FTIR spectroscopy as molecular fingerprint has been used to assess macromolecular and ele-mental stoichiometry as well as growth rates of phytoplankton cells. Chemometric models have been developed to extract quantitative information from FTIR spectra to reveal macro-molecular composition (of proteins, carbohydrates and lipids), C:N ratio, and growth potential. In this study, we tested these chemometric models based on lab-cultured algal species in mon-itoring changes of phytoplankton community structure in a hypertrophic lake (Lake Auensee, Leipzig, Germany), where a seasonal succession of spring green algal bloom followed by cya-nobacterial dominance in summer can be commonly observed. Our results demonstrated that green algae reacted to environmental changes such as nitrogen limitation (due to imbalanced nitrogen and phosphorus supply) with restricted growth by changing carbon allocation from protein synthesis to storage carbohydrates and/or lipids, and increased C:N ratio. By contrast, cyanobacteria proliferated under nitrogen limiting conditions. Furthermore, the FTIR-based growth potential of green alga matched well with the population biomass determined by the Chl-a concentration. However, the predicted growth potential based on FTIR spectroscopy cannot describe the realistic growth development of cyanobacteria in this lake. These results revealed that green algae and cyanobacteria have different strategies of C-allocation stoichi-ometry and growth patterns in response to environmental changes. These taxon-specific re-sponses may explain at a molecular level why green algae bloomed in the spring under condi-tions with sufficient nutrient, lower pH and lower water temperature; while cyanobacteria overgrew green algae and dominated in the summer under conditions with limited nutrient availability, higher pH and higher water temperature. In addition, the applicability of these chemometric models for predicting field cyanobacterial growth is of limited value. This may be attributed to other special adaptation properties of cyanobacterial species under stress growth conditions. We used flow cytometry to isolate functional algal groups from the water samples. Despite some drawbacks of the flow cytometry combined FTIR spectroscopy tech-nique, this method provides prospects of monitoring water quality and early warning of harmful algal blooms.

In the field of protein research in general and the pharmaceutical industry in particular, it is now necessary to perform measurements of the secondary structure of proteins on many samples simultaneously, for instance to screen for molecules that stabilize proteins or to evaluate the action of multiple environmental conditions. In this context, we have proposed a new approach to evaluate the secondary structure of proteins on a very large scale (approximately 2000 to 4000 samples / cm2), by combining infrared imaging and 2D printing of protein microarrays. In view of the large amount of data, in a first step, methods for automating the extraction of spectra of interest from microarray infrared images and for automating the processing of the spectra were developed. Since the estimation of the secondary structure from infrared spectra is based on the construction of prediction models by chemometric methods, a relevant set of proteins for calibration was mandatory. A protein bank consisting of 92 commercially available proteins, the structure of which was well characterized by X-ray crystallography, was established for this purpose. After the development of predictive models for secondary structure determination and the validation of the protein microarray approach, we tried to optimize the models to improve the secondary structure prediction by different approaches as secondary structure definition, partial deuteration or subtraction of side chain contribution to the spectra. On the other hand, dealing with non-native structures not present in the reference protein library was a challenge. We took the opportunity to analyze the structural modifications of a subset of our protein library subjected to moderate denaturation conditions. Multivariate curve resolution-alternating least squares (MCR-ALS) was used to model a new spectral component appearing in the protein set subjected to denaturing conditions, which could represent a potential spectroscopic marker of aggregation and could allow a semi-quantitative evaluation of the aggregation. While the assessment of secondary structure was well established in the first part of this work, tertiary structure and stability are also critical. Hydrogen / deuterium exchange (HDX) is a potential approach for studying the structure and dynamics of proteins. In the last part of this work, we built a device which allowed to follow the HDX exchange kinetics simultaneously on the entire microarray. In conclusion, protein microarray FTIR imaging opens the door to high throughput analysis of protein secondary structure without any labelling and would allow better understanding of three-dimensional structure and dynamics of proteins through recording HDX curves. / Dans le domaine de la recherche sur les protéines et de l'industrie pharmaceutique, il s’avère désormais nécessaire d'effectuer des mesures de la structure secondaire des protéines sur de nombreux échantillons simultanément, de cribler des molécules qui stabilisent les protéines, ou d'évaluer l'action de multiples conditions environnementales. Dans ce contexte, nous avons proposé une nouvelle approche pour évaluer la structure secondaire des protéines à très grande échelle (environ 2 000 à 4 000 échantillons / cm2), en associant l'imagerie infrarouge et l'impression 2D de damiers de protéines. Dans un premier temps, des méthodes d'automatisation de l'extraction des spectres d'intérêt à partir des images infrarouges des damiers et d'automatisation des spectres ont été développées. L'estimation de la structure secondaire à partir des spectres infrarouges étant basée sur la construction de modèles de prédiction à partir de méthodes chimiométriques, un ensemble pertinent de protéines pour l'étape de calibration était obligatoire. Une banque de protéines constituée de 92 protéines disponibles dans le commerce, dont la structure était bien caractérisée par cristallographie aux rayons X, a été constituée dans ce but. Après élaboration des modèles prédictifs de la structure secondaire et la validation de l'approche des damiers de protéines, nous avons tenté d'optimiser les modèles pour améliorer les prédictions de structure secondaire par différentes approches. D'autre part, traiter des protéines présentant une structure jamais rencontrée dans les structures natives de notre bibliothèque de protéines de référence constituait un défi. Nous avons saisi l'opportunité d'analyser les modifications structurales d'un sous-ensemble de notre bibliothèque de protéines, caractérisé par un contenu structurel secondaire très différent en le soumettant à des conditions de dénaturation modérées La méthode de résolution de courbes multivariées des moindres carrés alternés (MCR-ALS) a été utilisée pour modéliser une nouvelle composante spectrale apparaissant dans l'ensemble protéique soumis à des conditions dénaturantes, et a permis de révéler un marqueur spectroscopique potentiel d'agrégation protéique permettant une évaluation semi-quantitative de son contenu. Alors que l’évaluation de la structure secondaire a été bien établie dans la première partie de ce travail, la structure tertiaire et la stabilité sont également critiques. L'échange hydrogène / deutérium (HDX) est une approche potentielle pour l’étude de la structure et de la dynamique des protéines. Dans la dernière partie de ce travail, nous avons construit un dispositif qui a permis de suivre la cinétique d’échange HDX simultanément sur l'ensemble d’un damier. En conclusion, l'imagerie FTIR de damiers de protéines ouvre la porte à une analyse à haut débit de la structure secondaire des protéines et permettrait de mieux comprendre la structure et la dynamique tridimensionnelles grâce à l'enregistrement des courbes HDX. / Doctorat en Sciences / info:eu-repo/semantics/nonPublished

