In the medical world the precise identification of a disease can take longer than it is safe to wait to start treatment so there is a need for faster and more precise biosensors. Bond Rupture is a new sensor technique that maybe able to improve disease detection. It does this by inducing bonds to rupture from the surface, and also measuring the point at which this rupture occurs this enables the forces to be measured on the surface. Specifically, this project has focused on the application of Bond Rupture to detecting antigens when bound to a surface using their specific antibodies, and the idea that the rupture force of these antigens can also be measured. The sensor that this project is based around is the Quartz Crystal Microbalance (QCM), which oscillates horizontally when a voltage is applied, and can also be used to measure mass change on its surface via change in resonant frequency. The aim of this project was to investigate possible Bond Rupture detection methods and techniques and has involved the development of a high speed digital electronics system, for the purposes of inducing and detecting Bond Rupture. This has involved the development of a FPGA based high speed transceiver board which is controlled by a Digital Signal Processor (DSP), as well as the development of various graphical user interfaces for end user interaction. Bond rupture testing was carried out by rupturing beads from the surface of a QCM in an experiment taking as little as 20 seconds. The Bond Rupture effect has been observed via the high accuracy measurement of the frequency change while inducing Bond Rupture on the sensor, proving that the Bond Rupture effect indeed exists. The research performed is believed to be a world first in terms of the method used and accuracy acquired.

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Reversible changes in the self-organization of polysoaps may be induced by controlling their charge numbers via covalently bound redox moieties. This is illustrated with two viologen polysoaps, which in response to an electrochemical stimulus, change their solubility and aggregation in water, leading from homogeneously dissolved and aggregated molecules to collapsed ones and vice verse. Using the electrochemical quartz crystal microbalance (EQCM), it could be shown that the reversibility of this process is better than 95% in 16 cycles. /

A framework to compartmentalize microfluidic surfaces was developed. Substrates are separated from surface modifying agents with an intermediate binding layer (IBL). The IBL is comprised of two compounds which bind together using a non-covalent interaction; a host compound is immobilized on the substrate, and a guest compound is conjugated to the surface modifying agent. The primary benefit of the IBL architecture is adaptability: substrates and surface compounds become modular components with standard connectors. Beta-Cyclodextrin (BCD) and adamantane (AD) were selected as the model immobilized host and conjugated guest, respectively. A quartz crystal microbalance (QCM) was assembled and developed to study the BCD/AD complexation interaction. Kinetic, thermodynamic, and Langmuir isotherm data were reported for AD-derivatives binding with immobilized BCD. QCM was also used to investigate neutravidin (NA) binding onto AD-PEG and AD-PEG-biotin coatings immobilized to t-BCD surfaces. QCM was an effective platform to validate the use of BCD/AD as the IBL interaction prior to microfluidic implementation. The BCD/AD IBL was successfully demonstrated in a microfluidic environment. Microfluidic devices were fabricated using the soft-lithographic technique. Adapted surface modifications were visualized using fluorescein isothiocyanate (FITC) probes within the microfluidic device and detected using confocal laser scanning microscopy (CLSM). Surface modifications were applied to demonstrate the fundamental functions of surface passivation, specific binding, and visualization using the IBL architecture. Consistent with QCM data, AD-PEG passivated the surface and AD-PEG-biotin specifically bound NA to the BCD surface. Thus, an adaptable surface modification architecture for microfluidic applications was developed and demonstrated.

A framework to compartmentalize microfluidic surfaces was developed. Substrates are separated from surface modifying agents with an intermediate binding layer (IBL). The IBL is comprised of two compounds which bind together using a non-covalent interaction; a host compound is immobilized on the substrate, and a guest compound is conjugated to the surface modifying agent. The primary benefit of the IBL architecture is adaptability: substrates and surface compounds become modular components with standard connectors. Beta-Cyclodextrin (BCD) and adamantane (AD) were selected as the model immobilized host and conjugated guest, respectively. A quartz crystal microbalance (QCM) was assembled and developed to study the BCD/AD complexation interaction. Kinetic, thermodynamic, and Langmuir isotherm data were reported for AD-derivatives binding with immobilized BCD. QCM was also used to investigate neutravidin (NA) binding onto AD-PEG and AD-PEG-biotin coatings immobilized to t-BCD surfaces. QCM was an effective platform to validate the use of BCD/AD as the IBL interaction prior to microfluidic implementation. The BCD/AD IBL was successfully demonstrated in a microfluidic environment. Microfluidic devices were fabricated using the soft-lithographic technique. Adapted surface modifications were visualized using fluorescein isothiocyanate (FITC) probes within the microfluidic device and detected using confocal laser scanning microscopy (CLSM). Surface modifications were applied to demonstrate the fundamental functions of surface passivation, specific binding, and visualization using the IBL architecture. Consistent with QCM data, AD-PEG passivated the surface and AD-PEG-biotin specifically bound NA to the BCD surface. Thus, an adaptable surface modification architecture for microfluidic applications was developed and demonstrated.

