L'objectif de cette thèse réside notamment dans l'étude par diffusion Raman de la dynamique vibrationnelle de nanoparticules métalliques en matrice. Grâce au couplage des vibrations avec le plasmon de surface des particules (diffusion Raman résonnante), la diffusion est fortement amplifiée, ce qui conduit à un signal très intense au regard de la faible quantité de matière métallique présente dans les films nanocomposites étudiés. Les caractéristiques structurales de ces films diffèrent selon la méthode d'élaboration utilisée: source d'agrégats à vaporisation laser et co-déposition des particules et de la matrice par la technique LECBD, co-pulvérisation ionique du métal et de la matrice, ou encore fabrication de verres dopés. Les spectres Raman basse fréquence sont dominés par la bande correspondant à la diffusion par les vibrations quadrupolaires. Dans le cas de l'argent, la position de cette bande varie avec la taille des particules conformément aux prédictions du modèle de la sphère élastique, ainsi qu'avec la longueur d'onde d'excitation, ce qui reflète une sélection en forme des particules diffusant la lumière. Des mesures réalisées dans deux configurations de polarisation des lumières incidente et diffusée confirment cette hypothèse. Un effet de cohérence spatiale sur la diffusion Raman a été mis en évidence en comparant des spectres d'échantillons ayant ou non subis un recuit. L'origine de cet effet est justifiée par quelques considérations théoriques. La diffusion Raman par les vibrations radiales des particules, observée sur des échantillons traités thermiquement, donne lieu à une comparaison intéressante avec des résultats extérieurs, obtenus par une technique de spectroscopie résolue en temps. Le problème des particules mixtes est aussi abordé à travers l'étude de plusieurs systèmes bimétalliques formant, soit un alliage, comme l'or-argent, soit un «core-shell» lorsqu'il y a ségrégation des deux métaux, comme le suggèrent les mesures effectuées sur des particules d'argent-nickel et d'argent-cobalt. Ce travail de recherche a aussi fait l'objet d'une étude par diffusion haute fréquence sur les échantillons recuits de particules d'argent en matrice de silice. Une bande large, dont le maximum est localisé vers 1000 1/cm, est observée et présente des comportements, vis-à-vis de la taille des particules et de l'excitation, très semblables à ceux de la bande basse fréquence. Une discussion sur l'origine de cette diffusion attribuerait plutôt celle-ci à des excitations de paires électron-trou.

Ce travail de thèse présente une étude théorique, numérique et expérimentale de l'intégration sur un guide d'onde diélectrique de chaînes de nanoparticules d'or supportant des résonances " plasmon de surface localisé ". Les guides d'onde à plasmon de surface localisé procurent un confinement sub-longueur d'onde de la lumière, ce qui permet d'envisager la réalisation de composants optiques ultra-compacts. Cependant, leurs pertes optiques élevées restreignent leur application à de courtes distances de propagation, contrairement aux guides d'onde diélectriques. Une combinaison judicieuse des deux types de guide doit donc permettre de bénéficier de leurs avantages respectifs. Dans un premier temps, nous avons étudié théoriquement les propriétés des chaînes des nanoparticules grâce à un modèle analytique basé sur l'approximation de dipôles ponctuels couplés, que nous avons développé. Cette étude a permis de déterminer la forme et les dimensions des nanoparticules qui ont ensuite été introduites dans un logiciel de FDTD pour simuler le couplage entre la chaîne de nanoparticules et le guide diélectrique (SOI ou en Si3N4). De cette étude numérique, nous avons déduit les géométries des structures à fabriquer. Les structures réalisées ont été caractérisées à l'aide d'un banc de transmission résolue spectralement, mis en place pendant cette thèse, et d'un système de mesures en champ proche optique en collaboration avec le LNIO (Troyes). Pour la première fois, nous avons montré expérimentalement les propriétés d'une chaîne courte de nanoparticules intégrée sur un guide SOI, ainsi que le phénomène de guides couplés entre une chaîne longue de nanoparticules et un guide SOI. Une valeur record de la constante de couplage a été obtenue, et ce, aux longueurs d'onde des télécoms (proche infrarouge). L'énergie lumineuse transportée par le mode TE du guide SOI peut ainsi être entièrement transférée au guide plasmonique en 4 ou 5 nanoparticules, soit une distance de propagation de moins de 600 nm. Nous avons également étudié les propriétés de réseaux de Bragg à base de plasmon de surface localisé en confrontant les résultats de mesures de transmission résolue spectralement aux résultats théoriques d'un modèle analytique basé à la fois sur l'approximation de dipôle ponctuel en régime quasi-statique et la théorie des modes couplés. Ces travaux ouvrent la voie à des applications de pinces optiques, de capteurs ou de spaser, qui bénéficieront de l'intégration de nanoparticules métalliques dans les circuits photoniques.