<p>Traumatic brain injury (TBI) is characterized by a violent or sudden blow to the head that causes tearing or bruising of the brain tissue and its supporting blood vessels. Determination of the mechanical properties of gray and white matter is critical for the creation of computational models of healthy and TBI-damaged brain tissues. Current in vivo methods to characterize brain tissue, such as 3D amplified MRI (aMRI) and magnetic resonance elastography (MRE), are highly vulnerable to motion artifacts and have limited techniques to exert mechanical loads on the brain. Therefore, in vitro testing was employed to estimate the chemical composition of gray and white matter using Fourier Transform Infrared (FTIR) spectroscopy and the stress responses of the brain tissues to high compressive deformations via unconfined compression. Attenuated total reflectance (ATR) was run in conjunction with FTIR spectroscopy to eliminate the need for sample preparation. Unconfined compression of gray and white matter samples was performed to 70% of the total sample height at a constant strain rate of 0.35/s. Results showed significant increases in the absorbances of white matter (<em>p</em> < 0.05) in the characteristic lipid and carbohydrate regions of the FTIR spectra when compared to gray matter. Within the initial 10% toe-region of the stress-strain curve, white matter is observed to absorb significantly greater compressive loads (<em>p </em>< 0.05) than gray matter. These results indicate an incomplete characterization of brain tissue; therefore, additional in vitro and in vivo methods are still necessary, separately or in combination, to accurately characterize brain tissue mechanics in TBI and non-TBI patients.</p>

