Die Vorverarbeitung und Analyse von spektrometrischen und spektroskopischen Daten von Pflanzengewebe sind in den unterschiedlichsten Forschungsbereichen wie der Pflanzenbiologie, Agrarwissenschaften und Klimaforschung von großer Bedeutung. Der Schwerpunkt dieser Arbeit liegt auf der optimierten Nutzung von Daten von Pflanzengeweben, insbesondere der Daten gewonnen durch Matrix–Assistierte Laser–Desorption–Ionisierung Massenspektrometrie, Raman-Spektroskopie und Fourier-Transform-Infrarotspektroskopie. Die Klassifizierungsfähigkeit mit diesen Methoden wird insbesondere nach Kombination der Daten untereinander und mit zusätzlichen chemischen und biologischen Informationen verglichen. Die diskutierten Beispiele befassen sich mit der Untersuchung und Einordnung innerhalb einer bestimmten Pflanzenart, beispielsweise der Unterscheidung von Proben aus unterschiedlichen Populationen, Wachstumsbedingungen oder Gewebeunterstrukturen. Die Daten wurden mit sowohl mit explorativen Werkzeugen wie der Hauptkomponentenanalyse und der hierarchischen Clusteranalyse, als auch mit Methoden des maschinellen Lernens wie die Diskriminanzanalyse oder künstliche neuronale Netzwerke umfassten. Konkret zeigen die Ergebnisse, dass die Kombination der Methoden mit zusätzlichen pflanzenbezogenen Informationen in einer Konsensus-Hauptkomponentenanalyse zu einer umfassenden Charakterisierung der Proben führt. Es werden verschiedene Strategien zur Datenvorbehandlung diskutiert, um nicht relevante spektrale Information zu reduzieren, z.B. aus Karten von Pflanzengeweben oder eingebetteten Pollenkörnern. Die Ergebnisse dieser Arbeit weisen auf die Relevanz der gezielten Nutzung spektrometrischer und spektroskopischer Daten hin und lassen sich nicht nur auf pflanzenbezogene Themen, sondern auch auf andere analytische Klassifizierungsprobleme übertragen. / The pre-processing and analysis of spectrometric and spectroscopic data of plant tissue are important in a wide variety of research areas, such as plant biology, agricultural science, and climate research. The focus of the thesis is the optimized utilization of data from plant tissues, which includes data from Matrix-Assisted-Laser Desorption/Ionization time of flight mass spectrometry, Raman spectroscopy, and Fourier transform infrared spectroscopy. The ability to attain a classification using these methods is compared, in particular after combination of the data with each other and with additional chemical and biological information. The discussed examples are concerned with the investigation and classification within a particular plant species, such as the distinction of samples from different populations, growth conditions, or tissue substructures. The data were analyzed by exploratory tools such as principal component analysis and hierarchical cluster analysis, as well as by predictive tools that included partial least square-discriminant analysis and machine learning approaches. Specifically, the results show that combination of the methods with additional plant-related information in a consensus principal component analysis leads to a comprehensive characterization of the samples. Different data pre-treatment strategies are discussed to reduce non-relevant spectral information, e.g., from maps of plant tissues or embedded pollen grains. The results in this work indicate the relevance of the targeted utilization of spectrometric and spectroscopic data and could be applied not only to plant-related topics but also to other analytical classification problems.