<p>Immobilization of different bio- and organic molecules on solid supports is fundamental within many areas of science. Sometimes, it is desirable to obtain a directed orientation of the molecule in the immobilized state. In this thesis, the copper (I) catalyzed Huisgen 1,3-dipolar cycloaddition, referred to as a “click chemistry” reaction, was explored as a means to perform directed immobilization of small molecule ligands on gold surfaces. The aim was to synthesize alkyne- and azide-terminated alkanethiols that would form well-organized self assembled monolayers (SAMs) on gold from the commercially available substances orthoethylene glycol and bromo alkanoic acid. N-(23-azido-3,6,9,12,15,18,21-heptaoxatricosyl)-n-mercaptododekanamide/hexadecaneamide (n = 12, 16) were successfully synthesized and allowed to form SAMs of different compositions to study how the differences in density of the functional groups on the surface would influence the structure of the monolayer and the click chemistry reaction. The surfaces were characterized by different optical methods: ellipsometry, contact angle goniometry and infrared reflection-absorption spectroscopy (IRAS). The click reaction was found to proceed at very high yields on all investigated surfaces. Finally, the biomolecular interaction between a ligand immobilized by click chemistry on the gold surfaces and a model protein (bovine carbonic anhydrase) was demonstrated by surface plasmon resonance using a Biacore system.</p>

The study of optical phenomena related to the strong electromagnetic response of noble metals (silver (Ag) and gold (Au) being most popular) over the last couple of decades has led to the emergence of a fast growing research area called plasmonics named after 'surface plasmons' which are electron density waves that propagate along the interface of a metal and a dielectric medium. Surface plasmons are formed by the coupling of light to the electrons on the metal surface subject to the fulfillment of certain physical conditions and they are bound to the metal surface. Depending on whether the metallic medium is a continuous film or a structure having dimensions less than or comparable to the wavelength of the exciting light, propagating or localized surface plasmons can be excited. The structure can be either a hole or an arbitrary pattern in a metal film, or a metallic particle. An array of subwavelength structures can behave as an effective homogeneous medium to incident light and this is the basis of a new class of media known as metamaterials. Metallic metamaterials enable one to engineer the electromagnetic response to  incident light and provide unconventional optical properties like negative refractive index as one prominent example. Metamaterials exhibiting negative index (also called negative index materials (NIMs)) open the door for super resolution imaging  and development of invisibility cloaks. However, the only problem affecting the utilization of plasmonic media to their fullest potential is the intrinsic loss of the metal, and it becomes a major issue especially at visible-near infrared (NIR) frequencies. The frequency of the surface plasmon is the same as that of the exciting light but its wavelength could be as short as that of X-rays. This property allows light of a given optical frequency to be conned into very small volumes via subwave lengthmetallic structures, that can be used to develop ecient sensors, solar cells, antennas and ultrasensitive molecular detectors to name a few applications. Also, interaction of surface plasmons excited in two or more metallic subwavelength structures in close proximity inuences the far-eld optical properties of the overall coupled system. Some eects of plasmonic interaction in certain coupled particles include polarization conversion, optical activity and transmission spectra mimicking electromagnetically-induced transparency (EIT) as observed in gas based atomicsy stems. In this thesis, we mainly focus on the optical properties of square arrays of certain plasmonic structures popularly researched in the last decade. The structures considered are as follows: (1) subwavelength holes of a composite hole-shape providing superior near-eld enhancement such as two intersecting circles (called' double hole') in an optically thick Au/Ag lm, (2) double layer shnets, (3) subwavelength U-shaped particles and (4) rectangular bars. The entire work is based on electromagnetic simulations using time and frequency domain methods. Au/Ag lms with periodic subwavelength holes provide extraordinarily high transmission of light at certain