One of the most important volatiles in magma is water. In magma, water is incorporated in both the melt and in crystals, including hydrous and nominally anhydrous minerals (NAMs). The purpose of this study is to determine the role of magmatic water content in controlling volcano explosivity especially at Merapi volcano, Indonesia, which is one of the most active volcanoes in the world. Here I apply clinopyroxene from two types of eruption products, lava and ash, to test the magmatic water content in the Merapi 2010 eruption. Both oriented and unoriented crystals were analysed using Fourier-Transformed Infrared (FTIR) spectroscopy to establish the clinopyroxene’s crystal water content. By combining the water content of clinopyroxene and geochemical data obtained from EPMA analysis, the magmatic water content is then estimated by inserting the data into the equation of O’Leary et al. (2010) [lnD= -4.2(60.2)16.5(60.5) VI[Al3+]-1.0(60.2) [Ca2+]]. I also investigated clinopyroxene crystals that were experimentally rehydrated, including four oriented crystals from a Merapi 2010 eruption ash sample annealed at a temperature of 700°C and pressure of 1 atm. Magmatic water contents of Merapi 2010 from rehydration experiments were then compared to the Merapi 2006 magmatic water content which were treated under the same conditions. The results revealed a wide variation between samples and among crystals taken from the same sample. However, oriented samples yielded a smaller variation between minimum and maximum clinopyroxene crystal water content and, overall, ash samples yielded higher water content in clinopyroxene than lava samples. The rehydration experiment significantly amplified clinopyroxene crystal water content by 3 to 7-fold compared to the result without the rehydration procedure. Comparison of data between the 2006 and 2010 Merapi eruptions demonstrates that there was a significant difference in magmatic water contents with the 2010 eruption displaying more than twice as much magmatic water than the 2006 eruption. The result implies that magmatic water plays potentially a crucial role in controlling explosivity of Merapi eruptions. / Indonesien är det land i Världen som har den största befolkningen som lever inom 100 km av en aktiv vulkan. Merapi är en av de mest farliga vulkanerna i Indonesien, som också är en av de mest aktiva vulkanerna i Världen och ligger på ön Java runt 15-25 km från Yogyakarta med en total befolkningstäthet på 1000 personer per kvadratkilometer. Utbrott från Merapi har dödat cirka 5000 personer under de senaste 500 åren. Således är det viktigt att studera hur vulkanen beter sig och orsaken till utbrotten för att kunna vita förebyggande åtgärder för att minska antalet dödsfall eller till och med undvika dödsfall helt. Vulkanutbrott kontrolleras av många faktorer, en av faktorerna är flyktiga ämnen i magman och en av de viktigaste flyktiga ämnen är vatten. Det här projektet syftar till att ta reda på vattnets roll på explosiviteten hos utbrotten genom att undersöka eruptiva produkter från utbrotten av Merapi under 2006 och 2010 med hjälp av Fourier-Transformed Infrared (FTIR) spektroskopi. Experimentet använder normalt vattenfria mineraler (NAMs) så som klinopyroxen men vatten kan införlivas i NAMs genom att binda väte i kristallgitteret under kristalltillväxten. Tidigare studier har visat att vattenhalten i klinopyroxenkristall skulle kunna användas för att beräkna magmatisk vattenhalt och därmed jämföra den magmatiska vattenhalt mellan olika utbrott med olika explosivitet i samma vulkan, vilket kan indikera hur vattenhalten påverkar vulkanutbrotten. Magmatiskt vatteninnehåll beräknat utifrån klinopyroxenvattenhalten visade en variation mellan de undersöka proverna från samma utbrott, varför ytterligare undersökning genom rehydreringsexperiment gjordes genom annealing av proverna vid en temperatur av 700 °C och tryck vid 1 atm. Även om det var variation i magmatisk vattenhalt mellan proverna, så har utbrotten av Merapi under 2010 högre magmatiskt vatteninnehåll än utbrottet under 2006 med 3-7 gånger. Sammantaget har Merapi 2010 utbrottet högre explosivitet och högre magmatisk vattenhalt än 2006 utbrottet, vilket innebär att högre vattenhalt ger högre explosivitet. På detta sätt kontrollerade vattnet vulkanens explosivitet för Merapivulkanen.Nyckelord: Merapi vulkan, NA

Film thickness, free carrier concentration and free carrier mobility are critical figures of merit for silicon carbide epitaxial growth. Room temperature Fourier Transform Infrared (FTIR) reflection spectroscopy can estimate these parameters non-destructively and is capable of high-resolution wafer mapping. Commercially available equipment has greatly simplified the application of this technique by coupling a high performance automated spectrometer with model-based data analysis and interpretation based on the personal computer. While powerful numerical techniques run fast and efficient on modern computers, it is essential that low-order, well-conditioned models are needed. The observed reflectance spectrum is the result of reflection and refraction of light at different interfaces due to constructive and destructive interference. The estimation of film thickness and free carrier concentration for single epitaxial layers has been improved by studying the Longitudinal Optical Phonon Plasmon (LPP) coupled modes. However, the addition of multiple layers introduces many degrees of freedom, which complicates parameter extraction. The multiple epitaxial layer stacks studied were intended for Metal Semiconductor Field Effect Transistor (MESFET?s) on both conducting and semi-insulating substrates. The thickness estimation of the n-channel in the MESFET stack on semi-insulating substrate is improved by preconditioning the curve fit for plasma frequency obtained from doping estimation from capacitance voltage profiling or by observing an LPP- peak.