Spider silk is one of the most fascinating materials found in nature. Besides its properties like biodegradability, low immunoreactivity, and biocompatibility, especially the mechanical properties outperforming today’s artificial high-tech materials like Kevlar® are of great interest in biomedicine or material science. Spider silk comprises highly repetitive amino acid sequence motives, whose structure is accepted to be responsible for the extraordinary properties of spider silk. Typically, hydrophilic sequence motives alternate with hydrophobic ones making spider silk proteins resemble block copolymers. Additionally, the simple amino acid sequence and the possibility to form fibrillar structures are common characteristics of spider silk proteins as well as intrinsically disordered proteins (IDP) or protein regions (IDR). Both are suspected of being involved in the development of certain neurodegenerative diseases like Alzheimer´s disease. These aspects open promising possibilities of the use of spider silk proteins in nanotechnology, but also as model systems for the fibrillization processes of IDPs and IDRs, which are still unresolved today. Currently, most of the research and application is focused on 1-dimensional spider silk protein fibrils and fibers or 0-dimensional spider silk particles. However, 2-dimensional spider silk protein films or porous 3-dimensional objects are highly relevant platforms with the potential for cell-supporting scaffolds, biodegradable electrolyte materials in transistors, or e.g., planar drug-eluting implant coatings. Generally, the effects of sequence-based and external influences on the self-assembly and folding of spider silk proteins have not yet been fully elucidated in all of these various dimensional spider silk materials, even concerning IDP and IDR models. Thus, basic research regarding assembly and folding processes is still needed, especially in films. Particularly, 2-dimensional films allow a broad spectrum of (surface) analytical techniques, from whose outcome general structure-property relations of spider silk materials across all material dimensions can be obtained. In this work, engineered spider silk proteins, which are based on the consensus sequence motives in the spider silk fibroin (spidroin) 3 and 4 of the European garden spider Araneus diadematus (eADF4(Cx), eADF3(AQ)x, eADF3(QAQ)x) as well as blends of two short peptides with the respective aa sequence of the hydrophobic (pep-c) and hydrophilic (pep-a) part of eADF4(Cx) proteins were used. Spider silk-related proteins and peptides were dissolved in 1,1,1,3,3,3-hexafluoroisopropanol or formic acid, processed as thin films, and post-treated with methanol vapor to induce β-sheet formation. Dichroic FTIR-spectroscopy was used, a powerful tool for studying protein secondary structure formation and orientation. Proteins reveal characteristic amide bands, which are highly sensitive to the conformation of the protein backbone. In the course of this work, a set of components for the line shape analysis (LSA) of the Amide I band was developed. Therby, each component was assigned to a typical secondary structure allowing a quantitative determination of the respective portions and their structural orientation. Quantitative secondary structure portions and their orientation could be determined on this basis. Furthermore, a comprehensive study of folding and self-assembly-influencing parameters like hydrophobic and hydrophilic sequences, molecular weight, the repeating sequence motive order, the film thickness, surface topography, and the surface chemistry in engineered spider silk protein and spider silk protein-based films was carried out. In general, methanol vapor post-treatment induced the formation of β-sheet structures in all films, causing phase separation and the formation of spherical and filamentous structures. The phase separation upon post-treatment was influenced by the covalent connectivity between hydrophobic and hydrophilic sequence parts as well as the repeating sequence motives. In thin films, the increased flexibility of shorter peptides enabled the formation of multipack filaments instead of spherical structures, which were formed by higher molecular weight proteins with several inter-connected repeating sequence motives. Stamping wrinkled structures using poly(dimethylsiloxane) substrates was possible. Filamentous structures were successfully assigned to β-sheet rich structures using infrared nanospectroscopy for the first time. Further, enhanced surface hydrophobicity led to the clustering of β-sheet filaments. The β-sheet content could be controlled by the amount of hydrophobic sequences in thin films. With a higher amount of hydrophobic sequences in the proteins or blends, the β-sheet content increased until a maximum β-sheet content of around 60% was reached. Additionally, β-sheet formation could be suppressed by increasing substrate hydrophobicity or by decreasing the number of repeating sequence motives by going from protein-like folding to peptide-like self-assembly. The backfolding of proteins with covalently linked repeating sequence motives further promoted the formation of more