L’objectif de cette thèse est de synthétiser de nouvelles surfaces spécifiques nécessaires à l’immobilisation des biomolécules ; visant à développer à terme un biocapteur pour la détection de pathogènes en industrie agroalimentaire. Cette nouvelle procédure de fonctionnalisation de surface consiste d’une part à greffer des molécules organiques sur un substrat métallique à partir d’une réaction électrochimique et d’autre part de synthétiser un monomère photopolymérisable sur tout type de surface. Ces surfaces sont enfin utilisées pour immobiliser les biomolécules. Ce procédé ainsi développé permet d’éliminer les multiples étapes, l’utilisation excessive de réactifs observés dans les protocoles classiques de fonctionnalisation de surface pour la capture de microorganismes. Deux stratégies de fonctionnalisation ont été investiguées : la polymérisation sur une plaque de platine et le dépôt de monocouche sur une surface d’or. La fonctionnalisation de surfaces ainsi que l’immobilisation de biomolécules ont été caractérisées par la spectroscopie Raman, la microbalance à cristal de quartz, la microscopie à force atomique (AFM) pour le premier et en plus la microscopie à fluorescence pour le second. Les résultats de la fonctionnalisation de surfaces par dépôt de polymère ont montré, une déstabilisation du polymère en présence de l’eau. Afin d’optimiser la synthèse, nous avons travaillé en milieu inerte, sous alumine activée. De plus, on note une large couverture de la zone spectrale des biomolécules par les signaux du polymère ; Pour le dépôt de monocouche, l’on a obtenu une surface très réactive, homogène. La diffusion Raman est la principale technique de caractérisation utilisée. Elle présente l'avantage d'être une méthode de caractérisation physico-chimique non destructive et non invasive. Longtemps délaissée dans les sciences du vivant, cette méthode apparaît maintenant particulièrement prometteuse grâce à un développement récent de spectromètres intégrés performants. La diffusion Raman sur la monocouche déposée montre une intensité accrue des signaux par l’utilisation de la surface d’or et un spectre plus dégagé conduisant à l’identification aisée des biomolécules après fixation. Elle permet non seulement d’identifier les bandes de vibrations de chaque groupement mais aussi la conformation des structures. Les résultats d’immobilisation ont montré que l’accroche des biomolécules sur les surfaces fonctionnalisées était spécifique. La fonctionnalisation de surface d’or par dépôt de monocouche constitue finalement une technique très rapide à mettre en œuvre, peu coûteuse permettant d’ancrer efficacement les biomolécules et peut être utilisée pour diverses applications. La synthèse du monomère photopolymérisable a été abordée et est en cours d’investigation. / In food processing industry, detecting bacteria or viruses is crucial. Nowadays, it can be achieved with microbiological tests but, it requires several days. The objective of the project was to synthesize new specific surfaces capable of biomolecules immobilization in order to develop a biosensor for the detection of various pathogenics in food-processing industry. This new procedure of surface functionalisation consists on one hand in anchoring organic molecules on a metallic substrate by an electrochemical reaction and on the other hand to synthesize a photocrosslinkable monomer on every type of surface. These surfaces are finally used to immobilize biomolecules. Two strategies of surface functionalisation were investigated: the polymerization on a platinium surface and the deposition of monolayer on a gold surface. Both processes were characterized by spectroscopy Raman, Quartz Crystal Microbalance, Atomic Force Microscopy and Fluorescence Microscopy. The results of the functionalisation of surfaces by deposition of polymer showed a destabilization of the polymer in presence of water. To optimize the synthesis, we worked in sluggish middle, under activated alumina. Furthermore, we noted a wide coverage of the spectral zone of biomolecules by the signals of the polymer; For the monolayer deposition, we obtained a very reactive and homogeneous surface. The Raman spectroscopy was the main technique used to the characterization. It presented the advantage to be a non-destructive and non invasive physico-chemical method. This method seemed now particularly promising due to a recent development of successful integrated spectrometers. Raman Spectroscopy showed an enhanced intensity of the signals by the use of the gold surface and a more clear spectrum well-to-do identification of biomolecules after binding. It allowed not only the identification of the bands of vibrations of every connection but also the conformation of the structures. The results of the immobilization showed that the grafting of biomolecules on functionalised surfaces was specific and efficient. The functionalisation of gold surface by monolayer deposition constituted at the end an efficient and low cost technique allowing to anchor biomolecules and can be used for multitude applications. The last step consisting of the synthesis of photocrosslinkable monomer was started and still investigated.

