Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 132-140).

When and how life first emerged on the Earth is an area of intense research. Signs of the first life on Earth, including morphological fossils, are scarce and hard to interpret. An alternative approach is to study organic biomarkers, which are molecular fossils commonly considered as bona fide biosignatures. The main objective of the project is to develop an approach for analysis of single oil-bearing fluid inclusions and most importantly the detection of organic biomarkers in these inclusions. Analysis of oil-bearing fluid inclusions is advantageous since the inclusions may provide an uncontaminated sample source of Precambrian hopanes and steranes, which are key biomarkers for tracing the early evolution of life on Earth. Due to the presence of several inclusion generations, single inclusion analysis is desired in order to constrain biomarkers to specific inclusions. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) could be an excellent tool for analysis of these types of samples. The development of the approach for analysis of single oil-bearing inclusions was done in a two-step process; i) a number of crude oils were analysed with ToF-SIMS and gas chromatography mass-spectrometry (GC-MS) to facilitate interpretation of ToF-SIMS spectra of these types of samples and, ii) a procedure that combines micrographs with ion etching and ToF-SIMS analysis was developed for analysis of inclusions. The feasibility of the technique was demonstrated for oil inclusions from the Siljan impact crater in which hopanes and steranes where detected. Single oil-bearing fluid inclusions trapped in mid-Proterozoic sandstones from Northern Australia were subsequently analyzed, and steranes and hopanes were detected in these inclusions. If applied on older inclusions this approach may help answer some of the questions regarding the emergence and evolution of life on Earth, and if applied on extraterrestrial samples, also the possibility of life on other planets and moons. / Livets uppkomst och tidiga utveckling på jorden är ett hett forskningsfält. Hur och när livet och dess olika domäner (arkéer, bakterier och eukaryoter) uppstod på jorden är fortfarande oklart vilket beror på att de första tecknen på liv, vilka inkluderar morfologiska fossil, spårfossil och isotoper, är få och svåra att tolka. Ett alternativt sätt att studera det tidiga livet är att studera organiska biomarkörer som är organiska molekyler som anses unika för liv. Huvudmålet med projektet är att utveckla en metod som kan detektera organiska biomarkörer i enskilda oljebärande vätskeinneslutningar. Vätskeinneslutningar, som är små mängder vätska (picoliter) infångad in en sten, är intressanta då de är en potentiell provkälla för prekambriska (äldre än 500 miljoner år) biomarkörer, som hopaner och steraner, vilka används för att utforska livets tidiga utveckling på jorden. Analys av enskilda inneslutningar är emellertid oftast nödvändigt för att kunna tidsavgränsa biomarkörer. På grund av att de flesta inneslutningar är små (10 µm i diameter) är det inte möjligt att analysera en enskild vätskeinneslutning med standardtekniken gaskromatografi-masspektrometri (GC-MS). Time-of-flight secondary ion mass spektrometri (ToF-SIMS) med sin höga känslighet, höga massupplösning och kapacitet för 2D-representation av analysdata och djupprofilering av prover är en utmärkt teknik för analys av enskilda inneslutningar. Metoden för analys av enskilda inneslutningar utvecklades i två steg. Först analyserades ett antal råoljor med ToF-SIMS och GC-MS för att underlätta förståelsen av ToF-SIMS-spektra från dessa typer av prover. Därefter utvecklades en metod som bestod av mikroskopering för att lokalisera inneslutningen, jonetsning för att öppna inneslutningen och ToF-SIMS analys av det exponerade innehållet. Metoden testades framgångsrikt på enskilda inneslutningar i hydrotermala vener av flusspat och kalcit i ordovicisk (488-443 miljoner år sedan) kalksten. Därefter användes den utvecklade metoden för att analysera enskilda vätskeinneslutningar i 1,43 miljarder år gammal sandsten från norra Australien, i vilka hopaner och steraner detekterades. De detekterade steranerna visar att trots att havet under denna tid var syrefritt existerade det lokala syrerika miljöer där eukaryoter kunde överleva. Om den utvecklade metoden används på ännu äldre inneslutningar, vilka har daterats till 3,2 miljarder år, kan den komma att svara på några de mest fundamentala frågorna kring livets uppkomst och tidiga utveckling. Om metoden används på utomjordiska prover kan den svara på frågan om det finns liv på andra planeter eller månar. / At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Submitted.