antiparallel β-sheets. Antiparallel β-sheet formation was also favored when the portion of the hydrophilic, amorphous phase was increased. Micrometer thick films did not reveal any preferred alignment of β-sheets, while a general out-of-plane orientation of β-sheets could be obtained in all thin protein, peptide, and blend films. Z-axial orientation in films was increased by using short pep-c and pep-a peptides, higher molecular weight proteins or the deposition of monolayered films instead of thin multilayered films. Also, increased hydrophilicity of the substrate promoted the alignment of β-sheets perpendicular to the substrate surface. The folding kinetics and final domain size were found to be directly correlated. The amount of hydrophobic phase, backfolding, and increased flexibility due to low chain lengths increased the folding kinetics and led to smaller domain sizes. Thus, competing effects of backfolding and flexibility of the protein/peptide backbone could be rationalized. The film integrity and water contact angle were directly related to the β-sheet content and the molecular weight. Beyond the classical protein conformation and orientation analysis, the possibilities and limits of orientation analysis using dichroic attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy were elaborated on the seemingly ideal oriented polymer model system of end-grafted poly(N,N-dimethylaminoethylmethacrylate) chains. Such a system featured a polymer brush regime in the swollen state with z-axial orientation expected similarly high as thin spider silk films after ptm. Moreover, dichroic ATR-FTIR spectroscopy is a promising analytical method for closing gaps in the defined assignment of brush regimes. In summary, general models of the structure formation and self-assembly of spider silk protein in films depending on the parameters mentioned above could be developed and set in relation to IDP/IDR self-assembly by using dichroic FTIR spectroscopy as the basic analysis method. The herein postulated models on the molecular level contribute to the understanding and development of future industrial applications of spider silk protein-based materials and the clarification of unresolved questions regarding IDP and IDR systems.:Abstract V Kurzfassung IX List of Publications XIII Publications in Trade Journals XIII Presentations and Posters XIII Contribution to Joint Publications XV List of Abbrevations XVII List of Symbols XIX List of Figures XXV List of Tables XXXIII 1 Introduction and Motivation 1 2 Theory 5 2.1 Proteins and Peptides 5 2.1.1 General Definition of Proteins and Peptides 5 2.1.2 Structure of Globular Proteins 7 2.1.3 Protein Folding 10 2.1.4 Intrinsically Disordered Proteins and Protein Regions 11 2.2 Block Copolymers 14 2.3 Spiders and Spider Silks 17 2.3.1 Classification of Spiders 17 2.3.2 The Natural Spider Silk Spinning Process 18 2.3.3 Structure of Spider Silk and Spider Silk Proteins 19 2.3.4 Structure-Property Relationships of Spider Silk 21 2.4 Infrared Spectroscopy 23 2.4.1 Basic Principles of Infrared Spectroscopy 23 2.4.2 Basic Equipment and IR-Technologies 27 2.4.3 Orientation Analysis using Dichroic FTIR Spectroscopy 32 2.4.4 Infrared Spectroscopy of Proteins and Peptides 38 2.4.5 Quantitative Analysis of TRANS- and ATR-FTIR Protein Spectra 43 2.5 Electronic Circular Dichroism 46 2.5.1 Basics Principles of Circular Dichroism 46 2.5.2 Circular Dichroism of Proteins and Polypeptides 48 2.5.3 Spectra Analysis 50 2.6 Atomic Force Microscopy 51 2.6.1 Setup of Atomic Force Microscopes 51 2.6.2 Basic Principles of Atomic Force Microscopy 52 2.6.3 AFM Operation Modes 55 3 Experimental Section 57 3.1 Materials 57 3.1.1 Chemicals 57 3.1.2 Substrates 57 3.1.3 Film Preparation 58 3.2 Analytical Methods 60 3.2.1 Dichroic FTIR Spectroscopy 60 3.2.2 Atomic Force Microscopy 64 3.2.3 Electronic Circular Dichroism 64 3.2.4 Spectroscopic Ellipsometry 64 3.2.5 Infrared Nanospectroscopy 65 3.2.6 Grazing Incident Small Angle X-Ray Scattering 66 4 Results 67 4.1 Self-Assembly of eADF4(C16) Films 67 4.1.1 Motivation 67 4.1.2 Dichroic FTIR Spectroscopy Characterization of ß-sheet Orientation in Spider Silk Films on Silicon Substrates 68 4.2 Influence of the Hydrophilic and Hydrophobic Blocks on Peptide Self-Assembly 90 4.2.1 Motivation 90 4.2.2 β-Sheet Structure Formation within Binary Blends of Two Spider Silk Related Peptides 90 4.2.3 Influence of the Hydrophilic and Hydrophobic Blocks on the Inner Morphology in Spider Silk Protein Based Blend Films 122 4.3 Influence of the Sequence Motive Repeating Number on Spider Silk Protein Folding 123 4.3.1 Motivation 123 4.3.2 Influence of Sequence Motive Repeating Number on Protein Folding in Spider Silk Protein Films 124 4.4 Influence of the Module Order on Spider Silk Protein Self-Assembly 152 4.4.1 Motivation 152 4.4.2 Secondary Structure upon Post-treatment 153 4.4.3 β-Sheet Orientation after Post-treatment 157 4.4.4 Morphology and Surface Properties 158 4.4.5 Conclusion 160 4.5 Surface Induced Changes of Spider Silk Protein Self-Assembly 161 4.5.1 Motivation 161 4.5.2 Variation of the Substrate Surface Chemistry and Topography 161 4.5.3 Influence of the Surface Topography on Protein Self-Assembly 162 4.5.4 Influence of the Surface Chemistry on Protein Self-Assembly 164 4.5.5 Conclusion 169 4.6 Chances and Limits of Dichroic ATR-FTIR Spectroscopy 170 4.6.1 Motivation 170 4.6.2 Novel Insights into Swelling and Orientation of End-Grafted PDMAEMA Chains by In-Situ ATR-FTIR Complementing In-Situ Ellipsometry 171 5 Conclusion and Outlook 197 6 References 203 7 Appendix 219 8 Danksagung 227 9 Eidesstattliche Versicherung 229

