Dans ce travail, nous étudions l’adsorption de protéines sur des surfaces chimiquement contrôlées. Le but est d’établir le lien entre les propriétés physico-chimiques de la surface (hydrophobicité /charge) et la structure physique de protéines. Des couches auto-assemblées de thiols ayant des groupements terminaux différents sont formées sur des surfaces d’or (SAM) et servent de support à l’adsorption ou du greffage de protéines. Les SAM sont caractérisés, avant ou après l’adsorption de protéines, avec une combinaison de techniques. Des analyses ex situ sont réalisées, dans l’air, en spectroscopie infrarouge en lumière polarisée (PM-IRRAS) ou, sous ultra-vide, en spectroscopie des photoelectrons X (XPS) et en spectrométrie de masse d’ions secondaires (ToF-SIMS). L’analyse en composante principale (PCA) des résultats ToF-SIMS aide à révéler l’orientation des protéines adsorbées grâce à la répartition des fragments d’acides aminés. En microbalance à quartz avec mesure de la dissipation (QCM-D), l’adsorption des protéines est suivie in situ (i.e. en phase liquide). Deux protéines globulaires ayant des propriétés structurales différentes sont d’abord étudiées, la β-Lactoglobuline (βLG) est dite dure quand l’albumine de sérum bovin (BSA) est dite souple. Des orientations différentes sont proposées après adsorption sur les SAM. Un cas plus complexe est ensuite étudié avec l’adsorption ou le greffage d’un anticorps sur les surfaces. De nouveau, différentes orientations sont proposées et elles sont corrélées à des mesures de bio-reconnaissances. En conclusion, cette thèse établie une méthodologie de détermination directe et sans marquage de l’orientation de protéines adsorbées. / In this work we studied protein adsorption on chemically well-controlled surfaces. The focus is put on linking physico-chemical properties of surfaces (hydrophobicity/charge) to the structural properties of the adsorbed proteins. To this end, alkyl thiols differing by their end group were used to build self-assembled monolayers on gold substrates (SAM) that serve as templates for protein adsorption or covalent grafting. SAM surfaces before and after protein adsorption were characterized with a combination of techniques. Ex situ analysis were carried out, in air with polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS), or in vacuum using X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS). ToF-SIMS results were analyzed statistically in principal component analysis (PCA) to reveal preferential orientations based on amino acids fragments distributions. Protein adsorption was also followed directly in situ (i.e. in the liquid phase) with quartz crystal microbalance with dissipation monitoring (QCM-D). Two model proteins – β-Lactoglobulin (βLG) and bovine serum albumin (BSA) – were first studied. They are both model globular proteins with different structural properties (βLG is hard while BSA is soft). Different orientations were proposed for both proteins on each SAM surface. A more complex case was then studied with the adsorption and grafting of a monoclonal antibody on the SAM. Again differences in orientations were determined and correlated to biorecognition measurements. In conclusion, this thesis establishes a methodology for the direct label free determination of protein orientation on surfaces.

