Nisin, an amphiphilic, antimicrobial peptide, has been shown to integrate into the hydrophobic inner region of poly(ethylene oxide) (PEO) brush layers; however, the presence of integrated nisin may compromise the protein repulsive character of the PEO layer. In particular, the introduction of fibrinogen to nisin-loaded brush layers has been observed to cause changes consistent with partial elution of nisin and/or location of fibrinogen at the interface. Questions surrounding the possibility of fibrinogen adsorption warrant further investigation, as the location of procoagulant proteins at a peptide-loaded PEO layer would significantly reduce the viability of a medical device coating based on such an approach. In this work, the preferential location of fibrinogen at PEO brush layers was investigated by: detection of FITC-labeled fibrinogen after sequential introduction of nisin and labeled fibrinogen; measurement of changes in the zeta potential of PEO coated and uncoated surfaces following nisin, fibrinogen, and/or buffer challenges; and evaluation of adsorption and elution kinetics in label-free, sequential adsorption experiments using optical waveguide lightmode spectroscopy (OWLS). PEO layers were constructed through radiolytic grafting of Pluronic�� F108 or F68 onto silanized silica surfaces producing long-chain or short-chain PEO layers, respectively. Adsorption results indicated that sequential introduction of nisin and fibrinogen to PEO brush layers, based on F108, does not result in fibrinogen adsorption beyond that expected for a nisin-free PEO layer. No evidence of nisin entrapment in fibrinogen-repellent F68 layers was recorded. Low-level fibrinogen adsorption observed at F68 layers following the introduction of nisin was determined to be a result of nisin adsorption at (uncoated) defect regions on the surface. In conclusion, retention of PEO layer capacity for protein repulsion after nisin entrapment is owing to a steric repulsive barrier provided by PEO segments extending beyond the level of entrapped nisin. It was then hypothesized that the immobilized, pendant PEO chains will inhibit exchange of entrapped nisin by competing proteins, and therefore prolong nisin activity retention. In order to evaluate nisin function following its entrapment, the antimicrobial activity of nisin-loaded, F108-coated silica surfaces was evaluated against the Gram-positive indicator strain, Pediococcus pentosaceous. The retained biological activity of these nisin-loaded layers was evaluated after incubation in the presence of bovine serum albumin (BSA), for contact periods up to one week. Surfaces were withdrawn at selected times and placed on plates inoculated with P. pentosaceous to measure kill zone radius in order to quantify nisin activity. In the presence of BSA, F108-coated surfaces retained more antimicrobial activity than the uncoated, hydrophobic surfaces. These results strongly suggest that PEO brush layers may serve as a viable drug storage platform due to the retained non-fouling character after bioactive peptide entrapment and the prolonged peptide activity in the presence of other proteins. / Graduation date: 2013

No description available.

A novel photonic frequency discriminator has been developed. The discriminator utilizes a Mach Zehnder interferometer-assisted ring resonator to achieve enhanced linearity. A numerical frequency-domain two-tone test is performed to evaluate the unique design of the discriminator, particularly for suppression of the third order intermodulation distortion. The discriminator is switchable between linear-intensity and linear-field regimes by adjusting a phase delay on one arm of the Mach Zehnder interferometer. Through the simulation, the linear<intensity discriminator is shown to be advantageous. The discriminator is an optical ring resonator-Mach Zehnder interferometer synthesized passive filter. The ring resonator is made of Arsenic trisulfide (As2S3) and the bus waveguide is a Titanium<diffused Lithium niobate (LiNbO3) waveguide. This As2S3 ring-on-Ti:LiNbO3 hybrid structure offers electro-optic tunability of the device owing to a strong electro-optic effect of the substrate material. A large optical confinement factor achieved by vertical integration of the As2S3 strip waveguide on a LiNbO3 substrate enables a low loss ring resonator. The Mach Zehnder interferometer is formed by the optical path length difference of the birefringent LiNbO3 substrate instead of a physical Y-branch structure, which makes the fabrication tolerances relaxed. In order for this highly birefringent device to be characterized, each polarization mode must be measured separately. A novel algorithm which can measure the wavelength-swept Jones matrix including its phase response is devised. The efficacy of the algorithm is demonstrated by characterizing a ring resonator. Finally, the fabricated discriminator is fully characterized using the algorithm.