Thesis (MEng)--Stellenbosch University, 2015. / AFRIKAANSE OPSOMMING: Raadpleeg die volteks vir opsomming, asseblief. / ENGLISH ABSTRACT: Please refer to full text for abstract

The surface functionalisation of polyethylene and polypropylene by industrial and laboratory scale corona treatments and by laboratory flame treatment was studied. The surface sensitive techniques of X-ray photoelectron spectroscopy (XPS), attenuated total reflection infra-red spectroscopy (FTIR-ATR), contact angle measurement and electron microscopy (SEM and TEM) were employed. Corona and flame treatments resulted in incorporation of oxygen only into the surfaces of both polyethylene and polypropylene, resulting in improved surface wettabilities. A variety of oxygen functional groups were introduced by the two treatments. The industrial and laboratory scale treatments of both polymers were found to be similar in terms of the oxygen concentrations incorporated and surface wettabilities achieved. The presence of significant amounts of chain scission products were indicated on corona treated surfaces, while only minimal quantities were indicted on flame treated surfaces. This was attributed to their volatilisation during flame treatment. Introduction of sulfur dioxide into the flame and corona regions during treatment resulted in significant improvements in surface wettability. Incorporation of sulfur and nitrogen resulted from the presence of sulfur dioxide. A possible mechanism involving the formation of sulfonic acid groups and ammonium sulfonate groups was suggested. An oxidation depth model developed for use with variable take-off angle XPS showed that significantly deeper oxidation occurred in the presence of sulfur dioxide. Corona treatment was more effective in improving surface wettabilities than flame treatment, this being attributed to heat induced functional group reorientation during flame . treatment for polyethylene and to differences in surface chemistry resulting from the two treatments in the case of polypropylene. The surface wettability of poly ethylene was more readily improved than the surface wettability of polypropylene after all the treatments investigated. A method for estimating functional group concentrations using chemical derivatisation and contact angle measurement was developed. Functional group estimates for flame treated polyethylene were found to be in good agreement with chemical derivatisation used in conjunction with XPS measurements.

Στην παρούσα μεταπτυχιακή εργασία ειδίκευσης περιγράφεται η σύνθεση και ο χαρακτηρισμός νέων μεσοπορωδών βιοενεργών υλικών. Παρουσιάζονται οι συσχετιζόμενες με τα πορώδη/μεσοπορώδη υλικά έννοιες, οι ιδιότητες τους και διάφοροι τρόποι σύνθεσης τους. Εν συνεχεία, αναλύονται θέματα βιουλικών, δίνοντας έμφαση στις βιοϋάλους και τις ιδιότητες τους, και ειδικότερα στη βιονεργότητα, που αποτελεί την πιο χαρακτηριστική ιδιότητα αυτών, ενώ δίνεται έμφαση, επίσης στις διάφορες μεθόδους που χρησιμοποιούνται για την σύνθεση τους. Στην συνέχεια αναλύονται οι τεχνικές που χρησιμοποιήθηκαν για το χαρακτηρισμό των προαναφερθέντων υλικών καθώς και ο τρόπος λειτουργίας της κάθε τεχνικής. Επίσης, γίνεται αναφορά στα διαφορετικά χαρακτηριστικά των υλικών που μπορούν να μελετηθούν για κάθε τεχνική ξεχωριστά. Στο τελευταίο κεφάλαιο παρουσιάζεται αναλυτικά η διαδικασία διεξαγωγής των πειραμάτων, οι διάφοροι τρόποι σύνθεσης που χρησιμοποιήθηκαν, καθώς και σχολιασμός των αποτελεσμάτων. Τέλος, παρουσιάζονται τα συμπεράσματα που προέκυψαν από τα πειραματικά αποτελέσματα για την παρούσα μεταπτυχιακή εργασία. Επίσης γίνεται αναφορά και σε μελλοντικές κατευθύνσεις που περιλαμβάνουν την χρήση αυτών των υλικών σε σύνθετα υλικά για παλμική εναπόθεση με Laser και τεχνικές εναπόθεσης λεπτού υμενίου. / In this master thesis the synthesis and characterization of novel bioactive mesoporous materials is being reported. The notions related to porous/mesoporous materials, their properties and various synthetic methods are being discussed. Subsequently, the notion of “biomaterials” is further analyzed, focusing on bioglasses and their properties. The meaning of bioactivity is also analyzed as the most characteristic feature of bioglasses while various methods used for the synthesis of these are discussed. Following the techniques used to characterize these materials as well as the operating mode of each technique is discussed. In the last chapter, the experimental processes are reported as well as the results are being discussed. Finally, the conclusions of all the experiments and analysis are reported. Also, future directions include the usage of these materials in composite materials for laser ablation and thin film deposition techniques are mentioned.