My dissertation focuses on (i) the development of new analysis tools and methodologies for analyzing X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) data, and (ii) the comprehensive characterization of materials (nanodiamonds) using a multi-instrument approach. Chapter 1 contains (i) a discussion of the two techniques I focused on most in my work: XPS and ToF-SIMS, (ii) a discussion of the common chemometrics techniques used to analyze data from these methods, and (iii) the advantages/rationale behind the multi-instrument characterization of materials. Chapter 2 describes various good practices for obtaining reasonable peak fits in XPS, which can also be applied to peak fitting data from different techniques. To address the issue of user subjectivity/bias in XPS peak fitting, I introduce two less biased mathematical functions for characterizing XPS narrow scans, namely the equivalent width (EW) and the autocorrelation width (AW). These functions are discussed in Chapters 3 and 4. In Chapter 5, I then introduce uniqueness plots as simple and straightforward graphical tools for assessing the quality of XPS peak fits and for determining whether fit parameters are correlated. This tool is extensively used in spectroscopic ellipsometry, and the mathematics behind it is known in XPS. However, to the best of my knowledge, this graphical tool has never been applied to XPS. ToF-SIMS data analysis is somewhat challenging due to the enormous amounts of data that are collected, and also the matrix effect in SIMS. This amount of information is significantly increased when depth profiles are performed on samples. Chapter 6 discusses a new chemometrics tool that I introduce for analysis of complex data sets, with emphasis on XPS and ToF-SIMS depth profiling data. The new approach is called the Information Content (IC) or entropy, which is adapted from Claude Shannon's work on Information Theory. Chapter 7 then contains a presentation of the comprehensive characterization of five nanodiamond samples used to manufacture particles for liquid chromatography. The advantages of a multi-instrument approach for material characterization and the lack of comprehensive material characterization in the literature are emphasized. To the best of my knowledge this is the most comprehensive characterization of nanodiamonds that has been reported in the literature. Chapter 8 presents conclusions of my work and future work. This thesis also contains six appendices. Appendix 1 contains an article from a scientific magazine that I wrote to highlight the importance and applications of the EW and AW to characterize XPS narrow scans. Appendices 2-5 are application notes I wrote on separations I performed on a nanodiamond based HPLC column. Finally, Appendix 6 describes the ToF-SIMS analysis of the tungsten species in the nanodiamond samples characterized in Chapter 7.

abstract: Oxygen fugacity (ƒO2) is a thermodynamic variable used to represent the redox state of a material or a system. It is equivalent to the partial pressure of oxygen in a particular environment corrected for the non-ideal behavior of the gas. ƒO2 is often used to indicate the potential for iron to occur in a more oxidized or reduced state at a particular temperature and pressure in a natural system. Secondary ion mass spectrometry (SIMS) is a powerful analytical instrument that can be used to analyze elemental and isotopic compositional information about microscopic features within solid materials. SIMS analyses of the secondary ion energy distribution of semi-pure metals demonstrate that the energy spectrum of individual mass lines can provide information about alterations in its surface environment. The application of high-resolution (see Appendix C) energy spectrum calibrations to natural ilmenite led to the investigation of zirconium (90Zr+) and niobium (93Nb+) as potential indicators of sample ƒO2. Energy spectrum measurements were performed on an array of ilmenite crystals from the earth’s upper mantle retrieved from kimberlites and from a reduced meteorite. In all studied materials, variability in the peak shape and width of the energy spectra has been correlated with inferred sample ƒO2. The best descriptor of this relationship is the full-width at half-maximum (FWHM; see Appendix C) of the energy spectra for each sample. It has been estimated that a 1eV change in the FWHM of 93Nb+ energy spectra is roughly equivalent to 1 log unit ƒO2. Simple estimates of precision suggest the FWHM values can be trusted to  1eV and sample ƒO2 can be predicted to ±1 log unit, assuming the temperature of formation is known. The work of this thesis also explores the applicability of this technique beyond analysis of semi-pure metals and ilmenite crystals from kimberlites. This technique was applied to titanium oxides experimentally formed at known ƒO2 as well as an ilmenite crystal that showed compositional variations across the grain (i.e., core to rim chemical variations). Analyses of titanium oxides formed at known ƒO2 agree with the estimation that 1 eV change in the FWHM of 93Nb+ is equivalent to ~1 log unit ƒO2 (in all cases but one); this is also true for analyses of a natural ilmenite crystal with compositional variations across the grain. / Dissertation/Thesis / Masters Thesis Geological Sciences 2019