Nous proposons des liaisons optiques en Silicium à faible coût utilisant des longueurs d'onde de propagation de 650 à 850 nm. La création de circuits intégrés optoélectroniques à grande échelle et de bus de données optiques au sein même des circuits intégrés, utilisant des composés Silicium CMOS, ont été envisagées présentant une voie prometteuse [1] - [3]. Dans les dernières tentatives de réalisation de systèmes optoélectroniques en CMOS, les technologies était principalement orientée sur l'utilisation des longueurs d'onde à 1550 nm [4] - [6], principalement en raison de la facilité de conception et de fabrication des guides d'ondes dans ce régime de longueur d'onde. Cependant, aucune source optique rapide efficace et aucun photo-détecteur Si ne sont disponibles à cette longueur d'onde de 1550 nm. Aujourd'hui, les solutions pour surmonter le problème sont principalement axées sur l'intégration de sources optiques basées sur des éléments du groupe IIIV reportés sur Silicium par liaison moléculaire [7a] - [7b].Si la source optique, le détecteur, les guides d'ondes et les capteurs pouvaient être réalisés sur la même puce CMOS Silicium, par exemple à une longueur d'onde de 750 nm, divers systèmes micro-photoniques sur puces, légers et miniaturisés, pourraient être conçus et réalisés. Alors que les sources optiques au Silicium ne sont peut-être pas encore au niveau de performance requis pour les communications à très haut débit, les systèmes optoélectroniques "tout-Silicium" à faible coût restent encore un excellent point de départ. Ces sources pourraient également conduire à un nouveau champ qui pourrait s'appeler «microsystèmes photoniques Si» ouvrant la voie à de nouvelles applications et produits notamment pour l'optique médicale, biomédicale, les interconnexions optiques et la biophotonique. Ces systèmes ne nécessitent de bande passante à très haute fréquence pour émettre, et les puissances d'émission de nos diodes électroluminescentes (LED) à avalanche peuvent être suffisantes pour assurer le fonctionnement de tels systèmes. Ce travail de thèse de doctorat traite donc des liaisons optiques SiGe / Si à faible coût en utilisant des dispositifs Photonique-Microondes tels que une source à Diode Electro-Luminescente (DEL) à avalanche en Silicium (SiAvLED) et Silicium-Germanium intégrée en technologie bipolaire, des guides d'ondes optiques en Nitrure de Silicium et en Oxyde de Silicium, des phototransistors bipolaires à hétérojonction (HPT) SiGe. Ce travail se concentre sur l'intégration combinée de sources optiques à l'échelle micrométrique, de guides d'ondes optiques et de détecteurs sur une même puce pour former une liaison de communication complète pour diverses applications iv impliquant des liaisons de courte longueur d'onde (750 nm à 950 nm). Les progrès fournis par ce travail par rapport aux travaux antérieurs pourraient être synthétisés comme suit:• La source optique, le guide d'ondes et le détecteur ont tous été intégrés et alignés sur la même puce, dans une technologie industrielle RF bipolaire SiGe 0,35μm, pour former une liaison optique ou optique micro-onde complète sur puce à la longueur d'onde de 750 nm.• Une série de liaisons de communication optique de deuxième génération de 50μm de longueur, utilisant des longueurs d'onde de propagation de 650 à 850 nm, a été conçue et réalisée en technologie SiGe bipolaire également. Des sources optiques, des guides d'ondes et des détecteurs de dimensions micrométriques ont tous été intégrés sur la même puce pour former une communication complète sur les liaisons micro-optiques. Des LED Si à base d'avalanche (Si Av LED), des contacts Schottky, des stratégies de densification TEOS, des guides d'ondes à base de Nitrure de Silicium et des technologies de détection bipolaire SiGe de pointe ont été utilisées comme stratégies de conception clés.