La bio-détection de molécules reposant sur le phénomène de résonnance plasmon permet de détecter des espèces en utilisant les propriétés optiques de films métalliques. L’utilisation de ce type de capteurs nécessite néanmoins l’augmentation de leurs performances afin de détecter des concentrations faibles d’analyte dans des milieux complexes. L’assemblage de nanoparticules d’oxyde de fer sur des substrats d’or, en utilisant des groupements complémentaires spécifiques via la méthode de chimie « click », permet de contrôler leur distribution spatiale à la surface du substrat. Les propriétés magnétiques portées par les nanoparticules sont ainsi étudiées en fonction de leurs distances inter-particules ainsi que de leurs tailles. Par ailleurs, le plasmon de surface du substrat étant directement influencé par l’assemblage des nanoparticules, il sera possible de contrôler la sensibilité du capteur pour étudier la détection de différentes biomolécules impliquées dans des processus biologiques. La présence des nanoparticules augmente les propriétés optiques intrinsèques de la surface du substrat et la géométrie de l’assemblage permet d’augmenter la quantité de biomolécules détectées. / Biomolecular detection based on the surface plasmon resonance phenomenon allow detecting species by using the optics properties of metallic thin films. This kind of biosensors require the increase of their performances in order to detect low concentration analyte in complex medium. The assembly of iron oxide nanoparticles on gold substrates by using specific complementary groups via the “click” chemistry technique allows controlling their spatial distribution on the substrate surface. The magnetic properties carried by the nanoparticles are studied as function of their inter-particle distances and their sizes. Moreover, the surface plasmon of the substrate is directly influenced by the nanoparticle assembly and the control of the sensor sensitivity will be possible in order to study the detection of different biomolecules implies in biological processes. The presence of nanoparticles increases the intrinsic optical properties at the substrate surface and the geometry of the assembly allow increasing the number of biomolecules detected.

Dans cette thèse, nous associons mesures expérimentales et modélisation des données pour étudier l'émission spontanée d'émetteurs fluorescents en environnement nano-structuré. Le mémoire est organisé en deux parties.Dans la première partie, nous étudions le transfert d'énergie entre émetteurs fluorescents en environnement plasmonique et sur des distances micrométriques. Pour commencer, nous caractérisons le transfert d'énergie entre deux ensembles d'émetteurs situés en champ proche d'une surface d'argent. Nous déterminons ainsi la dépendance en distance du taux de transfert d'énergie sur des distances micrométriques. Nous couplons ensuite une boite quantique et une bille fluorescente à un nano-fil d'argent et nous étudions le transfert d’énergie entre ces deux émetteurs, distants de plusieurs micromètres. Nous démontrons notamment le clignotement corrélé de ces deux émetteurs grâce à l'étude de la fonction de corrélation de leur intensité de fluorescence.Dans la seconde partie, nous sondons les variations spatiales de densité locale d'états électromagnétiques induites par des environnements nano-structurés grâce à différentes techniques de microscopie à super-résolution. A l'aide d'un microscope à balayage, nous réalisons tout d’abord une étude en trois dimensions de l’interaction de champ proche entre une bille fluorescente et différentes antennes en silicium. Nous introduisons ensuite une technique stochastique permettant de déterminer expérimentalement la position et le taux d'amortissement de molécules uniques photo-activées, avec une précision de localisation de l'ordre de 10 nm. Enfin, nous utilisons l'information de Fisher afin d'estimer les bornes inférieures de l'erreur type des estimations de positions et de taux d'amortissement réalisées dans le cadre de mesures sur molécules uniques. / In this thesis, we perform experimental measurements and data modelling to investigate spontaneous emission of fluorescent emitters in nanostructured environments. The manuscript is organised into two main parts.In the first part, we study micrometre-range energy transfer between fluorescent emitters in plasmonic environments. First of all, we characterise plasmon-mediated energy transfer between ensembles of fluorescent emitters located in the near field of a silver film. We thus determine the distance dependence of the energy transfer rate over micrometre distances. We then couple a single quantum dot and a fluorescent nanobead to a silver nanowire and we study evidences of the energy transfer between the two emitters, separated by several micrometres. We notably demonstrate a correlated blinking of the two emitters through the study of the correlation function of their fluorescence intensity.In the second part, we probe sub-wavelength spatial variations of the local density of electromagnetic states induced by nanostructured environments by means of different super-resolution microscopy techniques. To start with, we perform a three-dimensional study of the near-field interaction between a fluorescent nanobead and different silicon nanoantennas using a scanning-probe microscope. We then introduce a stochastic technique to experimentally determine the position and the fluorescence decay rate of single photo-activated molecules, with a localisation precision of the order of 10 nm. Finally, we use the Fisher information to estimate lower bounds on the standard errors on position and decay rate estimates performed in the context of single-molecule microscopy.