wavelengths much larger than the dimension of the perforations or holes. The spectral positions of the maxima depend on the shape of the hole and the intra-hole medium, thereby making such lms function as a refractive index sensor in the transmission mode. The sensing performance of the double-hole geometry is analyzed in detail and compared to rectangular holes. Fishnet metamaterials are highly preferred when it comes to constructing a NIM at optical frequencies. A shnet design that theoretically oers a negative refractive index with least losses at telecommunication wavelengths (1.4 1.5 microns) is presented. U-shaped subwavelength metallic particles, in particular single-slit split-ring resonators (SSRRs), provide a large negative response to the magnetic eld of light at a specic resonance frequency. The spectral positions of the structural resonances of the U-shaped particle can be found from its array far field transmission spectrum at normal incidence. An effort is made to clarify our understanding of these resonances with the help of localized surface plasmon modes excited in the overall particle. From an application point of view, it is found that a planar square array of SSRRs eectively functions as an optical half-wave waveplate at the main resonance frequency by creating a polarization in transmission that is orthogonal to that of incident light. A similar waveplate eect can be obtained purely by exploiting the near-eld interaction of dierently oriented neighbouring SSRRs. The physical reasons behind polarization conversion in dierent SSRR-array systems are discussed. A rectangular metallic bar having its dipolar resonance in the visible-NIR is called a nanoantenna, owing to its physical length in the order of nanometers. The excitation of localized surface plasmons, metal dispersion and the geometry of the rectangular nanoantenna make an analytical estimation of the physical length of the antenna from the desired dipolar resonance dicult. A practical map of simulated resonance values corresponding to a variation in geometrical parameters of Au bar is presented. A square array of a coupled plasmonic system comprising of three nanoantennas provides a net transmission response that mimicks the EIT effect. The high transmission spectral window possesses a peculiar dispersion profile that enables light with frequencies in that region to be slowed down. Two popular designs of such plasmonic EIT systems are numerically characterized and compared. / <p>QC 20121017</p>

Livet tas för givet av de flesta. Det finns däremot många som ägnar stora delar av sitt liv för att försöka lösa dess mysterier. En del av lösningen ligger i att förstå hur alla molekyler är sammanlänkade i det gigantiska nätverk som definierar den levande organismen. Under det senaste seklet har en hel del forskning utförts för att kartlägga dessa nätverk. Resultatet av dessa mödor kan vi se i de läkemedel som vi har idag och som har utvecklats för att bota eller åtminstone lindra olika sjukdomar och tillstånd. Dessvärre finns det fortfarande många sjukdomar som är obotliga (t.ex. cancer) och mycket arbete krävs för att förstå dem till fullo och kunna designa framgångsrika behandlingar. Arbetet i denna avhandling beskriver en analytisk plattform som kan användas för att effektivisera kartläggningsprocessen; protein-mikroarrayer. Mikroarrayer är ytor som har mikrometerstora (tusendels millimeter) strukturer i ett regelbundet mönster med möjligheten att studera många interaktioner mellan biologiska molekyler samtidigt. Detta medför snabbare och fler analyser - till en lägre kostnad. Protein-mikroarrayer har funnits i ungefär ett decennium och har följt i fotspåren av de framgångsrika DNA-mikroarrayerna. Man bedömer att protein-mikroarrayerna har en minst lika stor potential som DNA mikroarrayerna då det egentligen är mer relevant att studera proteiner, som är de funktionsreglerande molekylerna i en organism. Vi har i detta arbete tillverkat modellytor för stabil inbindning av proteiner, som lämnar dem intakta, funktionella och korrekt orienterade i ett mikroarray format. Därmed har vi adresserat ett stort problem med protein mikroarrays, nämligen att proteiner är känsliga molekyler och har i många fall svårt att överleva tillverkningsprocessen av mikroarrayerna. Vi har även studerat en metod att tillverka mikroarrayer av proteiner bundna till strukturer, som modellerats att efterlikna cellytor. Detta är särkilt viktigt eftersom många (hälften) av dagens (och säkerligen framtidens) läkemedel är riktade mot att påverka denna typ av proteiner och att studera dessa i sin naturliga