This dissertation includes two research topics. This first topic focuses on fundamental studies of monolignols and lignin, including polymerization and degradation. The second part reports a polymeric material that was crosslinked but can be reprocessed. In order to understand lignin from a molecular level and promote biopolymer conversion, we investigated the dehydrogenative copolymerization and degradation of two monolignols: caffeyl (C) alcohol and p-coumaryl (H) alcohol. The copolymerization and degradation were monitored by a quartz crystal microbalance with dissipation (QCM-D). Atomic force microscopy (AFM) was applied to investigate the topologies of the copolymer and degraded films. Horseradish peroxidase (HRP) was used as the enzyme for the dehydrogenative polymerization of monolignols and chelator-mediated Fenton chemistry was used to degrade the lignin. With constant monolignol concentration, we found that as the fraction of H in the polymerization feed increased, the amount of lignin formed increased, and the films became more rigid. For the degradation process of the resultant lignins, the presence of more C-monolignol during polymerization facilitated greater degradation. This work demonstrated the chemical factors that influenced the physical properties of lignin and lignin degradation, which could impact biofuel production. We further investigated the surface-initiated dehydrogenative polymerization of a new monolignol 5-hydroxyconiferyl (5H) alcohol using a QCM-D. HRP was immobilized on gold sensors. Various experimental conditions were studied. The dehydrogenative polymerization of 5H-monolignol was influenced by the concentration of monolignols and temperature, but was not affected by the hydrogen peroxide concentration, which was different from other monolignols. We also compared the polymerization kinetics of 5H-monolignol and the topology of the resulting lignin thin films with other monolignols. Furthermore, we utilized enzymatic and chemical degradation methods to treat the 5H-lignin. The 5H-lignin film was degraded thoroughly via a chelator-mediated Fenton reaction. This study provided a comprehensive understanding of 5H-monolignol polymerization and degradation and could be used as a reference for the exploration of the applications of the 5H-monolignol. In this dissertation, a separate study involved a vitrimer. It was a crosslinked polymer, but could be reprocessed and reshaped. The new vitrimer was based on poly (methyl methacrylate-co-hydroxymethyl methacrylate). Aromatic disulfides that underwent a dynamic exchange reaction were incorporated as crosslinkers. The structure of the material was identified by proton nuclear magnetic resonance spectroscopy (1H NMR) and Fourier transform infrared spectroscopy (FTIR). Thermal properties and mechanical properties were studied through thermogravimetric analysis (TGA), dynamic mechanical analysis (DMA), and Instron tests. Furthermore, the chemical resistance was explored. Notably, that new material exhibited comparable mechanical performance for three cycles when reprocessed via a hot press to reprocess. / Doctor of Philosophy / Lignin is a complex phenylpropanoid polymer and is one of the most abundant biopolymers in nature. Conversion of lignin into biofuels or other fine chemicals has drawn significant attention in recent years. Understanding molecular details of lignin formation and degradation is of fundamental importance for the biorefinery. Although a number of studies have improved our knowledge about lignin, many important aspects remain unknown. Lignin arises from dehydrogenative polymerization of three types of monolignols, named p-coumaryl (H), coniferyl (G), and sinapyl (S) alcohols. Recently, a new monolignol, caffeyl (C) alcohol, has been found. In this work, the surface-initiated copolymerization of C-monolignol and H-monolignol was conducted through an in vitro synthesis. Furthermore, chelator-mediated Fenton reactions were applied to degrade the resulting lignin. The effect of C-lignin incorporation on degradation was studied. It was found that, when more C-lignin was incorporated, the percentage of degradation was larger. These findings are likely to guide the conversion of lignocellulosic biomass into value-added products. A new monolignol, 5-hydroxyconiferyl (5H) alcohol, was investigated in this dissertation. The surface-initiated dehydrogenative polymerization of 5H was conducted under various experimental conditions, including different temperature, monomer concentration, and hydrogen peroxide concentration. Furthermore, degradation by enzymatic and non-enzymatic methods were studied. It was found that the 5H-lignin was recalcitrant to enzyme, but can be degraded by a non-enzymatic procedure. The synthesis and degradation were monitored by a quartz crystal microbalance with dissipation (QCM-D), which is a label-free method and can provide real-time data. Thermosets are the materials that are chosen for many applications due to their structural stability and mechanical properties. However, due to their permanent crosslinkages, they cannot be reprocessed or recycled. In this dissertation, a new crosslinked polymer material called a vitrimer was reported. The material was developed based upon poly (methyl methacrylate) (PMMA) and aromatic disulfide linkages, which are exchangeable chemical bonds. The exchange reaction occurs very quickly at elevated temperature. As a result, the material can be easily reprocessed and also exhibited chemical stability and mechanical properties similar to conventional thermosets.