This thesis studies comparison and connection of two spectrometric methods – low energy ion scattering spektrometry (LEIS) and secondary ion mass spectrometry (SIMS). SIMS method, despite its many positive qualities, suffers of so called matrix effect, which makes quantifiaction of data very difficult. LEIS method on the other hand is immune to this effect and so it’s suitable completion of SIMS method. As a convenient sample have been chosen AlGaN samples with various concentration of gallium and aluminium. In the first part of thesis is introduced physical essence of SIMS and LEIS method, experimental details and studied samples. In second part of the thesis there’s a description of measurements and comparison of data gained by each method.

Die Erweiterung experimenteller Infrastrukturen um neuartige Sensor eröffnen die Möglichkeit, qualitativ neuartige Erkenntnisse zu gewinnen. Um diese Informationen vollständig zu erschließen ist ein Abdecken der gesamten Verarbeitungskette von der Datenauslese bis zu anwendungsbezogenen Auswertung erforderlich. Eine Erweiterung bestehender wissenschaftlicher Instrumente beinhaltet die strukturelle und zeitbezogene Integration der neuen Sensordaten in das Bestandssystem. Das hier vorgestellte Framework bietet durch seinen flexiblen Ansatz das Potenzial, unterschiedliche Sensortypen in unterschiedliche, leistungsfähige Plattformen zu integrieren. Zwei unterschiedliche Integrationsansätze zeigen die Flexibilität dieses Ansatzes, wobei einer auf die Steigerung der Sensitivität einer Anlage zur Sekundärionenmassenspektroskopie und der andere auf die Bereitstellung eines Prototypen zur Untersuchung von Rezyklaten ausgerichtet ist. Die sehr unterschiedlichen Hardwarevoraussetzungen und Anforderungen der Anwendung bildeten die Basis zur Entwicklung eines flexiblen Softwareframeworks. Um komplexe und leistungsfähige Applikationsbausteine bereitzustellen wurde eine Softwaretechnologie entwickelt, die modulare Pipelinestrukturen mit Sensor- und Ausgabeschnittstellen sowie einer Wissensbasis mit entsprechenden Konfigurations- und Verarbeitungsmodulen kombiniert.:1. Introduction 2. Hardware Architecture and Application Background 3. Software Concept 4. Experimental Results 5. Conclusion and Outlook / Novel sensors with the ability to collect qualitatively new information offer the potential to improve experimental infrastructure and methods in the field of research technology. In order to get full access to this information, the entire range from detector readout data transfer over proper data and knowledge models up to complex application functions has to be covered. The extension of existing scientific instruments comprises the integration of diverse sensor information into existing hardware, based on the expansion of pivotal event schemes and data models. Due to its flexible approach, the proposed framework has the potential to integrate additional sensor types and offers migration capabilities to high-performance computing platforms. Two different implementation setups prove the flexibility of this approach, one extending the material analyzing capabilities of a secondary ion mass spectrometry device, the other implementing a functional prototype setup for the online analysis of recyclate. Both setups can be regarded as two complementary parts of a highly topical and ground-breaking unique scientific application field. The requirements and possibilities resulting from different hardware concepts on one hand and diverse application fields on the other hand are the basis for the development of a versatile software framework. In order to support complex and efficient application functions under heterogeneous and flexible technical conditions, a software technology is proposed that offers modular processing pipeline structures with internal and external data interfaces backed by a knowledge base with respective configuration and conclusion mechanisms.:1. Introduction 2. Hardware Architecture and Application Background 3. Software Concept 4. Experimental Results 5. Conclusion and Outlook

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In this work the two experimental dental implant materials FAT and FAW, made of fluoroapatite particles embedded in polymer matrices, and films of the proteins lysozyme, amylase and bovine serum albumin (BSA), adsorbed to the two dental implant materials, were investigated with time-of-flight secondary ion mass spectrometry (ToF-SIMS) and the multivariate data analysis technique discriminant principal component analysis (DPCA).