Cette thèse présente la conception et la mise en œuvre d'un imageur CMOS pour être utilisé dans biocapteurs intégrés basés sur Résonance Plasmonique de Surface (SPR). Tout d'abord, les conditions optimales pour la résonance plasmon dans une interface compatible CMOS / post-CMOS sont obtenus par modélisation avec COMSOL. Deuxièmement, un imageur CMOS de Colonne Actif (CMOS-ACS) du 32x32 pixels est mis en œuvre sur une technologie CMOS 0,35 um. Dans une interface d'or-eau avec une excitation de prisme, on constate que pour les prismes avec des indices de réfraction de 1,55 et 1,46, le couplage optimal avec le plasmon est obtenu pour des films d'or d'une épaisseur de 50 et 45 nm, respectivement. Dans ces conditions, environ 99,19% et 99,99% de l'énergie de la lumière incidente est transférée à le surface plasmon pour les deux prismes respectivement, à condition que la lumière incidente, avec une longueur d'onde de 633 nm, arrive avec un angle d'incidence de 68,45° et 79,05° respectivement. Il est également obtenu qu'un changement de RIU 10-4 de l'indice de réfraction du milieu diélectrique, produit un changement de 0,01 ° dans l'angle de résonance de plasmons qui, dans un schéma de modulation d'intensité de lumière produit une variation de 0,08% dans la lumière réfléchie au photodétecteur. En ce qui concerne le imageur CMOS, une photodiode n-well/p-substrate est choisi comme l'élément de photodétection, en raison de sa faible capacité de jonction, ce qui conduit à un rendement élevé et le gain de conversion élevé comparativement à une photodiode n-diff/p-substrate. Des simulations sur ordinateur avec Cadence et Silvaco produit une capacité de jonction de 31 FF et 135 fF respectivement. Le pixel de l'imageur est basé sur une configuration à trois transistors (3T) et présente un facteur de remplissage de 61%. Le circuit de lecture utilise une technique de capteur de colonne actif (ACS) pour réduire le bruit à motif fixe (Fixed Pattern Noise ou FPN en anglais) liée au le Capteur à Pixels Actif (APS) traditionnelle. En outre, Non-Corrélés Echantillonnage Double (Non-Correlated Double Sampling ou NCDS en anglais) et Delta double échantillonnage (DDS) sont utilisés comme techniques de réduction du bruit. Un montage optique expérimental est utilisé pour caractériser les performances de l'imageur, et nous avons obtenu un gain en conversion de 7,3 uV/e-, une capacité de jonction de la photodiode de 22 fF, un bruit de lecture de 324,5 uV, ce qui équivaut à 45 électrons, et une gamme dynamique de 50,5 dB. Les avantages de l'ACS et NCDS-DDS sont observées dans le niveau faible de FPN du pixel et de la colonne, avec une valeur de 0,09% et 0,06% respectivement. Le travail présenté dans cette thèse est une première étape vers l'objectif de développer une plateforme entièrement intégrée SPR pour biocapteurs, incorporant source de lumière, l'interface SPR, canal microfluidique, les éléments d'optique et imageur CMOS. / This dissertation presents the design and implementation of a CMOS imager for use in integrated biosensors based on Surface Plasmon Resonance. First, the optimal conditions for plasmon resonance in a CMOS/Post-CMOS compatible interface are obtained by COMSOL modelling. Second, a 32x32-pixel CMOS-Active Column Sensor (CMOS-ACS) is implemented on 0.35 um CMOS technology. In a gold-water interface with prism excitation, it is found that for prisms showing refractive indexes of 1.55 and 1.46, optimal plasmon coupling is obtained for gold films with thicknesses of 50 and 45 nm respectively. Under these conditions, approximately 99.19% and 99.99% of the incident light's energy is transferred to the surface plasmon for both prism respectively, provided that the incident light, with a wavelength of 633 nm, arrives with incidence angles of 68.45° and 79.05° respectively. It is also obtained that a change of 10-4 RIU in the refractive index of the dielectric medium, produces a change of 0.01° in the plasmon resonance angle, which under a light intensity modulation scheme produces a change of 0.08% in the reflected light's energy reaching the photodetector. Concerning the CMOS imager, a n-well/p-substrate photodiode is selected as the photosensing element, due to its low junction capacitance, which results in high efficiency and high conversion gain compared to the n-diff/p-substrate photodiode. Computer simulations with Cadence and Silvaco produced a junction capacitance of 31 fF and 135 fF respectively. The imager's pixel is based on a three-transistor (3T) configuration and shows a fill factor of 61%. The readout circuitry employs an Active Column Sensor (ACS) technique to reduce the Fixed Pattern Noise (FPN) associated with traditional Active Pixel Sensors (APS). Additionally, Non-Correlated Double Sampling (NCDS) and Delta Double Sampling (DDS) are used as noise reduction techniques. An experimental optical setup is used to characterize the performance of the imager, obtaining a conversion gain of 7.3 uV/e-, a photodiode junction capacitance of 21.9 fF, a read noise of 324.5 uV, equivalent to ~45 e- and a dynamic range of 50.5 dB. The benefits of ACS and NCDS-DDS are observed in the low pixel and column FPN of 0.09% and 0.06% respectively. The work presented in this thesis is a first step towards the goal of developing a fully integrated SPR-biosensing platform incorporating light source, SPR interface, microfluidic channel, optical elements and CMOS imager.

