Le but de cette thèse est de concevoir une puce à sucres, compatible avec un système optique d'imagerie en résonance des plasmons de surface (SPRi), afin d'analyser simultanément de multiples interactions protéine/oligosaccharide en temps réel. La réalisation d'un système modèle, ayant comme sucre sonde, l'héparine, est proposée. La modification du sucre par un pyrrole permet de le déposer sur une surface d'or par électrocopolymérisation. Cette chimie nécessite la construction de molécules « pyrrole - bras espaceurs » compatibles avec les propriétés des sucres utilisés. La puce utilisable en SPRi est ensuite fabriquée par électrocopolymérisations successives. Ces plots formés peuvent être caractérisés par MEB et par AFM. Des expériences préliminaires utilisant des traceurs fluorescents ont permis de valider le système ainsi que la chimie proposée ; la fluorescence observée est spécifique de l'interaction biologique grâce à la présence de négatifs. Les études d'interactions biologiques suivies par SPRi ont alors été réalisées ; la sensibilité de l'interaction est confirmée. Grâce à l'acquisition en temps réel des interactions, les cinétiques d'association et de dissociation du complexe oligosaccharide/protéine sont observées puis optimisées. De plus, les puces fabriquées sont régénérables mais aussi réutilisables sur plusieurs mois, ce qui permet l'étude des paramètres chimiques et biologiques. Cette approche est appliquée finalement à plusieurs problématiques biologiques.

L'objectif de cette thèse est de contrôler les propriétés optiques des nanoparticules d'or greffées de polymère en modulant les propriétés structurales de la couche protectrice de polymères. Des nanoparticules greffées de polymères thermosensibles avec une large gamme de masse molaire et différents degrés d'hydrophobicité sont synthétisées par la méthode de " grafting-to ". La DNPA est utilisée pour caractériser les propriétés structurales de la couche protectrice de polymère. Les spectres d'absorption sont modélisés en utilisant la théorie de Mie. Nous démontrons que la sensibilité de la SPR à la propriété diélectrique du solvant diminue progressivement avec la fraction volumique de la couche de polymère jusqu'à devenir quasi-nulle; dans ce dernier cas de figure, la SPR est dite " gelée " par la couche de polymère. Un déplacement significatif de la bande de SPR vers le rouge est induit (un changement de couleur se produit) dû à une transition de collapse de la couche de polymère avec la température. La gamme de température pour induire ce déplacement dépend du degré d'hydrophobicité du polymère et de la salinité. Une partie important de cette thèse est également consacrée aux propriétés des nanoparticules d'or greffées de polymères à l'interface air-eau. La technique de Langmuir est utilisée pour former des films minces dont la distance entre particule est contrôlée par la compression, la longueur des chaînes du polymère greffé et la température. Les propriétés structurales des films minces sont étudiées en déterminant la conformation de la couche de polymère greffée et l'organisation du cœur de l'or par la réflectivité de neutron et de X, respectivement. Les mesures de réflectivité nous permettent également d'évaluer et d'améliorer la stabilité des films minces pour un meilleur control de la distance entre particule, aspect important pour l'optimisation de la SPR. Enfin, les propriétés optiques des nanoparticules d'or à l'interface sont mesurées par des mesures de transmission.

Ruttningen av trafik i IP-nätverk sker ofta med hjälp av bågvikter som bestämmer vilken väg trafiken tar (kortastevägruttning). Problemet här är att avgöra ifall det existerar en uppsättning vikter givet ett önskat ruttningsschema. Den hör rapporten undersöker prestandan hos ett antal modeller och optimeringsprogram avsedda att lösa denna typ av problem som ofta kallas inversa kortastevägruttningsproblemet. Undersökningen visar att det existerar en stor skillnad mellan modellerna och optimeringsprogrammen och att modellen baserad på cykelbaser löst med CPLEXdualopt lösaren är snabbast. / The routing of traffic in IP networks is often done with a set of weights that determinewhich way the traffic will go (shortest path routing). The problem here is todetermine if there exists a set of weights for a desired routing pattern. This thesis willinvestigate the performance of a number of different models and solvers for solvingthis type of problem which is usually called the inverse shortest path routing (ISPR)problem. The models tested are the same as described in [1]. The different solversused are mainly the linear CPLEX solvers but also a few multi commodity networksolvers. The tests showed that there is a big performance difference between the models andsolvers and that the cycle bases model solved with the CPLEX dualopt solver wasthe fastest overall.

The design of optimal strictly positive real (SPR) compensators using numerical optimization is considered. The plants to be controlled are linear and nonlinear flexible manipulators. For the design of SISO and MIMO linear SPR controllers, the optimization objective function is defined by reformulating the H2-optimal control problem subject to the constraint that the controllers must be SPR. Various controller parameterizations using transfer functions/matrices and state-space equations are considered. Depending on the controller form, constraints are enforced (i) using simple inequalities guaranteeing SPRness, (ii) in the frequency domain, or (iii) by implementing the Kalman-Yakubovich- Popov lemma. The design of a gain-scheduled SPR controller using numerical optimization is also considered. Using a family of linear SPR controllers, the time dependent scheduling signals are parameterized, and the objective function of the optimizer seeks to find the form of the scheduling signals which minimizes the manipulator tip tracking error while minimizing the control effort.

It is well known boronic acids have its unique chemistry and related applications in organic synthesis. The boronic acid functionally group also plays very important roles in medicinal chemistry and chemical biology. For example, boronic acids have been developed as potential therapeutic agents, chemical biology tools. All these applications are directly related to the unique electronic and chemical properties of the boronic acid group. Herein, several application of boronic acids have been studied: 1) several groups of compounds were found as bacterial quorum sensing inhibitors; 2) a boronate compound was developed as a probe for detecting reactive oxygen species (ROS); and 3) boronic acid-modified aptamers can be used for glycoprotein recognition.