Pseudoexfoliation (PEX) syndrome is an age-related condition characterized by the production and accumulation of extracellular fibrillary material in the anterior segment of the eye. PEX predisposes for several pathological conditions, such as glaucoma and complications during and after cataract surgery. The pathogenesis of PEX is not yet fully understood. It is multifactorial with genetics and ageing as contributing factors. We aimed to study the proteome in aqueous humor (AH) in PEX in order to increase the knowledge about its pathophysiology. Therefore, we developed sampling techniques and evaluated separation methods necessary for analyzing small sample volumes. Other objectives were to study the lens capsule in eyes with PEX regarding small molecules, and to investigate the association between PEX and cataract surgery in a population-based 30-year follow-up study. Samples of AH from eyes with PEX and control eyes were collected during cataract surgery. In pooled, and individual samples, various liquid based separation techniques and high resolution mass spectrometry were utilized. For quantitation, various methods for labeling, and label free techniques were applied. Lens capsules were collected from some of the patients, and analysed by imaging mass spectrometry. A cohort of 1,471 elderly individuals underwent a comprehensive ophthalmological examination at baseline. Medical information was obtained by questionnaires, and from medical records. Incident cases of cataract surgery were identified by review of medical records. In the initial study, several techniques were explored for protein detection, and a number of proteins were identified as differentially expressed. In the individually labelled samples, changes in the proteome were observed. Eyes with PEX contained higher levels of proteins involved in inflammation, oxidative stress, and coagulation, suggesting that these mechanisms are involved in the pathogenesis in PEX. The levels of β/γ-crystallins were significantly increased in PEX, which is a novel finding. In the lens capsules from individuals with PEX, changes in the lipid composition was observed with time-of-flight secondary ion mass spectrometry. These changes remain to be elucidated. By multivariate analysis, lens opacities were the first, and PEX the second most important predictor for cataract surgery, the later accounting for a 2.38-fold increased risk for cataract surgery.