Thymidylate kinase (TMK) is a key enzyme for DNA synthesis. It occurs at the junction of the de novo and salvage pathways for the synthesis of deoxythymidine triphosphate (dTTP). Its inhibition affects cell viability, thereby making it an important target for the development of anticancer, antibacterial and antiparasitic drugs. This thesis describes the analyses of the sequence, structure and dynamics of thymidylate kinase to obtain insights into its function. Two thermophilic variants of the enzyme were chosen for our studies. The studies provide valuable insights about the active site residues and the mechanism of catalysis, which have implications in protein engineering and design of specific inhibitors. Following is a chapter-wise description of the overall layout of the thesis. Chapter 1 | Introduction: This chapter provides a brief survey of the literature on TMKs and the scope of the work presented in the thesis. TMK belongs to the nucleoside monophosphate kinase (NMPK) family of enzymes, which includes adenylate kinase (AMK), guanylate kinase (GMK), uridylate kinase (UMK) and cytidylate kinase (CMK). The NMPK family of enzymes is associated with the reversible transfer of the terminal phosphoryl group from a nucleoside triphosphate (NTP) (usually adenosine triphosphate, i.e., ATP) to a nucleoside monophosphate (NMP). The identity of the NMP substrate varies among different enzymes. NMPKs share a common Rossmann fold and are comprised of a conserved P-loop, Lid region, CORE and NMP domains. The enzymes in the NMPK family also contain structurally similar active site architecture. Besides the three signature motifs, there are other conserved residues at the active site of TMK which are involved in interactions with the substrates ATP and dTMP. Despite the overall similarity, TMKs exhibit significant variations in sequence, residue conformation, substrate specificity and oligomerization mode. However, the residues responsible for these differences have not been studied. This thesis describes a comprehensive analysis of the sequence space of TMKs to detect the residues involved in such diversity. Subsequently, TMKs from a thermophilic archaeon (Sulfolobus tokodaii) and a hyperthermophilic bacterium (Aquifex aeolicus) were chosen for biochemical characterization and structural studies. Of these, the Sulfolobus tokodaii TMK (StTMK) has low sequence identity to the other TMKs of known three dimensional (3D) structures. Crystal structure analyses depicted the presence of some novel structural features and provided insights into the role of a conserved Arginine residue in function, which was verified through computational studies and mutagenesis experiments. Finally, the study on Aquifex aeolicus TMK resulted in multiple crystal structures of the apo form and different holo forms. These helped us to understand the mechanistic details of TMK-mediated catalysis, namely, the order of substrate binding and the reaction mechanism for phosphate transfer. Chapter 2 | Materials and Methods: This chapter provides a brief description of the procedures used to carry out the thesis work. The protein samples were purified to a high degree using column chromatography, and the purity was assessed using SDS-PAGE (sodium dodecyl sulfate polyacrylamide gel electrophoresis) analysis. Circular dichroism (CD) spectroscopy was employed to assess if the purified protein was well-folded. The pure and properly folded protein samples were used in further experiments. Differential scanning fluorimetry (DSF) was performed to determine the melting temperature of the thermophilic protein. MicroScale Thermophoresis (MST) and Surface Plasmon Resonance (SPR) were carried out to detect protein-substrate interactions. The protein samples were crystallized using the hanging drop vapour diffusion and microbatch under-oil techniques using commercially available crystallization screens, and the conditions which gave crystals were further optimized. Diffraction data, collected at either the home source or the synchrotron, were processed and scaled. Subsequently, phase information was obtained using the molecular replacement (MR) calculations. The MR solution was refined till convergence and its geometry was validated using different softwares. Finally, molecular dynamics (MD) simulations were performed to study the functionally important motions in the protein. Chapter 3 Insights into substrate specificity and oligomerization mode of Thymidylate Kinases from sequence evolution and conformational dynamics: Thymidylate kinase homologs exhibit significant variations in sequence, residue conformation, substrate specificity and oligomerization mode. However, the influence of sequence evolution and conformational dynamics on its quaternary structure and function has not been studied before. Based on extensive sequence and structure analyses, our study detected several non-conserved residues which are linked by co-evolution and are implicated in the observed variations in flexibility, oligomeric assembly and substrate specificity among the homologs. These lead to differences in the pattern of interactions at the active site in TMKs of different specificity. The method was further tested on thymidylate kinase from Sulfolobus tokodaii (StTMK) which has substantial differences in sequence and structure compared to other TMKs. Our sequence analyses pointed to a more flexible dTMP-binding site in StTMK compared to the other homologs, which was also indicated in MD simulations on the protein 3D structure. Binding assays proved that the protein can accommodate both purine and pyrimidine nucleotides at the dTMP binding site with comparable affinity. Additionally, the residues responsible for the narrow specificity of Brugia malayi TMK, whose three dimensional structure is unavailable, were detected. Our study provides a residue-level understanding of the differences observed among TMK homologs in previous experiments. It also illustrates the correlation among sequence evolution, conformational dynamics, oligomerization mode and substrate recognition in thymidylate kinases and detects co-evolving residues that affect binding, which should be taken into account while designing novel inhibitors. Chapter 4 | Biochemical and Structural characterization of a thermophilic variant of thymidylate kinase: This chapter reports the biochemical characterization and crystal structure determination of thymidylate kinase from the hyperthermophilic organism Sulfolobus tokodaii (StTMK) in its apo and ADP-bound forms. Our study describes the first three-dimensional structure of an archaeal TMK. The different structures had resolution ranging between 1.60 Å and 2.40 Å. StTMK is a thermostable enzyme with a melting temperature of 85.3 °C, as observed from thermal unfolding studies. The protein exists as a dimer in solution. A coupled enzyme assay, performed using thermo-stable lactate dehydrogenase (TtLdh) and pyruvate kinase (TtPk) from Thermus thermophilus, showed that StTMK has optimum activity at 80 °C. Despite the overall similarity to homologous TMKs, StTMK structures revealed several residue substitutions at the active site. However, enzyme assays demonstrated specificity to its natural substrates ATP and dTMP. A novel insertion (9 residues long) is observed in the C-terminal stretch of the Lid region. However, it is relatively rigid, which may be attributed to the presence of two proline residues and a hydrogen bond with an arginine residue in the α4/α5 loop. The C-terminus of the α2 helix points away from the Lid region in StTMK to avoid steric clashes with the Lid insertion. The main chain dihedral angles of the conserved Arg in the DRX motif are in the disallowed region of the Ramachandran plot in all holo TMK structures, wherein it forms several conserved hydrogen bonds with residues in the P-loop, α4 helix and α7 helix, as well as with the phosphate groups of both the substrates. A similar feature is observed in some of the StTMK structures. However, torsion angles in the allowed region of the Ramachandran plot are observed in one chain each in two of the apo structures. Further, conformational rearrangements of this Arg and its neighboring residues at the binding site of the second substrate are observed. The functional implication of this variation is described in the next chapter (chapter 5). Chapter 5 | Role of a conserved active site Arginine residue in Thymidylate kinase: Analysis of the structures of StTMK revealed multiple conformational states of Arg93 which is located at the reaction centre and is a part of the highly conserved DRX motif. Conformational heterogeneity of Arg can also be observed in some structures of Staphylococcus aureus and human TMK. However, the functional implication of this feature has not been probed before. The rearrangements of Arg93 are accompanied by related changes in the conformations of its neighbouring residues at the active site. This leads to three distinct conformational states in the dTMP-binding site, namely ‘Arg in’, ‘Arg intermediate’ and ‘Arg out’. Only the ‘Arg in’ state was found to be suitable for the proper positioning of the α-phosphate group of dTMP at the active site. This is hindered in the ‘Arg out’ and ‘Arg intermediate’ states. MD simulations showed that the torsion angles of the DRX Arg can sample between allowed and disallowed values in the apo-protein, with a preference for the catalytically suitable disallowed conformation in the holo-protein. Computational alanine scanning and MM/PBSA binding energy calculation further revealed the importance of Arg93 side chain in substrate binding. Subsequent site directed mutagenesis at this position to an Ala resulted in the loss of activity. Our work provides the first experimental evidence for the functional importance of Arg93 and gives insight into its regulatory role in the catalytically competent placement of dTMP. Our study also has implications for the development of potent inhibitors to lock the enzyme in the catalytically non-productive state. Chapter 6 | Characterizing active site dynamics from structural studies on the Intermediates along the reaction coordinate of a hyperthermophilic Thymidylate Kinase: TMK belongs to the family of nucleoside monophosphate kinases (NMPKs), several of which undergo structure-encoded conformational changes to perform their function. However, the absence of three dimensional structures for all the different reaction intermediates of a single TMK homolog hinders a clear understanding of its