De façon évidente, la pratique industrielle de la cristallisation ne peut éviter la présence d'impuretés indésirables produites suite aux nombreuses réactions chimiques précédant les étapes de cristallisation. Même en quantités infimes, les impuretés présentes dans les jus mères peuvent affecter de façon considérable la cristallisation et la qualité du produit obtenu. Dans ce contexte, les technologies de mesures en ligne fournissent un apport considérable en permettant l'obtention d'informations riches, en temps réel et de façon quasi-continue sur l'évolution des phases liquide et dispersée. L'objectif du présent travail est la compréhension des effets des impuretés sur les produits de cristallisations discontinues. Des expériences sont effectuées, sur une installation-pilote, en vue d'étudier les effets des paramètres opératoires de cristallisation de l'oxalate d'ammonium monohydrate pur et en présence de sulfate de nickel (impureté) sur la taille et la forme des cristaux produits. Pour cela, deux techniques analytiques in situ, la spectroscopie ATR FTIR pour la mesure de sursaturation et l'analyse d'image in situ pour l'évaluation des distributions des tailles des cristaux, seront utilisées. A partir des données expérimentales obtenues, nous proposons des modèles cinétiques de nucléation (primaire et secondaire) et de croissance tenant compte de l'action des impuretés et décrivant l'adsorption de celles-ci à la surface des cristaux. Ces modèles sont ensuite exploités pour la mise en place de simulations fondées sur les équations de bilans de populations.L'originalité de l'approche adoptée réside dans l'emploi du modèle classique de Kubota - Mullin, modifié par l'ajout d'une variable temporelle permettant la prise en compte de la durée d'exposition de chaque cristal aux impuretés. Les résultats de simulation obtenus décrivent de façon satisfaisante l'évolution temporelle de la sursaturation et de la distribution de taille des cristaux.

Worldwide, 3.575 million people die each year from water-related diseases. The water and sanitation crisis claims more lives than any warfare and is predicted to be one of the biggest global challenges of this century. The rapid, accurate detection of viral pathogens from environmental samples is an ongoing and pertinent challenge in biological engineering. Currently employed methods are lacking in either efficiency or specificity. Here we explore a novel method for virus detection and concurrently use this method to learn more about the very early stages of the virus infection process. The method combines Fourier transform infrared (FTIR) spectroscopy, a method of visualizing molecules based on changes in vibration of particles, and mammalian cells as the biosensor. This method is used to detect and investigate viruses from the family picornaviridae, chosen due to their public health burden and their widespread presence in environmental samples, especially water sources. This family includes the Polioviruses, echoviruses and Coxsackieviruses, among others, many of which are human pathogens.The research outlined in this dissertation is aimed at developing and implementing a new cell-based biosensor that combines the advantages of FTIR spectroscopy with the ability of buffalo green monkey kidney (BGMK) cells to sense diverse stimuli, including infective enteroviruses. The goal of developing this biosensor is outlined in the first paper. The second paper focuses on the application of advanced statistical methods to analyze the spectra to discriminate different viral infections in BGMK cells. Finally, we designed a non-reactive metal biochamber to use with attenuated total reflectance-FTIR. This allowed near-continuous acquisition of real-time spectral data for the study of biochemical changes in mammalian cells caused by poliovirus (PV1) infection. This system is capable of tracking changes in cell biochemistry in minute intervals for many hours at a time.This work demonstrates the feasibility of FTIR spectroscopy in combination with the broad sensitivity of mammalian cells for potential use in the detection of infective viruses from environmental samples. We envision this method being extended to high throughput, automated systems to screen for viruses or other toxins in drinking water systems and medical applications.