• Le logiciel de simulation R-soft (Beam Prop) a été utilisé comme outil de simulation / We propose a low cost full-silicon optical links utilizing 650 – 850 nm propagation wavelengths. The creation of large-scale opto-electronic integrated circuits and optical data “highways” inCMOS integrated circuitry, utilizing Si CMOS compounds, have been envisioned and hold much promise [1] - [3] The latest attempts for realizing optoelectronic systems in CMOS technology have until now mainly been focused on utilizing wavelengths at 1550 nm [4] - [6], mainly because of the ease of design and fabrication of waveguides in this wavelength regime. However, no effective high-speed optical sources and Si detectors are available at this 1550nmwavelength. Today solutions to overcome the problem are mostly focused on the integration of group III-V elements based optical sources on Silicon through molecular bonding [7a] – [7b]. If optical sources, detectors, waveguides, and sensors could be realized on the same Si CMOS chip at, say, 750 nm wavelength, various low power consuming, light and miniature on-chip-based micro-photonic systems can be designed and realized. While Silicon optical sources may not yet be at the required performance level for very-high speed communications, the low cost “all silicon”opto-electronic systems still remain a great grail. These sources could lead as well to new field that could be appropriately named “Si photonic microsystems” opening the route to new sensing applications and products especially for the medical, biomedical optics, optical interconnect and bio-photonics field. These systems also do not require ultrahigh frequency bandwidths to transmit, and the emission powers of our avalanche Si light-emitting diodes(LEDs) may be sufficient to sustain the operation of such systems. This PhD thus deals with low cost SiGe/Si optical links using Microwave-Photonics devices such as, Bipolar integrated SiAvLED, Silicon Nitride and Silicon Oxide optical waveguides, SiGeHPTs, Si and SiGe/Si LEDs. It focuses on the combined integration of micron-scale optical sources, optical waveguides and detectors on the same chip to form a complete communication link for various applications involving short wavelength links (750nm to 950nm). The progress provided by this PhD to previous works could be synthesized as below:• Optical source, waveguide and the detector were all integrated and aligned on the same chip, in an industrial based technology, to form complete on-chip micro-optical links at750nm wavelength, with a SiGe radio frequency (RF) 0.35µm bipolar process.• A series of second generation of on-chip optical communication links of 50µm length, utilizing 650 – 850 nm propagation wavelengths, have been designed and realized inSiGe. Micron dimensioned optical sources, waveguides and detectors were all integrated ion the same chip to form a complete communication on-chip micro-optical links. Avalanche based Si LEDs (Si Av LEDs), Schottky contacting, TEOS densification strategies, Silicon-Nitride based waveguides, and state of the art SiGe bipolar detector technologies were used as key design strategies.• R-soft simulation software (Beam Prop) was used as a mathematical capable simulation tool to model various Silicon-Nitride optical waveguide structures, before the designing, the fabrication, characterization and testing of the device. Various device structures were modeled, simulation iterations were performed on several optical waveguide designed structures before the device design, and the devices were tested experimentally.• Best performances of the designed on-chip optical links show a conversion loss as low as30dB from source to detector with up to 500MHz in cut off frequency. The good alignment and the good efficiency of each device are then clearly achieved. Higher frequency performances are also envisaged from preliminary measurements

Biodesulfurization (BDS) is an alternative to hydrodesulfurization (HDS) as a method to remove sulfur from crude oil. Dibenzothiophene (DBT) was chosen as a model compound for the forms of thiophenic sulfur found in fossil fuels; up to 70% of the sulfur in petroleum is found as DBT and substituted DBTs; these compounds are however particularly recalcitrant to hydrodesulfurization, the current standard industrial method. My thesis deals with enhancing BDS through novel strains and through nanotechnology. Chapter highlights are: Chapter 2. My first aim was to isolate novel aerobic, mesophilic bacteria that can grow in mineral media at neutral pH value with DBT as the sole sulfur source. Different natural sites in Iran were sampled and I enriched, isolated and purified such bacteria. Twenty four isolates were obtained that could utilize sulfur compounds. Five of them were shown to convert DBT into HBP. After preliminary characterization, the five isolates were sent to the Durmishidze Institute of Biotechnology in Tbilisi for help with strain identification. Two isolates (F2 and F4) were identified as Pseudomonas strains, F1 was a Flavobacterium and F3 belonged to the strain of