miljö är därför väldigt relevant. I ett annat projekt har vi använt protein mikroarrayer för att detektera fyra vanliga droger (heroin, amfetamin, ecstasy och kokain). Detektionen baseras på användandet av antikroppar som lossnar från platser på ytan när de kommer i kontakt med ett narkotikum. Detta koncept kan enkelt utvecklas till att detektera mer än bara fyra droger. Vi har även lyckats att parallellt mäta förekomsten av en annan typ av förening på mikroarray ytan, nämligen det explosiva ämnet trinitrotoluen (TNT). Detta visar på en mångsidig plattform för detektionen av i princip vilken typ av farlig eller olaglig substans som helst - och på en yta! Vi föreställer oss därför att möjliga tillämpningsområden finns inom brottsbekämpning, i kampen mot terrorism och mot narkotikamissbruk etc. Mikroarrayerna har i denna avhandling utforskats med optiska metoder som tillåter studie av omärkta proteiner, vilket resulterar i så naturliga molekyler som möjligt. / Life is a thing taken for granted by most. However, it is the life-long quest of many to unravel the mysteries of it. Understanding and characterizing the incomprehensively complex molecular interaction networks within a biological organism, which defines that organism, is a vital prerequisite to understand life itself. Already, there has been a lot of research conducted and a large knowledge has been obtained about these pathways over, especially, the last century. We have seen the fruits of these labors in e.g. the development of medicines which have been able to cure or at least arrest many diseases and conditions. However, many diseases are still incurable (e.g. cancer) and a lot more work is still needed for understanding them fully and designing successful treatments. This work describes a generic analytical tool platform for aiding in more efficient (bio)molecular interaction mapping analyses; protein microarray chips. Microarray chips are surfaces with micrometer sized features with the possibility of studying the interactions of many (thousands to tens of thousands) (bio)molecules in parallel. This allows for a higher throughput of analyses to be performed at a reduced time and cost. Protein microarrays have been around for approximately a decade, following in the footsteps of the, so far, more successfully used DNA microarrays (developed in the 1990s). Microarrays of proteins are more difficult to produce because of the more complex nature of proteins as compared to DNA. In our work we have constructed model surfaces which allow for the stable, highly oriented, and functional immobilization of proteins in an array format. Our capture molecules are based on multivalent units of the chelator nitrilotriacetic acid (NTA), which is able to bind histidine-tagged proteins. Furthermore, we have explored an approach for studying lipid membrane bound systems, e.g. receptor-ligand interactions, in a parallelized, microarray format. The approach relies on the addressable, DNA-mediated adsorption of tagged lipid vesicles. In an analogous work we have used the protein microarray concept for the detection of four common narcotics (heroin, amphetamine, ecstasy, and cocaine). The detection is based on the displacement of loosely bound antibodies from surface array positions upon injection of a specific target analyte, i.e. a narcotic substance. The proof-of-concept chip can easily be expanded to monitor many more narcotic substances. In addition, we have also been able to simultaneously detect the explosive trinitrotoluene (TNT) along with the narcotics, showing that the chip is a versatile platform for the detection of virtually any type of harmful or illegal compound. This type of biosensor system is potentially envisaged to be used in the fight against crime, terrorism, drug abuse etc. Infrared reflection absorption spectroscopy together with ellipsometry has been used to characterize molecular layers used in the fabrication processes of the microarray features. Imaging surface plasmon resonance operating in the ellipsometric mode is subsequently used for functional evaluation of the microarrays using a well-defined receptor-ligand model system. This approach allows simultaneous and continuous monitoring of binding events taking place in multiple regions of interest on the microarray chip. A common characteristic of all the instrumentation used is that there is no requirement for labeling of the biomolecules to be detected, e.g. with fluorescent or radioactive probes. This feature allows for a flexible assay design and the use of more native proteins, without any time-consuming pretreatments.