STUDIES OF INTERACTION OF SMALL MOLECULES WITH WATER CONDENSED MEDIA<br /><br /> The present work reports experimental and theoretical studies of the intermolecular interactions in condensed water media. The chemical objects comprise pristine ice and polar organic substances: acetone, acetaldehyde, methanol and chloroform and bi-component water-organic deposits. The experimental part of the studies includes the Fourier Transform Infrared Reflection Absorption spectral (FTIR RAS) examination of the processes of film growth by vapor deposition on cold metal substrate and subsequent annealing. The theoretical studies include <em>ab initio</em> (<em>MP2</em>) and semi-empirical (<em>B3LYP</em>) calculations on the small water and water-organic clusters and classical molecular dynamics simulations of the adsorption of inert guests (Xe/Rn) on the ice surface. The FTIR RA spectral studies reveal that depending on the deposition conditions condensed water media exist in two principal structural forms: noncrystalline and polycrystalline. The former is characterized by porous structure while the latter exists as a non-porous medium with smooth external interface. On annealing, characteristic spectral changes indicate on a rapid crystallization occurring at a certain temperature range. The initial adsorption of organic molecules is accompanied by the hydrogen-bonded coordination between the functional group of organic species and non-coordinated hydroxyl group of the ice surface, the topology of which depends on the electronic properties of the functional group. The computational studies of small water-organic clusters reveal, in particular, two major coordination minima for carbonyl group: a single hydrogen-bonded in-plane complex and a double hydrogen-bonded in-plane complex. The classical molecular dynamics of Xe/Rn species on the ice interface is consistent with two distinctly different surface adsorption sites: one that delocalized over the entire surface and one that confined to small opening in the top ice layer, disrupted by the thermal molecular motion. The penetration barrier is associated with van der Walls repulsion of guest species from the ordered water hexagonal arrangement. A thermo-disruption of latter leads to a rapid diffusion of guest species inside ice medium.

Cette thèse s’inscrit dans le cadre d’une cotutelle internationale entre l’institut FEMTO-ST à Besançon en France et l’université de Sherbrooke au Canada. Elle porte sur l’élaboration d’un biocapteur, potentiellement à bas coût, pour la détection de pathogènes dans les secteurs de l’agroalimentaire, de l’environnement et de la biosécurité. Le modèle biologique visé est la bactérie Escherichia coli, dont les souches pathogènes sont responsables, chaque année et partout dans le monde, de plusieurs crises sanitaires liées à une mauvaise gestion des produits de consommation ou des installations de conditionnement ou de traitements de ces produits. L’utilisation de biocapteurs pour une détection rapide, sensible et sélective d’organismes pathogènes répond ainsi aux inquiétudes quant aux risques d’infection pour la population. La structure du capteur consiste en une fine membrane en arséniure de gallium (GaAs) vibrant sur des modes de cisaillement d’épaisseur générés par champ électrique latéral via les propriétés piézoélectriques du matériau. Nous montrons dans ce travail que le biocapteur offre également des possibilités de microfabrication, de biofonctionnalisation et de régénération intéressantes pour la conception d’un dispositif à bas coût. Le transducteur a été réalisé via des technologies de microfabrication utilisées en salle blanche avec une mise en parallèle des méthodes d’usinage par voie chimique et par plasma, l’objectif étant d’obtenir des membranes minces, planes et avec un état de surface de haute qualité. Une interface fluidique a été mise au point de façon à approvisionner de manière homogène le capteur en fluide. Par ailleurs, nos études se sont portées sur la fonctionnalisation biochimique de l’interface de bioreconnaissance sur l’arséniure de gallium et sa caractérisation fine par les techniques de spectroscopie infrarouge à transformée de Fourier (FTIR). Les résultats de cette étude ont permis de progresser sur la compréhension fondamentale du phénomène d’auto-assemblage de molécules sur GaAs. Un effort particulier a été mis en œuvre pour développer des biointerfaces de haute densité offrant une immobilisation optimale des immunorécepteurs biologiques. Parmi les différentes méthodes de régénération de la biointerface, le procédé de photo-oxydation UV en milieu liquide a démontré un fort potentiel pour des applications de capteurs réutilisables. Enfin, le transducteur a été caractérisé électriquement sous différents environnements. L’impact sur