Rhodococcus. The definite identification of isolate F5 was not successful but with high probability it was a known strain. Since no new strains were apparently discovered, I did not work further in this direction. Chapter 3. In a second approach I studied the desulfurization ability of Shewanella putrefaciens strain NCIMB 8768, because in a previous investigation carried out at Cranfield University, it had been found that it reduced sulfur odour in clay. I compared its biodesulfurization activity profile with that of the widely studied Rhodococcus erythropolis strain IGTS8. However, S. putrefaciens was not as good as R. erythropolis. Chapter 4 and 5. I then turned to nanotechnology, which as a revolutionary new technological platform offers hope to solve many problems. There is currently a trend toward the increasing use of nanotechnology in industry because of its potentially revolutionary paths to innovation. I then asked how nanotechnology can contribute to enhancing the presently poor efficiency of biodesulfurization. Perhaps the most problematic difficulty is how to separate the microorganisms at the end of the desulfurization process. To make BDS more amenable, I explored the use of nanotechnology to magnetize biodesulfurizing bacteria. In other words, to render desulfurizing bacteria magnetic, I made them magnetic by decorating their outer surfaces with magnetic nanoparticles, allowing them to be separated using an external magnet. I used the best known desulfurizing bacterial strain, Rhodococcus erythropolis IGTS8. The decoration and magnetic separation worked very well. Unexpectedly, I found that the decorated cells had a 56% higher desulfurization activity compared to the nondecorated cells. I proposed that this is due to permeabilization of the bacterial membrane, facilitating the entry and exit of reactant and product respectively. Supporting evidence for enhanced permeabilization was obtained by Dr Pavel Grigoriev, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino. In Chapter 6, to optimize attachment of the nanoparticles to the surface of the bacteria I created thin magnetic nanofilms from the nanoparticles and measured the attachment of the bacteria using a uniquely powerful noninvasive optical technique (Optical Waveguide Lightmode Spectroscopy, OWLS) to quantify the attachment and determine how the liquid medium and other factors influence the process.

No description available.

Dans les prochaines décennies, les limites des systèmes de communications optiques actuels seront atteintes à moins d'adopter de nouvelles solutions. L'une d'elles est l'utilisation d'une nouvelle plage spectrale autour de 2 µm stimulée par l'apparition des amplificateurs fibrés dopés thulium. Dans ce manuscrit, nous nous y intéresserons dans le cadre de transmissions très courtes distances sur puces photoniques. Divers matériaux, dont le dioxyde de titane, seront ainsi explorés.Ce travail de thèse a deux principaux objectifs. D'une part, il vise à démontrer que le dioxyde de titane (TiO2), matériau encore peu exploré, est prometteur pour des applications télécoms en le comparant à des plateformes plus matures. D'autre part, il tend à introduire la bande spectrale autour de 2 µm comme une solution à envisager pour les télécommunications de nouvelle génération.Plus précisément, la première partie de cette thèse a pour but de développer une technique pour coupler efficacement la lumière dans les structures en TiO2). Pour la première fois, une configuration faisant appel à un réseau métallique enterré a été évaluée numériquement avant d'être caractérisée expérimentalement. La seconde partie présente des transmissions télécoms haut-débit (10 Gbit/s) autour de µm réalisées sans erreurs dans des guides d'ondes sub-longueur d'onde ou multimodes en dioxyde de titane, silicium ou silicium-germanium. Pour terminer, des fonctions non-linéaires sont explorées sur ces puces photoniques. Il a été ainsi démontré une conversion en longueurs d'onde à 2 µm atteignant -10dB sur silicium ou la génération du premier supercontinuum s'étalant du visible à 2 µm dans un guide d'onde en TiO2. / In the next decades, the limits of current optical communication systems will be reached unless new solutions are adopted. On of them is the use of a new spectral range around 2 µm enabled by the emergence of thulium-doped fiber amplifiers. In this thesis, we will focus on it in the context of very short distances transmissions on photonic