This thesis demonstrates the application of biosensor technology for molecular biology investigations, utilizing a surface plasmon resonance based optical device for mass sensitive detection of biomolecular interactions at a chipsurface. Oligonucleotide model systems were designed for analysis of the action of DNA manipulating enzymes. DNA ligation, DNA cleavage and DNA synthesis could be quantitatively monitored in real-time. A protocol for DNA minisequencing was also established based on prevention of chain elongation by incorporation of chain-terminators. Determinations of affinities for short oligonucleotides hybridizing to an immobilized target were performed with various sequence content, length, temperature and degree of complementarity. The decrease in affinity for hybridizations involving mismatch situations was found to be strongly dependent on the relative position of the mismatch. Interestingly, also end-mismatches were clearly detectable. The stabilization effect achieved upon co-hybridization of two adjacently annealing short oligonucleotide modules (modular primer effect) was also investigated for different module combinations and hybridization situations. The modular concept of hybridizations was subsequently demonstrated to result in enhanced Capture of single stranded PCR products. The sequence based DNA analysis, first introduced with oligonucleotide modelsystems, was extended to the scanning and screening formutations in PCR amplified DNA from clinically relevant samples. Several different formats were investigated, eitherwith the PCR products immobilized on the chip and oligonucleotides injected or vice versa. Again, mismatch discrimination could be observed for wild type and mutant specific oligonucleotides hybridizing to the targets. The experimental set-up for mutation detection was further developed by the introduction of a subtractive mismatch sensitive hybridization outside the instrument and a subsequent determination of the relative amounts of remain ingoligonucleotides with analytical biosensor monitoring of hybridizations between fully complementary oligonucleotides. In conclusion, the applied technology was found to be a suitable tool for a wide range of molecular biology applications, with emphasis on hybridization analysis and mutation detection. / QC 20100611

Immobilization of different bio- and organic molecules on solid supports is fundamental within many areas of science. Sometimes, it is desirable to obtain a directed orientation of the molecule in the immobilized state. In this thesis, the copper (I) catalyzed Huisgen 1,3-dipolar cycloaddition, referred to as a “click chemistry” reaction, was explored as a means to perform directed immobilization of small molecule ligands on gold surfaces. The aim was to synthesize alkyne- and azide-terminated alkanethiols that would form well-organized self assembled monolayers (SAMs) on gold from the commercially available substances orthoethylene glycol and bromo alkanoic acid. N-(23-azido-3,6,9,12,15,18,21-heptaoxatricosyl)-n-mercaptododekanamide/hexadecaneamide (n = 12, 16) were successfully synthesized and allowed to form SAMs of different compositions to study how the differences in density of the functional groups on the surface would influence the structure of the monolayer and the click chemistry reaction. The surfaces were characterized by different optical methods: ellipsometry, contact angle goniometry and infrared reflection-absorption spectroscopy (IRAS). The click reaction was found to proceed at very high yields on all investigated surfaces. Finally, the biomolecular interaction between a ligand immobilized by click chemistry on the gold surfaces and a model protein (bovine carbonic anhydrase) was demonstrated by surface plasmon resonance using a Biacore system.

Cancer is the main cause of death in economically developed countries and the second leading cause of death in developing countries. Along with today’s knowledge that more than two hundred different diseases lie in the category of this prognosis there is an urge for more detailed and case-specific treatments to replace the dramatic actions of available radiation- and chemotherapy, which in many cases do not make a difference between healthy and cancer cells. The transcription factor and onco-protein c-Myc has, after being extensively studied during the past decades, become a prognostic marker for almost all cancer forms known. Still, many questions remain regarding how c-Myc interacts with its many different target proteins involved in cell-cycle regulation, proliferation and apoptosis. Current cell biology states that one of the regulating proteins, hPin1, interacts with c-Myc in a phosphorylation-dependent manner which appears to direct the correct timing of c-Myc activation and degradation through the ubiquitin/proteasome-pathway. The critical phosphorylation sites, T58 and S62, are located in the Myc-Box-I (MBI) region, a highly conserved sequence strongly coupled to aggressive tumourigenesis by hotspot mutations. Interestingly, preliminary results in the Sunnerhagen group suggested that MBI alone did not bind hPin1, suggesting hPin1 targeting a site distal from the residues to be phosphorylated. In this thesis, results from Surface Plasmon Resonance (SPR) and Nuclear Magnetic Resonance (NMR) show that the docking WW-domain of hPin1 binds unphosphorylated c-Myc at a region distal from the phosphorylation site, including residues 13-34. Furthermore, SPR experiments revealed that hPin1 binds unphosphorylated c-Myc with apparently greater affinity and with much slower kinetics than phosphorylated c-Myc. Thus, hPin1 recognition and interaction with c-Myc appears not to be dependent on phosphorylation of c-Myc prior binding. The newly identified binding region of c-Myc, located N-terminal of MBI, may further increase the understanding of protein degradation control and c-Myc function. The studies presented in this thesis provide a brick in the puzzle of c-Myc and hPin1 coupled oncogenesis for further development of new therapeutic strategies.

