001). For overlayers adsorbed on Rh and Ru, the interplay between these two parameters can result in corrugation of the overlayer, i.e. a surface with bonding and non-bonding areas. The amplitude of corrugation is increasing with the strength of interfacial interaction. The corrugated BN overlayer (BN nanomesh) was used as a template for the growth of two-dimensional and highly dispersive Au nanoparticles. In addition, the inert BN nanomesh was used as a substrate for the deposition of pentacene molecules that conform to the corrugated surface while preserving the herringbone crystal structure. The coadsorption of oxygen and Co clusters on the nanomesh was investigated. Oxygen was utilized to lower the Co surface energy, i.e. to prevent Co agglomeration. It is observed that the smaller Co clusters intercalate through the BN overlayer upon soft annealing. Beside the surface structure, the substrate induced surface reactivity of the MG overlayer was employed to promote the hydrogenation of graphene on Pt, Ir and Ni. The graphene layer adsorbed on Pt and Ir shows higher H uptake than MG/Ni. Furthermore the uptake increases with the size of the bonded graphene. The small H uptake for MG/Ni was attributed to the electron localization in the C-Ni bonds.