chips. Various materials, mainly titanium dioxide (TiO2), will be explored.This thesis work has two main objectives. On the one hand, it aims to demonstrate that a material relatively unexplored, titanium dioxide, is promising for telecom applications by comparing it to more mature plateforms. On the other hand, it tends to introduce the spectral band around 2 µm as a solution to be considered for next-generation communications.More precisely, the first part of this thesis aims to develop a technique to efficiently couple light in TiO2 structures. For the first time, a configuration using a buried metallic grating was evaluated numerically and then characterized experimentally. The second part presents error-free high-speed (10 Gbit/s) telecom transmissions around 2 µm carried out in subwavelength or multimode waveguides in titanium dioxide, silicon or silicon-germanium. Finally, nonlinear functions are explored on the photonic chips. Thus, it has been demonstrated a wavelength conversion at 2 µm reaching -10dB on a silicon waveguide or the first supercontinuum generation spreading from visible to 2 µm wavelength in a TiO2 waveguide.

Le contexte de cette thèse couvre les dispositifs photoniques hybrides III-V sur silicium. L’étude porte sur l’intégration par collage de matériau à base d'InP sur le silicium, puis la conception d’un guide optique comportant une nanostructuration qui permettra la sélection en longueur d’onde dans un laser DFB hybride. Enfin, on étudie les étapes technologiques de fabrication d’un laser hybride injecté électriquement fonctionnant dans le domaine spectral 1.55µm, et on caractérise les dispositifs. Pour associer les matériaux III-V sur Si, nous avons développé le collage sans couche intermédiaire que l’on nomme collage hétéroépitaxial ou oxide-free. Ce collage est reporté dans la littérature comme présentant une meilleure qualité électrique. Nous avons établi les conditions de préparation permettant d’obtenir des surfaces parfaitement désoxydées, et les conditions de recuit conduisant à une interface hybride sans oxyde et sans dislocation. Mais ce recuit est réalisé à température assez élevée (~450-500°C). Nous avons alors développé le collage avec une fine couche intermédiaire d’oxyde réalisé à plus faible température -300°C- qui présente l'avantage d'être compatible avec la technologie CMOS. Nous avons étudié différentes approches pour élaborer et activer une couche d’oxyde très fine (~3nm), de façon à obtenir une surface collée sans zones localement non collées. Le collage est dans les deux cas réalisé sous vide dans un équipement de type Bonder Suss SB6e. La qualité structurale de l’interface a été observée par STEM et la qualité mécanique du joint de collage a été caractérisée par indentation. Une méthode originale de mesure quantitative et locale de l’énergie du joint de collage a été développée. La qualité optique des couches collées a été étudiée par la mesure de la photoluminescence de puits quantiques placés proches du joint d’interface. En conséquence du collage sans couche intermédiaire ou avec une couche très fine, le design du mode optique est de type double-cœur, qui ne nécessite pas de taper. Le guide optique Si est de type shallow ridge, le confinement latéral étant assuré par un matériau nanostructuré à une période sub-longueur d’onde. Ce matériau fonctionne comme un matériau effectif uniaxe pour lequel on a calculé les indices optiques ordinaire et extraordinaire selon la géométrie de la nanostructuration. On peut rajouter sur cette nanostructuration une super-périodicité qui conduit à un fonctionnement sélectif en longueur d’onde. Le comportement modal du guide est simulé à l'aide du logiciel COMSOL Multiphysics, le comportement spectral est simulé par FTDT 3D. Nous avons validé la pertinence de ce design en mesurant la transmission de guides hybrides. Ce design sera inclus dans un laser et permettra d’obtenir une émission monofréquence de type DFB. Nous avons développé les étapes technologiques nécessaires à la fabrication d’un laser hybride à base d'InP sur Silicium fonctionnant en injection électrique. Nous avons mis en oeuvre de nombreuses techniques, et développé plusieurs procédés spécifiques, en particulier, des procédés de gravure sèche de type Inductive Coupled Plasma Reactive Ion Etching ICP-RIE pour la gravure de la nanostructuration dans le silicium, et pour la gravure du mésa du laser. La présence des 2 matériaux III-V et Si dans le