Surface plasmon-polaritons are optical surface waves formed through the interaction of photons with free electrons at the surface of metals. They offer interesting applications in a broad range of scientific fields such as physics, chemistry, biology, and material science. However, many of such applications face limitations imposed by the high propagation losses of these waves at visible and near-infrared wavelengths, which result mainly from power dissipation in the metal. In principle, the propagation losses of surface plasmon-polaritons can be compensated through optical amplification. The objective of this thesis is to provide deeper insights on the physics of surface plasmon-polariton amplification and spontaneous emission in surface plasmon-polariton amplifiers through theoretical and experimental vehicles applied (but not necessarily restricted) to a particular plasmonic mode termed long-range surface plasmon-polariton. On the theoretical side, the objective is approached by developing a realistic theoretical model to describe the small-signal amplification of surface plasmon-polaritons in planar structures incorporating dipolar gain media such as organic dye molecules, rare-earth ions, and quantum dots. This model takes into account the inhomogeneous gain distribution formed near the metal surface due to a non-uniform excitation of dipoles and due to a position-dependent excited-state dipole lifetime that results from near-field interactions between the excited dipoles and the metal. Also, a theoretical model to describe the amplified spontaneous emission of surface plasmon-polaritons supported by planar metallic structures is developed. This model takes into account the different energy decay channels into which an exited dipole located in the vicinity of the metal can relax. The validity of this model is confirmed through experimentation. On the experimental side, the objective is approached by providing a direct experimental demonstration of complete loss compensation in a plasmonic waveguide. The experiments are conducted using the long-range surface plasmon-polariton supported by a symmetric thin gold waveguide incorporating optically pumped organic dye molecules in solution as the gain medium. Also, an experimental study of spontaneous emission in a long-range surface plasmon-polariton amplifier is presented. It is shown that this amplifier benefits from a low spontaneous emission into the amplified mode, which leads to an optical amplifier with low noise characteristics. The experimental setup and techniques are explained in detail.

Les métamatériaux électromagnétiques sont des composites artificiels, constitués de résonateurs etayant des propriétés optiques n'existant pas à l'état naturel. Cette thèse est consacrée à lafabrication et caractérisation de tels matériaux. Pour cela des particules métalliques coeur-écorce(d'or ou d'argent enrobées de silice) sont assemblées par la technique de Langmuir-Blodgett afin deformer des réseaux denses en monocouche et en multicouches. Ces nanoparticules jouent le rôle derésonateurs grâce à la présence de la résonance plasmon et l'écorce de silice permet de contrôler ladistance entre particules. Nous avons ainsi réalisé des matériaux dont la distance entre lesrésonateurs et la fraction métallique varient. Les analyses spectro-photométriques des films obtenus,notamment en réflexion normale, nous ont permis d'extraire les propriétés optiques de nosmatériaux. Pour cela nous avons proposé un modèle phénoménologique dans lequel nousdéfinissons la permittivité de la couche effective comme étant celle de la matrice à laquelle s'ajouteun oscillateur de Lorentz décrivant la présence d'une résonance plasmon. Nous avons pu ainsimontrer expérimentalement qu'il était possible d'obtenir des métamatériaux d'indice de réfractioninférieur à 1 quand la fraction de métal dans le matériau est suffisamment importante.