functional mechanism. We herein report the different conformational states along the reaction coordinate of a hyperthermophilic TMK from Aquifex aeolicus, determined via X-ray diffraction and further validated through normal mode studies. The analyses implicate an arginine residue in the Lid region in catalysis, which was confirmed through site-directed mutagenesis and subsequent enzyme assays on the wild type protein and mutants. Further, the enzyme was found to exhibit broad specificity towards phosphate group acceptor nucleotides. Our comprehensive analyses of the conformational landscape of TMK, together with associated biochemical experiments, provide insights into the mechanistic details of TMK-driven catalysis, for example, the order of substrate binding and the reaction mechanism for phosphate transfer. Such a study has utility in the design of potent inhibitors for these enzymes. Finally, the implications of the work described in this thesis and its future applications have been discussed in the section titled ‘Future prospects’. The work described in chapters 3 – 6 have been published in peer reviewed journals. Additionally, the author was involved in several collaborative projects which also resulted in publications (reprints attached in appendix).

abstract: Gold-silver alloy nanoparticles (NPs) capped with adenosine 5'-triphosphate were synthesized by borohydride reduction of dilute aqueous metal precursors. High-resolution transmission electron microscopy showed the as-synthesized particles to be spherical with average diameters ~4 nm. Optical properties were measured by UV-Visible spectroscopy (UV-Vis), and the formation of alloy NPs was verified across all gold:silver ratios by a linear shift in the plasmon band maxima against alloy composition. The molar absorptivities of the NPs decreased non-linearly with increasing gold content from 2.0 x 108 M-1 cm-1 (fÉmax = 404 nm) for pure silver to 4.1 x 107 M-1 cm-1 (fÉmax = 511 nm) for pure gold. The NPs were immobilized onto transparent indium-tin oxide composite electrodes using layer-by-layer (LbL) deposition with poly(diallyldimethylammonium) acting as a cationic binder. The UV-Vis absorbance of the LbL film was used to calculate the surface coverage of alloy NPs on the electrode. Typical preparations had average NP surface coverages of 2.8 x 10-13 mol NPs/cm2 (~5% of cubic closest packing) with saturated films reaching ~20% of ccp for single-layer preparations (1.0 ~ 10-12 mol NPs/cm2). X-ray photoelectron spectroscopy confirmed the presence of alloy NPs in the LbL film and showed silver enrichment of the NP surfaces by ~9%. Irreversible oxidative dissolution (dealloying) of the less noble silver atoms from the NPs on LbL electrodes was performed by cyclic voltammetry (CV) in sulfuric acid. Alloy NPs with higher gold content required larger overpotentials for silver dealloying. Dealloying of the more-noble gold atoms from the alloy NPs was also achieved by CV in sodium chloride. The silver was oxidized first to cohesive silver chloride, and then gold dealloyed to soluble HAuCl4- at higher potentials. Silver oxidation was inhibited during the first oxidative scan, but subsequent cycles showed typical, reversible silver-to-silver chloride voltammetry. The potentials for both silver oxidation and gold dealloying also shifted to more oxidizing potentials with increasing gold content, and both processes converged for alloy NPs with >60% gold content. Charge-mediated electrochemistry of silver NPs immobilized in LbL films, using Fc(meOH) as the charge carrier, showed that 67% of the NPs were electrochemically inactive. / Dissertation/Thesis / M.S. Chemistry 2014

Submitted by Irene Nascimento (irene.kessia@ufpe.br) on 2017-01-30T18:17:26Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) DISSERTACAO_LEO_DEFESA - FINAL - CATALOGADA PDF.pdf: 4585329 bytes, checksum: 4b70c80127866cd2da97a6217bb6a34f (MD5) / Made available in DSpace on 2017-01-30T18:17:27Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) DISSERTACAO_LEO_DEFESA - FINAL - CATALOGADA PDF.pdf: 4585329 bytes, checksum: 4b70c80127866cd2da97a6217bb6a34f (MD5) Previous issue date: 2016-08-16 / CNPQ / Um dos principais desafios no projeto de sensores baseados em Ressonância de Plasmons de Superfície — RPS — é maximizar sua sensibilidade. Neste trabalho é proposto o uso de dois algoritmos heurísticos, Monte Carlo e Enxame de Partículas, para otimização de sensores baseados em RPS em interfaces planares, i.e, nas configurações de Kretschmann e de Otto, sem o auxílio da aproximação lorentziana para a curva de ressonância. Devido à natureza probabilística dos algoritmos, consegue-se obter um método simples e robusto para atingir essa otimização. É feita uma comparação quanto à eficiência computacional dos algoritmos em relação ao método tradicional de otimização, ficando demonstrado que o método de Enxame de Partículas é o mais eficiente em relação às outras técnicas. Com o emprego desse método, a dependência espectral dos parâmetros ótimos é obtida para sensores utilizando vários metais nas configurações de Kretschmann e de Otto, tanto para aplicações em meios gasosos quanto em meios aquosos. Um aplicativo foi desenvolvido e sua funcionalidade demonstrada, que pode ser