La stabilité d'un verre est liée à sa composition et l'environnement contrôle son altération. Pour les verres historiques, les polluants organiques émis par les vitrines en bois interviennent dans leur altération. Ce travail étudie les mécanismes d'altération des acides acétique et formique et du formaldéhyde sur des objets de musée et des verres vieillis artificiellement, de composition sodique. Après détermination de la composition par microsonde électronique, la décomposition des spectres Raman a servi à établir des corrélations entre composition et structure des verres, et à interpréter les variations de structure entre verre sain et altéré. La structure des objets altérés par les polluants est caractéristique d'une altération par lixiviation, où seuls les silicates liés aux alcalins sont transformés en silanols, qui polymérisent par la suite. Les profils de concentrations SIMS de verres vieillis en atmosphères artificielles et réelles ont permis de suivre l'altération en fonction du temps, l'humidité et la concentration en polluants. Le film d'eau formé à la surface par l'humidité et son acidité contrôlent l'altération par lixiviation des alcalins et hydratation du verre. Le formaldéhyde n'agit pas sur la réaction de lixiviation tandis que les acides l'accélèrent et l'amplifient. Quelques soient les proportions des polluants, les composés formates prédominent dans les produits cristallins, même en faible concentration d'acide formique. L'humidité et la température fluctuante des musées entretiennent la réaction de lixiviation. L'évidence du rôle néfaste des polluants organiques acides dans l'altération des verres sodiques permettra d'améliorer leur conservation.

<p>This work focuses on the surface and interfacial characterisation of silane films of a non-organofunctional silane, 1,2-bis(triethoxysilyl)ethane (BTSE), and an organofunctional silane, γ-mercaptopropyltrimethoxysilane (γ-MPS), deposited on Al, Zn and Al-43.4Zn-1.6Si (AlZn) alloy coated steel. Furthermore, a tribological study of a vegetable oil coupled to an aluminium surface pre-treated with γ-MPS is presented and, finally, the tribological response of thin organic coatings exposed to a sliding contact as evaluated by surface analysis is discussed. The main analyses techniques used were time-of-flight secondary ion mass spectrometry (ToF-SIMS), Auger electron spectroscopy (AES) and x-ray photoelectron spectroscopy (XPS). </p><p>The results presented in this thesis show that the combination of ToF-SIMS, AES and XPS analysis can be used in order to obtain useful and complementary information regarding the surface and interface characteristics of silane films and organic coatings deposited on metal substrates.</p><p>The major result regarding the silane films is that the silane film composition/structure is not dependent of pH-value during deposition or type of metal substrate. The presence of Si-O-Me ion fragments in the ToF-SIMS spectra is a strong indication that a chemical interaction between the silane film and the metal substrate exists. Furthermore, it has been shown that it is possible to bond a vegetable oil to a thiol functionalised aluminium surface and to produce a coating thick enough to obtain desired friction and wear characteristics. Finally, the use of ToF-SIMS analysis makes it possible to distinguish between mechanical and tribochemical wear mechanisms.</p>

A study of the effect of catalyst properties on the synthesis of carbon nanotubes (CNTs) is done in this thesis. Three different metal alloy catalysts, Fe/Ti, Ni/Ti, Co/Ti, have been studied. Various atomic concentrations and thicknesses were cosputter deposited on clean Si wafers using AJA Orion 4 RF Magnetron sputter deposition tool at 5mtorr and 17��C, and the films were characterized using a scanning electron microscope, Energy-dispersive X-ray spectroscopy. All the alloys have been annealed at 650��C and 3 torr in an argon atmosphere at 100 SCCM, followed by ammonia gas plasma etch at different powers at 3 torr and 50 SCCM NH��� flow in a modified parallel plate RF chemical vapor deposition tool for 1 minute. The influence of plasma power, thickness of catalyst and concentration of Ti the secondary metal in the alloy composition, on the surface morphology of the catalyst are investigated by characterizing them with atomic force microscopy. The study has shown that the surface roughness is affected by Ti concentration, thickness and plasma power. The 35 W power NH��� plasma produced rougher surfaces when compared to the 75 W NH��� plasma. The result is interpreted as follows: ion bombardment leads to greater etching of the catalyst surface. Thus, plasma power must be optimized for catalyst thin film and etch time. The study has provided an in depth analysis and understanding of the various factors that influence catalyst surface morphology which can be applied into further study for optimizing parameters for synthesis of single walled CNTs. Following this, a study on catalysts for CNT synthesis was performed using Plasma enhanced chemical vapor deposition and characterized by scanning electron microscope. CNTs were synthesized on Ni, Ni-Ti, Co, Co-Ti and Fe catalyst. Ni, Ni-Ti catalyst produced forest like vertically aligned CNTs whereas Co, Co-Ti produced vertically aligned free standing CNTs. The growth was dense and uniform across the substrate. Initial growth runs on Fe, Fe-Ti alloy did not produce any CNTs until catalyst was restructured with a thicker Ti under layer after an investigation using Secondary ion mass spectrometry of suspected Fe catalyst poisoning due to reaction with Si substrate. A room temperature run was carried out on annealed and plasma etched Ni catalyst and no CNTs were produced indicating the importance of substrate temperature of CNTs. A deeper understanding of factors of influence on CNTs such as catalyst types, structure/morphology, and substrate temperature has been achieved with this study. / Graduation date: 2013