la réponse du résonateur des paramètres électriques, mécaniques et thermiques de ces milieux a été évalué afin de simuler le comportement du dispositif en condition réelle. / Abstract : This PhD thesis was realized in the context of a cotutelle program between FEMTO-ST institute in France and the University of Sherbrooke in Canada. The thesis addresses the development of a potentially low cost sensor dedicated for detection of pathogens in food industry processing, environment and biosafety sectors. Such a sensor could serve detection of Escherichia coli bacteria whose pathogenic strains are the source of foodborne illnesses encountered worldwide every year. Hence, biosensor devices are needed for a rapid, sensitive and selective detection of pathogens to avert, as soon as possible, any sources of contamination and prevent outbreak risks. The design of the sensor consists of a resonant membrane fabricated in gallium arsenide (GaAs) crystal that operates at shear modes of bulk acoustic waves generated by lateral field excitation. In addition to the attractive piezoelectric properties, as shown in this work, fabrication of a GaAs-based biosensor benefits from a well-developed technology of microfabrication of GaAs, as well as biofunctionalization and the possibility of regeneration that should result in cost savings of used devices. The transducer element was fabricated by using typical clean room microfabrication techniques. Plasma and wet etching were investigated and compared for achieving thin membranes with high quality surface morphology. At the same time, we designed and fabricated fluidic elements that allowed the construction of a flow cell chamber integrated in the sensor. Extensive research was carried out with a Fourier transform infrared spectroscopy (FTIR) diagnostic tool to determine optimum conditions for biofunctionalization of the GaAs surface. This activity allowed to advance the fundamental knowledge of self-assembly formation and, consequently, fabrication of high density biointerfaces for efficient immobilization of selected bioreceptors. Among different biochip regeneration methods, it has been demonstrated that liquid UV photooxidation (liquid-UVPO) has a great potential to deliver attractive surfaces for re-usable biochips. Finally, operation of the transducer device was evaluated in air environment and in various liquid media, simulating real conditions for detection.

Fourier Transform Infrared spectroscopy is used as a diagnostic tool in biological and physical sciences by characterizing the samples based on infrared light-matter interaction. In the case of biological samples, Activation of Jurkat T-cells in culture following treatment with anti-CD3 (Cluster of Differentiation 3) antibody is detectable by interrogating the treated T-cells using the Attenuated Total Reflection - Fourier Transform Infrared (ATR-FTIR) Spectroscopy technique. Cell activation was detected within 75 minutes after the cells encountered specific immunoglobulin molecules. Spectral markers noted following ligation of the CD3 receptor with anti CD3 antibody provides proof-of-concept that ATR-FTIR spectroscopy is a sensitive measure of molecular events subsequent to cells interacting with anti-CD3 Immunoglobulin G (IgG). ATR-FTIR spectroscopy is also used to screen for Colitis in chronic (Interleukin 10 knockout) and acute (Dextran Sodium Sulphate-induced) models. Arthritis (Collagen Antibody Induced Arthritis) and metabolic syndrome (Toll like receptor 5 knockout) models are also tested as controls. The marker identified as mannose uniquely screens and distinguishes the colitic from the non-colitic samples and the controls. The reference or the baseline spectrum could be the pooled and averaged spectra of non-colitic samples or the subject’s previous sample spectrum. The circular dichroism of titanium-doped silver chiral nanorod arrays grown using the glancing angle deposition (GLAD) method is investigated in the visible and near infrared ranges using transmission ellipsometry and spectroscopy. The characteristics of these circular polarization effects are strongly influenced by the morphology of the deposited arrays. Studies of optical phonon modes in nearly defect-free GaN nanowires embedded with intrinsic InGaN quantum dots by using oblique angle transmission infrared spectroscopy is described here. These phonon modes are dependent on the nanowire fill-factor, doping densities of the nanowires and the presence of InGaN dots. These factors can be applied for potential phonon based photodetectors whose spectral responses can be tailored by varying a combination of these three parameters. The optical anisotropy along the growth (c-) axis of the GaN nanowire contributes to the polarization agility of such potential photodetectors.