executado diretamente via web, com base na metodologia proposta, para otimização de sensores RPS em interfaces planares. / One of the main challenges in the design of surface plasmon resonance – SPR – sensor systems is to maximize their sensitivity. In this work one proposes the use of two heuristic algorithms, Monte Carlo and Particle Swarm, for optimization of SPR sensors in planar interfaces, i.e, in the Kretschmann and Otto configurations, without use of the Lorentzian approximation to the resonance curve. Because of the probabilistic nature of the algorithms, one manages to obtain a simple and robust method to achieve optimization. A comparison is made on the computational efficiency of the algorithm relative to the traditional method of optimization, showing that the particle swarm optimization method is more efficient compared to other techniques. By employing this method, the spectral dependence of optimum parameters is obtained for sensors using a wide range of metal films in the Kretschmann and Otto configurations, both for applications in gaseous an in aqueous media. An app was developed and its functionality can be demonstrated, by direct execution via web, based on the proposed methodology for optimization of SPR sensors on planar interfaces.

O incessante aumento do volume de informações produzido por uma sociedade cada vez mais informatizada tem elevado drasticamente os requisitos quanto ao desenvolvimento de dispositivos capazes de suportar velocidades de operação cada vez mais elevadas em tamanhos cada vez mais reduzidos. No entanto, a contínua redução do tamanho desses dispositivos, celebrado através da lei de Moore, também produz um indesejável aumento na produção de calor durante a operação dos mesmos, comprometendo seu desempenho global. Uma alternativa promissora para aliviar, ou mesmo superar, estas limitações é oferecida pelos dispositivos ópticos integrados. No entanto, todo esse avanço esbarrava no fato de que as dimensões de tais dispositivos estavam restringidas fundamentalmente ao que é largamente conhecido como limite de difração (LD). Uma maneira de contornar essa limitação é obtida através da utilização de Plásmon Poláritons de Superfície, ou SPPs, que, de maneira simplificada, são ondas que se propagam ao longo da superfície de um condutor depositado sobre um dielétrico. Estas são essencialmente ondas de luz que são localizadas na superfície por causa de sua interação com os elétrons livres do condutor. Nesta interação, os elétrons livres respondem coletivamente oscilando em ressonância com a onda de luz. No presente trabalho, o fenômeno de geração de SPPs é estudado teoricamente e aplicado na modelagem de diversas estruturas de interesse científico e tecnológico, tais como acopladores direcionais e ressoadores. O objetivo principal é a obtenção de estruturas capazes de proporcionar propagação de SPPs por longas distâncias, permitindo, assim, estender ainda mais o leque de possíveis aplicações. As estruturas são investigadas prioritariamente no COMSOL Multiphysics, um aplicativo baseado em elementos finitos que permite solução vetorial de problemas eletromagnéticos. Os resultados obtidos até o momento permitem afirmar que o conceito de SPP de longa distância (long range SPP, LRSPP) podem ser aplicados com sucesso a estruturas geometricamente complexas como os ressoadores em anel e acopladores direcionais. / The continuous growth of knowledge produced by a society with increasing access to information technologies has demanded the development of communication devices capable of supporting high processing speeds at more and more reduced sizes. Nevertheless, the continuous reduction of the size of these devices, celebrated by the Moore\'s law, has also produced an undesirable increase of heat produced during the operation of the device itself, compromising its overall performance. A promising alternative to alleviate, or even overcome, these limitations has been offered by photonic integrated circuits. However, all the advance of photonic devices was restricted to what is known as diffraction limit. A fascinating way of circumventing this limit is now available to the scientific community, and consists in the generation of Surface Plasmon Polariton (SPP) waves. In a simplified manner, SPP waves are waves that propagate along a metal/dielectric interface. These waves are essentially localized at the metal/dielectric interface because of the interaction of light with free electrons of the metal. In this interaction, the free electrons respond collectively and oscillate resonantly with the incident light. In the present work, the phenomenon of SPP generation is theoretically investigated and applied to the modeling of several structures, such as directional couplers and resonators. The primary goal of this work is to design structures capable propagating SPP waves for long distances, known as long range SPP (LRSPP). The structures are investigated mostly with COMSOL Multiphysics, a finite elements based software that allows for the vectorial solution of electromagnetic problems. The results obtained so far are extremely encouraging, and prove that the LRSPP concept can be successfully applied to geometrically complex structures, such as couplers and ring resonators.