Les conditions sévères de fonctionnement des réacteurs du futur, Génération-IV, -haute température et fortes irradiations-nécessitent le développement de matériaux adaptés. Les aciers ODS (Oxide Dispersion Strengthened) sont des candidats très compétitifs pour le gainage du combustible en raison de leurs excellentes propriétés de gonflement et de fluage. Ces atouts majeurs sont induits par la fine dispersion de nanoparticules d’oxydes (Y, O, Ti) obtenue par co-broyage de poudres de la matrice et d’oxyde dont les conditions sont à optimiser pour maitriser la distribution en taille et composition de ces nanoparticules. Dans l’objectif de mieux comprendre le mécanisme de formation de ces nanoparticules à l’échelle atomique, la présente thèse met à profit l’utilisation de la spectroscopie d’annihilation de positons (PAS) et de la spectrométrie de masse d’ions secondaires pour étudier l’interaction des défauts lacunaires avec des solutés Y, O et Ti et évaluer leur rôle dans la formation des nanoparticules. Les irradiations avec des ions He ont été effectuées pour révéler les propriétés des défauts lacunaires et les implantations d’Y, Ti, O ont été réalisées pour étudier les interactions de ces éléments Y, Ti, O avec les lacunes dans la matrice de fer. La distribution des défauts en profondeur indique la présence de défauts lacunaires avec une taille plus petite dans la région où la concentration d’Y, Ti, O est la plus élevée. Cet effet est plus prononcé pour O, Y et Ti respectivement. Il est expliqué par la formation de V-X (X=O, Y, Ti) complexes qui réduisent la probabilité de la mobilité et d’agglomération des défauts lacunaires. Les recuits des échantillons implantés Y et O révèlent que des complexes O-lacune sont mobiles à température ambiante, et que l’yttrium ne diffuse pas jusqu’à 550°C alors que des complexes Y-lacunes sont encore détectés comme cela est attendu par des résultats théoriques. Un modèle des premières étapes de la nucléation des nanoparticules est proposé en utilisant les résultats obtenus dans cette thèse. / The severe operating conditions of the future nuclear reactor, Generation-IV, -high temperature and high irradiation damage-, require the adapted materials development. Oxide-dispersion strengthened (ODS) alloy is one of the most potential candidates expected to be used for fuel cladding material because of their outstanding swelling and creep properties. Their excellent properties are induced by the fine dispersion of oxide nanoparticles (Y, O, Ti), obtained by mechanical alloying of steel and oxide powders and which has to be better mastered. But the atomic scale clustering mechanism of these nanoparticles is not yet cleared. In this context, the present thesis using positron annihilation spectroscopy (PAS) and secondary ion mass spectrometry (SIMS) sheds light on the interaction of vacancy defects with Y, O and Ti solutes to better understand their roles in the nanoparticles formation. The He irradiations have been performed to reveal the vacancy defects properties and Y, Ti, O implantations realized to study the Y, Ti, O-vacancy interactions in bcc Fe matrix. In all cases, the defects depth distribution shows a lower size of vacancy defects in the region where the concentration of the incident ions Y, Ti and O is the highest. This effect of the ions on the damage formation is more pronounced for respectively O, Y and Ti. It is explained by the formation of V-X (X=O, Y, Ti) complexes which reduce the mobility and agglomeration probability of the vacancy defects. The annealing of the Y and O implanted samples reveals that some O-vacancy complexes are mobile at room temperature and Y doesn’t diffuse up to 550°C whilst Y-vacancy complexes remain as it is expected from theory. A model of the first steps of the ODS nanoparticles nucleation is proposed by using the results obtained in this thesis.

Progress in chemomechanical functionalization was made by investigating the binding of molecules and surface coverage on the silicon surface, demonstrating functionalization of silicon with gases by chemomechanical means, analyzing atomic force microscopy probe tip wear in atomic force microscopy (AFM) chemomechanical nanografting, combining chemomechanical functionalization and nanografting to pattern silicon with an atomic force microscope, and extending chemomechanical nanografting to silicon dioxide. Molecular mechanics of alkenes and alkynes bound to Si(001)-2x1 as a model of chemomechanically functionalized surfaces indicated that complete coverage is energetically favorable and becomes more favorable for longer chain species. Scribing a silicon surface in the presence of ethylene and acetylene demonstrated chemomechanical functionalization with gaseous reagents, which simplifies sample cleanup and adds a range of reagents to those possible for chemomechanical functionalization. Thermal desorption spectroscopy was performed on chemomechanically functionalized samples and demonstrated the similarity in binding of molecules to the scribed silicon surface and to the common Si(001)-2x1 and Si(111)-7x7 surfaces. The wearing of atomic force microscope probe tips during chemomechanical functionalization was investigated by correlating change over time and force with widths of created lines to illustrate the detrimental effect of tip wear on mechanically-driven nanopatterning methods. In order to have a starting surface more stable than hydrogen-terminated silicon, silicon reacted with 1-octene was used as a starting surface for AFM chemomechanical functionalization, producing chemomechanical nanografting. Chemomechanical nanografting was then demonstrated on silicon dioxide using silane molecules; the initial passivating layer reduced the tip friction on the surface to allow only partial nanografting of the silane molecules. These studies broadened the scope and understanding of chemomechanical functionalization and nanografting.