As the two most abundant natural polymers on earth, cellulose and chitin have attracted increasing attention as a source of renewable energy and functional materials. Thin films of cellulose and chitin are useful for studying interactions of these materials with other natural and synthetic molecules via techniques such as quartz crystal microbalance with dissipation monitoring (QCM-D) and surface plasmon resonance (SPR). Because of the difficulty of extracting native cellulose, regenerated cellulose (RC), sulfated nanocrystalline cellulose (SNC), and desulfated nanocrystalline cellulose (DNC) thin films are often studied in its place. In this work, QCM-D solvent exchange studies showed that water contents of RC, SNC and DNC films were proportional to the film thickness (d). Accessibility and degradation of the films was further analyzed via substrate exposure to cellulase. Cellulase adsorption onto RC films was independent of d, whereas cellulase adsorption onto SNC and DNC films increased with d. Enhanced access to guest molecules for SNC and DNC films relative to RC films revealed they are more porous. The porosity of these cellulose films aided in understanding the observed differences of xyloglucan (XG) adsorption onto their surfaces. Xyloglucan adsorption onto RC, SNC, and DNC was studied by QCM-D and SPR. The amount of adsorbed XG increased in the order RC < SNC < DNC. XG adsorption onto RC films was independent of d, whereas XG adsorption was weakly dependent upon d for SNC films and strongly dependent upon d for DNC films. However, XG adsorbed onto "monolayer" thin films of RC, SNC, and DNC in approximately the same amount. These results suggested that the morphology and surface charge of the cellulose substrate had a limited effect upon XG adsorption and that accessible surface area of the cellulose film may be the factor leading to apparent differences in XG adsorption for different surfaces. The porosity and surface charge of SNC films presented a unique opportunity to examine polyelectrolyte adsorption and subsequent dewatering of the SNC substrate. The adsorption of a series of cationically derivatized dextran (cDex) polyelectrolytes with various degrees of substitution (DS) onto SNC was studied using QCM-D and SPR. As the hydrophobic character of the cDex samples increased, the water content of the adsorbed cDex layer decreased. For cDex with the greatest hydrophobic content, nearly 50% by mass of the initial water present in the porous SNC film was removed upon cDex adsorption. This study indicated that the water content of the film could be tailored by controlling the DS and hydrophobic character of the polyelectrolyte. This work also presents the first report of smooth, homogeneous, ultrathin chitin films, opening the door to surface studies of binding interactions, adsorption kinetics, and enzymatic degradation. The chitin films were formed by spincoating trimethylsilyl chitin onto gold or silica substrates, followed by regeneration to a chitin film. The utility of these chitin films as biosensors was evident from QCM-D and SPR studies that revealed bovine serum albumin adsorbed as a monolayer. / Ph. D.