Afin de développer des capteurs ultrasensibles des substrats fiables pour la diffusion Raman exaltée de surface (SERS) ont été fabriqués. Les deux meilleurs candidats de matériaux constituant les nanoparticules pour des substrats SERS sont l’argent et l’or. L’argent présente un meilleur facteur d’exaltation de l'intensité Raman et l’or est stable dans les milieux biologiques. C’est pourquoi la combinaison de ces deux métaux dans des nanostructures bimétalliques semble être une approche prometteuse qui combine les propriétés de surface de l’or et d’exaltation de l’argent. Le recuit thermique des couches métalliques minces est utilisé comme une technique simple et peu coûteuse. Cette dernière permet d’élaborer des substrats homogènes et reproductibles de nanoparticules bimétalliques or-argent ayant un facteur d’exaltation importante. Ces nanoparticules gardent leurs propriétés d’exaltation même après une année de fabrication. En jouant sur la composition de nanoparticules bimétalliques il est possible d’avoir une résonance de plasmons de surface localisés (LSPR) sur tout le spectre visible. Ces substrats sont caractérisés par une exaltation SERS supérieure lorsque la résonance plasmon est plus proche de la longueur d'onde d'excitation Raman. En outre, les nanoparticules bimétalliques de différentes tailles, compositions ont été réalisés par lithographie électronique. L’étude systématique de leurs propriétés plasmoniques et de leur exaltation SERS a révélé une conservation du lien entre résonance plasmon et signal SERS / Driven by the interest in finding ultrasensitive sensors devices, reliable surface enhanced Raman scattering (SERS) based substrates are fabricated. Silver and gold nanoparticles are two of the best candidates for SERS substrates where Ag nanoparticles exhibit large enhancing ability in Raman intensity while Au nanostructures are stable in biological systems. Hence, combining the two metals in bimetallic nanostructures appeared to be a promising approach in order to sum the merits of Au surface properties and Ag enhancing ability. Thermal annealing of thin metallic films is used as a simple and relatively inexpensive technique to elaborate homogenous and reproducible Ag/Au bimetallic nanoparticles SERS substrates with high enhancing ability. The fabricated nanoparticles proved their enhancing stability even after one year of fabrication. Manipulating the composition of Ag/Au bimetallic NPs resulted in tuning the Localized Surface Plasmon Resonance (LSPR) over the whole visible spectrum, where the substrates are characterized with higher SERS enhancement when they exhibit LSPR closer to the Raman excitation wavelength. Additionally, bimetallic nanoparticles patterns with different size, composition and lattice constants have been conducted by electron beam lithography. The systematic study of their interesting plasmonic and SERS enhancing properties revealed maintenance in the LSPR-SERS relation by changing the nanoparticle size

Les avancées récentes de la nanofabrication ont permis de faire émerger un nouveau champ de recherche, celui des nanocapteurs. En particulier, le nanocapteur plasmonique dont le principe utilise l’effet SERS (Diffusion Raman Exaltée de Surface) commence à s’imposer. En effet, ce capteur permet d’amplifier la signature d’une molécule jusqu’à un facteur de 1012 et fournit une véritable empreinte digitale de chaque molécule. La sensibilité du capteur dépend des propriétés optiques des Nanoparticules Métalliques (NPMs) qui sont liées aux propriétés physiques et structurales de ces dernières. Ainsi, la maîtrise de la fabrication de NPMs est un réel défit pour des multiples applications nanotechnologiques. Dans ce contexte, nous avons développé une approche originale de fabrication de NPMs organisées par auto-assemblage de polymère. Il s’agit d’introduire de manière contrôlée des interactions physiques qui se manifestent lors de la fabrication par une nano-séparation de phase au sein du matériau. Ceci se traduit par un nanstructuration du polymère et une auto-organisation très spécifique du précurseur métallique qui se transforme spontanément en NPMs. Les investigations expérimentales en considérant les différents facteurs physico-chimiques impliqués, nous ont permis d’identifier les paramètres clés de cette structuration et de hiérarchiser leur influence sur les dimensions structurales et la réponse optique des NPMs. Finalement, la capacité du nanocapteur à détecter de faibles traces (<10-13 M) de polluants organiques a été démontrée / The recent advances in nanofabrication techniques have allowed for the emergence