This work focuses on the emission processes of metal-organic clusters MmMen, (M is the organic molecule and Me the metal atom) ejected from self assembled monolayers (SAMs) of alkanethiols on gold after keV ion bombardment. These aggregates are often observed upon energetic ion bombardment of strongly bound molecules like SAMs. The explanation of this effect remains elusive, especially for large clusters as those observed in our study. The emission of these clusters is investigated using ToF-SIMS under 15 keV Ga+ bombardment. In particular, we have measured the energy distributions (KEDs), which are informative of the physical processes of sputtering. We have probed both the influence of the intermolecular forces and the adsorbate-metal bonding on the cluster ion emission. Importantly, our KEDs revealed that a significant fraction of MmMen clusters is formed via the metastable decay of larger aggregates in the acceleration section of the spectrometer. This is the experimental evidence that another cluster formation channel has to be considered in addition to the recombination mechanisms proposed by other groups. In parallel to these experiments, we have used classical molecular dynamics (MD) simulations to model an overlayer of octanethiols on gold. A realistic potential has been used including long-range forces between the hydrocarbon chains of the alkanethiols. Our key finding concerns the emission of large clusters which were not observed under sub-keV projectile impact. Statistically, they are predominantly formed in high yield events, where many fragments and (supra)molecular species are ejected. From the microscopic viewpoint, these events mostly stem from the confinement of the projectile and recoil atom energies in a finite nanovolume of the surface. As a result of the high local energy density, molecular aggregates desorb from an overheated liquid-like region surrounding the impact point. In summary, from a combined experimental and computational study we have shown that analytical models involving linear collision cascades and recombination processes are insufficient to describe metal-thiolate cluster emission from SAMs under keV ion bombardment. The detailed MD investigation have allowed us to obtain a general picture of the emission of these aggregates in which the mechanisms at play are reminiscent of those high yields events (megaevents) with non linear effects used usually to account for large (bio)molecule desorption.

With increasing miniaturization in microelectronics the wirebonds used in IC packages are witnessing a thrust towards fine pitch wirebonding. To have a precise control over loop height of the wirebond for fine pitch wirebonding, it is imperative to do mechanical characterization of the wirebond. The present work studies the mechanical properties of gold wire and wirebond using nanoindentation. The wirebond specimen surface was planarized using mechanical polishing. The loop height of the gold wirebond is directly proportional to the length of the heat affected zone (HAZ) above the ball of gold wirebond. Metallographic preparation of gold wirebond cross section reveals the presence of undesirable coarse grain structure in HAZ due to recrystallization and grain growth in the gold wire adjacent to the ball. The recrystallization temperature of our gold wire was found using D.S.C. to be 340.66°C. The doping elements present in the gold wire used, were identified using TOF-SIMS. Nanoindentation of the gold wire was done at different maximum loads to observe the hardness variation with load. The nanoindentation of gold wirebond has confirmed a v-shaped hardness profile in the HAZ. The hardness minima for the particular gold wire used with a ball size ratio of 2.4 was observed at distance of 160-170 µm from the neck of the ball. The elastic modulus was found to vary randomly and to be independent of the microstructure in the wirebond. A yield stress profile based on empirical hardness-yield strength correlation has been predicted for the gold wirebond. / Singapore-MIT Alliance (SMA)