Résumé : Lors de l’utilisation de la radiation pour le diagnostic et le traitement du cancer, l’ADN est une cible importante due à son rôle dans la division cellulaire. La radiation y dépose de l’énergie par production abondante (10[indice supérieur 5] e[indice supérieur −]/MeV) d’électrons de basse énergie (EBE) (<50 eV) menant à la production de radicaux et à la dissociation de molécules. Une meilleure compréhension de ces phénomènes physico-chimiques mènera au développement de nouvelles stratégies en radioprotection et en radiothérapie. Il est primordial d’identifier et de quantifier ces dommages initiaux. Suite à des résultats obtenus par des expériences récentes (Li et al., 2010) sur des couches minces d’ADN irradiées par des EBE dans le vide, nous suggérons que certains produits désorbent en quantité significative. Nous proposons une méthode pour mesurer cette perte de matière en utilisant une balance à quartz pour mesurer in situ les changements de masse totale. Ce mémoire présentera la conception et la construction de l’appareil ainsi que les résultats d’irradiation de la thymine et de la thymidine. À 25 ◦ C, le taux de perte de masse spontanée des échantillons joue un rôle important pour les petites molécules comme la thymine (126 uma). L’irradiation augmente d’abord ce taux qui diminue d’un facteur 5 à 15 après une exposition prolongée, signe de modifications notables de l’échantillon. Pour des molécules plus imposantes comme la thymidine (242 uma), il n’y a pas de désorption spontanée et le taux de désorption induite par des électrons de 50 eV est de 0,4 ± 0,1 uma/e[indice supérieur -]. Cette méthode, nécessaire à la calibration d’autres expériences réalisées par HPLC et spectrométrie de masse, permet de compléter la quantificationdes fragments, qui peuvent aussi être l’origine de lésions subséquentes. / Abstract : DNA is the principle target of radiotherapy (RT) due to its crucial role in cellular growth and function. Ionizing radiation (IR) delivers its energy into the cell and its nucleus via sequential ionization events that produce many low-energy electrons (LEE)(10[superscript 5]e[superscript −] per MeV) which drive subsequent molecular dissociations and the formation of radicals and other reactive species. Since a better understanding of these mechanisms is needed to develop new strategies for radioprotection and RT, it is essential to identify and to quantify the initial damage induced by IR. Recent chromatographic (HPLC) analysis of short oligonucleotide irradiated with LEE in vacuo (Li et al., 2010) revealed that only ∼30 % of the loss of intact molecules could be explained by the formation of identifiable radiation products. We hypothesize that electron stimulated desorption (ESD) may account for some of the unexplained loss of the missing molecules. Here we propose a new experimental method to quantify this loss using a quartz crystal microbalance to measure in situ the total mass change due to ESD. This thesis describes the design and the construction of the novel apparatus and presents results for LEE irradiated thymine (thy) and thymidine (dT). We find that at 25 ◦ C, the thermal-induced mass loss is important for small molecules such as thy (126 amu). Upon irradiation at 50 eV, the rate of mass loss initially increases, but then decreased by factors between 5 and 15 indicating structural changes occurring at the sample surface. For larger molecules such as dT (242 amu), there is no thermal evaporation at 25 ◦ C and the LEE induced rate of desorption at 50 eV is 0.4 ± 0.1 amu/e[superscript -]. This work is needed to calibrate HPLC and mass spectrometry experiments allowing us to quantify the fragment species produced by LEE that are expected to induce further and biologically significant damage.

Nanostructured, porous materials offer great promise for application in areas such as energy storage, photovoltaics, and catalysis. These materials are often difficult to characterize because they are structurally and compositionally inhomogeneous, and disordered with features to small to be resolved by scanning probe techniques such as atomic force microscopy (AFM) and scanning electron microscopy (SEM). These shortcomings require that new techniques be developed that can be applied to real world systems to elucidate how the interplay of material composition and structure alters their performance. Towards this end, the development of a hybrid quartz crystal microbalance/ ellipsometric porosimetry (QCM/EP) technique is being pursued to facilitate the determination of a number of material parameters such as porosity, pore size distribution, and surface area. Additionally, the use of adsorbate probe molecules of varying polarity gives further information about adsorbate-surface interactions and surface chemistry characteristics. Simultaneous acquisition of both mass-based and refractive index based adsorption isotherms fosters mechanistic understanding about the behavior of adsorbates confined in mesopores while at the same time reducing the uncertainty in the analysis of the optical parameters acquired via ellipsometry. To highlight the power of this approach, studies of TiO₂ and TiC, electrode materials as model systems will be presented that have helped us validate measurement and modeling protocols for extracting physical properties. / text