of novel sensing approaches. Amongst these various approaches, Surface Enhanced Raman Spectroscopy (SERS) via the use of plasmonic substrates has received wide-spread attention due to its many interesting proper-ties. In fact, plasmonic substrates enhance the Ra-man signal up to 12 orders of magnitude, paving the path for single molecule detection. Nevertheless, the sensitivity of this technique is strongly affected by the physical and structural properties of the metallic nanoparticles (MNPs). Thus, the mastering of the MNPs fabrication is a major challenge for various nanotechnological applications.In this context, we have developed a novel approach for the fabrication of organized NMPs through poly-mer self-assembly. The fabrication technique con-sists on controlling the physical interactions which occur during the fabrication through a nanophase separation in the polymer solution. This results in a nanostructuring of the polymer and a strong self-organization of the metallic precursor which is rapidly reduced into the MNPs. Experimental investigations of the different physical and chemical processes in play allow for a better understanding of the various keystone parameters of the nanostructuring as well as for determining their influences on the dimensions and optical response of MNPs. Finally, the fabricated plasmonic substrate demonstrated SERS limits of detection down to 10-13 M

La réponse optique de nano-objets métalliques et semi-conducteurs a été étudiée par spectroscopie par modulation spatiale (SMS), une technique permettant de détecter des nano-objets individuels et d'en mesurer quantitativement la section efficace d'extinction. Dans le cadre de ce travail, nous avons systématiquement corrélé ces mesures optiques à une caractérisation bi- voire tridimensionnelle de leur morphologie, permettant une comparaison précise des mesures avec des simulations numériques. Le premier volet de cette thèse décrit une étude détaillée de l'effet de la déposition de nano-objets métalliques de forme allongée (nanobâtonnets et nanobipyramides) sur un substrat absorbant. Nos expériences montrent qu'elle conduit à un élargissement de la résonance plasmon de surface, dont l'ampleur dépend fortement de la forme et de l'encapsulation des nano objets. En combinant la SMS avec une approche pompe-sonde, nous avons pu mesurer la réponse ultrarapide de nano-bipyramides d'or individuelles, qui contient une contribution de plusieurs de leurs modes de vibration, permettant d'accéder à leur fréquence et taux d'amortissement, en s’attachant en particulier à l'effet d'une encapsulation diélectrique des bipyramides. Au cours de cette thèse, nous avons étendu l'application de la SMS à des nano-objets très allongés avec une dimension micrométrique (nanofils et nanopointes), dans le but notamment d'étudier leur réponse optique, leur interaction avec une nanoparticule d’or et d’obtenir des informations sur leur profil d'absorption, une information essentielle pour l'interprétation d'expériences d'émission électronique (effet de champ) ou ionique (tomographie de sonde atomique) / The optical response of metallic and semi-conductor nano-objects has been studied by spatial modulation spectroscopy (SMS), a technique allowing to detect single nano-objects and to quantitatively measure their extinction cross-sections. During my thesis, we have systematically correlated these optical measurements with the 2D or 3D characterization of their morphology, allowing a precise comparison of the measurements with numerical simulations. The first part of my PhD thesis describes a detailed study of the effect of the deposition of elongated nano-objects on an absorbing substrate. Our experiments show a spectral broadening of the surface plasmon resonance, whose extent highly depends on the shape and the encapsulation of the nano-objects. By combining SMS with a pump-probe approach, we were able to measure the ultrafast response of single gold nano-bipyramids. This response contains a contribution from several vibration modes, allowing extraction of their frequencies and damping times. In particular, we have addressed the effect of a dielectric encapsulation of bipyramids on their vibrational quality factors. During this thesis, we extended the use of SMS to very elongated nano-objects with a micrometric dimension (nanowires and nanotips), with the goal of studying their optical response, their interaction with a gold nanosphere and obtaining information on their absorption profile, as required to interpret electronic (field effect) or ionic (atom-probe tomography) emission experiments