Protein-protein and protein-molecule interactions are complicated phenomena due to the tendency of proteins to change shape and function in response to their environment. Protein aggregation whether onto surfaces or in solution, can pose numerous problems in industry. Surface plasmon resonance (SPR) devices and quartz crystal microbalances (QCM) are two real-time, label free methods that can be used to detect the interactions between molecules on surfaces. These devices often employ self-assembled monolayers (SAMs) to produce specific surfaces for studying protein-protein interactions. The objective of this work was to develop methodologies utilizing SPR to better understand protein-protein and protein-molecule interactions with possible applications in the food and separation industrial sectors. A very well characterized whey protein, β-lactoglobulin (BLG), is used in numerous applications in the food industry. BLG can undergo different types of self-aggregation due changes in external environment factors such as buffer strength, pH or temperature. In this work, a hydrophilic SAM was developed and used to study the interaction and non-specific adsorption of BLG and palmitic acid (PA), a molecule which is known to bind to BLG. It was found that PA tended to reduce BLG conformational changes once on the surface, resulting in a decrease in its surface adhesion. Fluorescent excitation emission matrices (EEM’s) using a novel fluorescence probe technique were utilized to detect protein on the surface as well as conformational changes on the surface of the sensor, although the extent these changes could not be quantified. Another whey protein, α-lactoglobulin (AL), was utilized as a surrogate protein to study the adsorption of colloidal/particulate and protein matter (CPP) extracted from filtration studies of river water. A large fraction of natural organic matter (NOM), the major foulant in membrane based water filtration, is CPP and protein. Understanding the interactions between these components is essential in abating NOM membrane fouling. Several SPR methods were investigated in order to verify the interactions. A mixture of AL and CPP particles in solution prevented the non-specific adsorption of AL to the SAM surface. This change in association was then detected through SPR. Fluorescent EEM’s of the sensor surface verified that CPP and AL bound to the surface. This finding has fundamental significance in the interpretation of NOM-based membrane fouling. To better understand the mechanisms behind non-specific adsorption, a mechanistic mathematical model was developed to describe the adsorption of BLGs onto the hydrophilic SAM. The resulting model performed well in terms of predicting adsorption based on SPR data. The model incorporated the monomer-dimer equilibrium of BLG in solution, highlighting the impact of protein aggregation on non-specific adsorption mechanisms. For future studies, improvement in fluorescent FOP surface scan methodology would help identify different protein/molecules and conformations on the surface.

The design of optimal strictly positive real (SPR) compensators using numerical optimization is considered. The plants to be controlled are linear and nonlinear flexible manipulators. For the design of SISO and MIMO linear SPR controllers, the optimization objective function is defined by reformulating the H2-optimal control problem subject to the constraint that the controllers must be SPR. Various controller parameterizations using transfer functions/matrices and state-space equations are considered. Depending on the controller form, constraints are enforced (i) using simple inequalities guaranteeing SPRness, (ii) in the frequency domain, or (iii) by implementing the Kalman-Yakubovich- Popov lemma. The design of a gain-scheduled SPR controller using numerical optimization is also considered. Using a family of linear SPR controllers, the time dependent scheduling signals are parameterized, and the objective function of the optimizer seeks to find the form of the scheduling signals which minimizes the manipulator tip tracking error while minimizing the control effort.

Identification of pathogens living in biofilms of chronic infections has been difficult with PCR, serological, biochemical and culture techniques. The study aims at the detection of bacterial pathogens in biofilms of biological secretions using SPR analysis Biacore. The antibodies were developed by isolating mononuclear lymphocytes from the blood of the patients who sustained systemic infection. The isolated lymphocytes had antibody secreting B cells (plasma cells) which were identified using flow cytometry analysis. The antibodies produced (n=4) were used to immobilize CM5 chip of Biacore to detect the bacteria in ulcer secretions with wound secretions of healthy volunteers as controls. The results from Surface Plasmon Resonance (SPR) analysis and culture technique were compared and statistically there was no significant difference obtained. The results from present study suggest that SPR analysis could be used as an alternative system for detection of bacteria in poly-microbial samples and detect the organisms that might not be discovered by culture or PCR method.

The Microelectronics Group has been researching sensors useful for detecting and quantifying events in biological molecular chemistry, for example, binding events. Our previous research has been based primarily on quartz resonators. This thesis describes the results of our initial research of Surface Plasmon Resonance (SPR) based technology. This study contains the design and implementation of a fully functional SPR biosensor with detailed disclosure of monolayer construction, digital hardware interfaces and software algorithms for process the SPR sensors output. An antibody monolayer was constructed on the biosensor surface with the goal of setting the strengths, weaknesses and limitation of measuring molecular events with SPR technology. We documented several characteristics of molecular chemistry that directly effect any measurements made using Surface Plasmon Resonance technology including pH, free ions, viscosity and temperature. Furthermore, the component used in our study introduced additional limitations due to wide variations amongst parts, the constraint of a liquid medium and the large surface area used for molecular interrogation. We have identified viable applications for this sensor by either eliminating or compensating for the factors that affect the measured results. This research has been published at the inaugural IEEE sensors conference and to our knowledge is the first time a biosensor has been constructed by attaching a sensor to a PDA and performing all signal processing, waveform analysis and display in the PDAs core processor.

No description available.