No description available.

No description available.

The Al₂SiO₅ polymorphs have been examined to provide new insights into their chemical bonding, their crystal chemistry, their equations of state, and the incorporation of water in the form of hydroxyl in their structures. The Al₂SiO₅ polymorphs provide a unique structural assemblage for a crystal chemical examination due to the variation in Al coordination in the structures where Al is in 4-fold, 5-fold, and 6-fold in sillimanite, andalusite, and kyanite, respectively. Consequently, the Al₂SiO₅ polymorphs have been examined with a combination of experimental (high pressure X-ray diffraction and Polarized FTIR spectroscopy) and theoretical (VASP and Crystal 98) methods. An experimental high pressure X-ray diffraction study on andalusite and sillimanite has constrained their equation of state and the pressure derivatives of their bulk modulus with pressure. Additionally, the effect of pressure on the crystal structures has been examined, where the main structural response is compression of the AlO₆ octahedra. Comparatively, compression of the AlO₆ octahedra in andalusite is more anisotropic, while the major direction of axial compressibility in both structures is dependent on the orientation of the AlO6 octahedra. In order to better understand the crystal chemistry of the Al-O and Si-O bonds in the polymorphs, ELF isosurfaces were examined. ELF isosurfaces represent a graphical representation of the localized electron probability density. Six distinct types of ELF isosurfaces were observed in the Al₂SiO₅ polymorphs resulting from differences in the geometry, coordination, and coordinated cation atomic number surrounding the oxygens within the crystal structures. The ELF was also shown to be isostructurally related to electron density difference maps. In a combined experimental and theoretical investigation of the Al₂SiO₅ polymorphs, potential protonation sites within the crystal structures were determined at an atomic level with polarized FTIR spectroscopy and analysis of (3,-3) critical points of the negative Laplacian. The polarized FTIR spectra indicate the orientation of the OH dipole in the three polymorphs and the (3,-3) critical points indicate regions of locally concentrated electron density. Potential protonation sites were determined based on the value of the negative Laplacian, the underbonded nature of the oxygens, and the number of surrounding cations. / Ph. D.

High molecular weight star-shaped polystyrenes were prepared via the coupling of 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) terminated polystyrene oligomers with divinylbenzene (DVB) in m-xylene at 138 °C. Linear polystyrene oligomers (Mn = 19,300 g/mol, Mw/Mn = 1.10) were synthesized in bulk styrene using benzoyl peroxide in the presence of TEMPO at approximately 130 °C. In situ mid-infrared spectroscopy was successfully utilized to follow initiation, monomer conversion, and polymer formation. Real-time data allowed for the determination of apparent rate constants of 2.1E-5 s⁻¹ at 132 °C and 1.2E-5 s⁻¹ at 126 °C from the profile of the decaying styrene vinyl carbon-hydrogen (=CH₂) absorbance at 907 cm⁻¹. Coupling of the TEMPO terminated oligomers under optimum conditions resulted in a compact and dense product with a number average molecular weight exceeding 300,000 g/mol (Mw/Mn = 3.03) after 24 h, suggesting the formation of relatively well-defined star-shaped polymers. Synthetic factors that affected the molecular weight, yield, and composition of maleic anhydride (MAH), norbornene (Nb), and tert-butyl 5-norbornene-2-carboxylate (NbTBE) terpolymers were investigated. Pseudo first order kinetic analysis using in situ FTIR indicated that the observed rate of reaction was a strong function of the Nb/NbTBE ratio with a maximum of 6.7E-5 s⁻¹ for a 50/0/50 Nb/NbTBE/MAH monomer ratio and a minimum of 1.1E-5 s⁻¹ for a 0/50/50 Nb/NbTBE/MAH ratio. Polymer yields were also observed to be a function of the Nb/NbTBE ratio and also decreased with increasing NbTBE. Calculated work of adhesion values (Wadh) values were observed to increase as the content of NbTBE was increased. 193 nm photoresist formulations incorporating polymers with high NbTBE content showed increased imaging performance using 193 nm light and successfully produced sharp and defined features as small as 110 nm, which was demonstrated via scanning electron microscopy (SEM). Additional functionality was introduced via the copolymerization of MAH with several norbornene (Nb) derivatives that were synthesized from facile Diels-Alder cycloaddition reactions of cyclopentadiene with a-olefins containing electron withdrawing groups. Subsequent hydrolysis of the anhydride offered further versatility and provided an avenue to introduce aqueous base solubility into Nb/MAH copolymers. / Ph. D.

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.