Some collision cascades, induced by keV polyatomic projectiles, result in the emission of multiple secondary ions. Such co-emissions imply that the ejecta originate from molecules co-located within the nano-volume perturbed by a single projectile impact. The relevance for the chemical analysis of nano-domains depends on the effectiveness of the projectile to cause co-emission of two or more secondary ions. This research examines how projectile characteristics, i.e. the energy and number of constituent atoms in the projectile, influence multiple secondary ion emission, or "superefficient" events. In addition we examine the relevance of this technique for nanostructure investigation. Yields have been measured for multi-ion emission events as a function of projectile characteristics. The data show that some collision cascades are "superefficient". For example, in a four-ion emission event, the yield for the phenylalanine quasi-molecular ion is two orders of magnitude larger from Au4+ impacts than from equal velocity Au+ projectiles. Yields for the co-emission of two phenylalanine quasi-molecular ions from "super-efficient" events have been measured. This case is particularly productive in that the detection of two analytically significant ions is recorded from a single event. Large increases (one to two orders of magnitude) in co-emitted ion yields were observed with increasing projectile energy and complexity. Correlation coefficients were calculated for the co-emission of two Ph ions, their behavior suggests differences in emission pathways for bombardment by atomic and polyatomic projectiles. Finally, we use this methodology to investigate surface structural effects on the occurrence of "super-efficient" events. The results indicate that it is possible to distinguish between two phases of a chemical compound although the stoichiometry remains the same. These results confirm previous predictions concerning the chemical nature of these "super-efficient" events. Also shown is that they are sensitive to the surface nanoenvironment. This approach extends the technology of Secondary Ion Mass Spectrometry by providing a methodology for probing surface nano-domains at the sub100 nm level.

Le but de ce travail est d’étudier l’effet de la vapeur d’eau contenue dans le plasma sur la composition et la vitesse de dépôt des couches minces d’oxynitrures de chrome déposées par pulvérisation cathodique magnétron réactive avec l’air contenant différentes teneurs en vapeur d’eau (humidité relative). Les techniques d’analyses par faisceau d’ions énergétiques : RBS et réactions nucléaires nous ont permis de déterminer les concentrations relatives des éléments déposés. Les profils d’hydrogène et d’azote ont été déterminés par RNRA et Tof- SIMS. La liaison chimique a été identifiée par LEEIXS et XPS. Les mesures XPS ont dévoilé la présence d’une phase autre que Cr, CrN, Cr2O3 et CrO2 ; cette nouvelle phase possède une stoechiométrie (CrO2)3-N. La teneur en Cr et ses composés varie en fonction du flux et de l’humidité relative de l’air. En mode métallique de la pulvérisation cathodique, la stoechiométrie Cr2O3 est majoritaire en coexistence avec de faibles teneurs et CrN, CrO2 et (CrO2)3-N alors qu’en mode composé, c’est la stoechiométrie CrO2 qui prédomine./ The aim of this work is to study the stoichiometry of chromium oxynitride thin films deposited by reactive magnetron sputtering in presence of air with various relative humidities. Ion Beam Analysis methods: RBS (Rutherford Backscattering Spectroscopy) and resonant nuclear reaction (RNRA) were used to determine the thickness and the composition of the films. Hydrogen and nitrogen profiles were obtained by RNRA and Tof-SIMS. The chemical bonds were investigated by XPS and LEEIXS. The chromium metallic and chromium compounds concentrations were measured versus the flow and relative humidity of the air. During sputtering in metallic mode, Cr2O3 stoichiometry is observed with low contents of CrN, CrO2 and (CrO2)3-N whereas in compound mode the CrO2 stoichiometry predominates.