dispositif hybride rend ces étapes complexes. Les premiers résultats peuvent être améliorés en optimisant la technologie des contacts. Un design permettant de s’affranchir de la pénalité thermique présenté par tous les dispositifs ayant les 2 contacts électriques du coté du matériau III-V a été proposé, exploitant le passage du courant à l’interface hybride III-V / Si, ce qui est possible dans le cas du collage oxide-free. Cette approche ouvre des perspectives d’intégration au-delà de la photonique. / This work contributes to the general context of III-V materials on Silicon hybrid devices for optical integrated functions, mainly emission/amplification at 1.55µm. Devices are considered for operation under electrical injection, reaching performances relevant for data transfer application. The main three contributions of this work concern: (i) bonding InP-based materials on Si, (ii) nanostructuration of the Si guiding layer for spatial and spectral control of the guided mode and (iii) technology of an hybrid electrically injected laser, with a special attention to the thermal budget. Bonding has been investigated following two approaches. The first one we call heterohepitaxial or oxide-free bonding, is performed without any intermediate layer at a temperature ~450°C. This approach has the great advantage allowing electrical transport across the interface, as reported in the literature. We have developed oxide-free surface preparation for both materials, mainly InP-based layers, and established bonding parameter processing. An in-depth STEM and RX structural characterization has demonstrated an oxide-free reconstructed interface without any dislocation except on one or two atomic layers which accommodate the large lattice mismatch (8.1%) between InP and Si. Photoluminescence of quantum wells intentionally grown close to the interface has shown no degradation. We have also developed an oxide-based bonding process operated at 300°C in order to be compatible with CMOS processing. The original ozone activation of the very thin (~5nm) oxide layer we have proposed demonstrates a bonding surface without any unbonded area due to degassing under annealing. We have developed an original method based on nanoindentation characterization in order to obtain a quantitative and local value of the surface bonding energy. Related to the absence or to the very thin intermediate layer between the two materials, our modal design is based on a double core structure, where most of the optical mode is confined in the Si guiding layer, and no taper is required. The Si waveguide on top of the SOI stack is a shallow ridge. A nanostructured material on both sides of the waveguide core ensures the lateral confinement, the nanostructuration geometry being at a sub-wavelength period in order to operate this material well below its photonic gap. It behaves as an uniaxial material with ordinary and extraordinary indices calculated according to the structuration geometry. Such a structuration allows modal and spectral control of the guided mode. 3D modal and spectral simulation have been performed. We have demonstrated, on a double-period structuration, a wavelength selective operation of hybrid optical waveguides. Such a double-period geometry could be included in a laser design for DFB operation. This nanostructuration has larger potential application such as coupled waveguides arrays or selective resonators. We have developed all the technological processing steps for an electrically injected hybrid laser fabrication. Main developments concern dry etching, performed with the Inductive Coupled Plasma Reactive Ion Etching ICP-RIE technique of both the nanostructuration of the Silicon material, and the mesa of the hybrid laser. Efficient electrical contacts fabrication is also a complex step. First lasers operating performances could be improved. We have investigated a specific design in order to overcome the thermal penalty encountered by all the hybrid devices. This penalty is due to the thick buried oxide layer of the SOI stack that prevents heating related to the current flow to be dissipated. Taking advantage of the electrical transport we have shown at the oxide-free interface, we propose a design where the n-contact is defined on the guiding Si layer, suppressing thermal heating under electrical operation. Such an approach is very promising for densely packed hybrid devices integrated with associated electronic driving elements on Si.