Photonic crystal waveguide (PCW) based device has been used in many applications in recent years due to its unique slow light effect. In this work, the application of PCW on sensing is presented. First, we present a PCW structure based Infrared (IR) spectroscopy combining with slot structure which has a large electric field enhancement for light-matter interaction for chemical sensing. The slow light effect and the electric field enhancement of our designed structure greatly enhance the absorption factor of chemical analytes by 1000. We then use multimode interference (MMI) optical splitter and Y junction combiner to connect two PCWs to show multiplexed detections of two chemicals on a single chip. Our results show the detection is down to 1 ppb for xylene in water and 100ppm for methane in nitrogen. We also present PCW microcavities structure for biological sensing in our work. Due to its high quality factor and easier immobilization of biomaterials, we are able to use ink jet printing method to bind the biomaterials on top of our chip. We choose linear-type 13 (L13, missing 13 holes) microcavities to do the biosensing for antibodies and cancer cell lysates because of its higher sensitivity combining with slow light effect. Our work achieves the cancer cell lysates detection down to 2 cells/μl., and further applications will be presented in our group in the future. / text

This thesis describes work carried out to demonstrate the use of photonic crystal fibres for the study of photochemistry reaction kinetics and fluorescence spectroscopy. Photonic crystal fibre allows the guidance of light, in a well-defined mode, over long path lengths. When the fibre’s microstructure is filled with a sample solution this, therefore, provides a greatly increased measurement path length and greater light-sample interaction than is possible in conventional spectroscopic systems, leading to enhanced sensitivity whilst greatly reducing the required sample volumes. The use of photonic crystal fibre as a micro reaction chamber for carrying out photochemical reactions and the study of their kinetics was achieved through monitoring the photoisomerisation of two azobenzene-based dyes, Disperse Red 1 and Disperse Orange 1, using real-time UV/Vis absorption spectroscopy. Both the 488 nm excitation laser and the broadband light source for the measurements were co-coupled through the fibre, giving perfect overlap of both with the sample. The fibre used for the measurements was a hollow core kagomé-type fibre with a core diameter of 19μm, giving a sample volume of 2.8 nL cm-1. The 30 cm path-length of the fibre allowed the use of sample concentrations down to 5×10-6 M, over an order of magnitude lower than in a conventional 1cm cuvette, with a sample volume of 90 nl in the core, a reduction of five orders of magnitude over conventional measurements. The kinetics of the photoisomerisation from the trans to the cis isomers of the dyes and the thermally driven cis-to-trans isomerisation could be tracked on the ms timescale, using a grating spectrometer which recorded the entire absorption spectrum of the dye. The data were numerically fitted using a custom model to take into account the properties of the fibre system. This led to the calculation of rate constants for the isomerisation processes in good agreement with those previously measured for these dye systems in bulk solution. Furthermore, the measurement of the dyes in pentane, in which they are highly insoluble, could be achieved due to the low concentrations that could be used; such measurements have not previously been reported. For the study of photonic crystal fibre as a system for the excitation and collection of fluorescence, two types of fibre were used; the same kagomé hollow-core fibre used for the photochemistry absorption measurements and a suspended-core “Mercedes” fibre. This allowed for the excitation of fluorophores in two contrasting environments. In the kagomé fibre fluorophores in bulk solution are excited whilst, in the Mercedes fibre, only fluorophores either on or in close proximity to the silica core interact with the evanescent field of the excitation light. The Fluorescein fluorophore was used initially to measure the detection limits in both fibre types and limits of 2x10-11 M in the kagomé and 10-9 M in the Mercedes fibre were obtained. This equates to 106 molecules in the kagomé fibre, which displays the lower detection limit due to greater light-sample interaction. Two-photon excitation of the Fluorescein fluorophore was then carried out using a mode-locked Ti-Sapphire laser as an excitation source, demonstrating the ability of the fibre system to sustain two-photon excitation of a long (30 cm) path length. The two-photon measurements showed remarkable detection sensitivity allowing detection of fluorescence from 10-9 M solutions of Fluorescein, showing the potential of using PCF for two-photon based experiments which are of particular interest in fields such as photodynamic therapy. A further study was carried out, using the two fibre types, for measurement of the fluorescence lifetime of the Rhodamine B fluorophore. Unperturbed lifetimes could be measured in the fibres showing no interference from the fibre. The measurements confirmed, in reference to known lifetime values, that in the kagomé fibre the excited fluorophores are in the bulk solution with only a minor influence from surface effects, whilst in the Mercedes fibre all of the excited molecules experience interaction with the surface of the silica core. This, therefore, gives a method of locating the fluorophores with respect to the fibre surface and the ability to choose between measurement of bulk solution and long path-length evanescent field-induced fluorescence.

Les travaux effectués dans le cadre de cette thèse s'inscrivent dans la suite des travaux réalisés par l'INL (Institut des Nanotechnologies de Lyon) sur les résonateurs optiques à base de cristaux photoniques membranaires pour la réalisation de composants actifs ou passifs intégrés sur silicium. Ces travaux se concentrent particulièrement sur le contrôle des propriétés de propagation des modes et des résonances guidés s'établissant dans les cristaux photoniques membranaires. Ils s'appuient notamment sur la nature partiellement ou totalement guidée de ces modes, ainsi que des propriétés de symétrie des structures (ou au contraire de dissymétrie) afin de pouvoir générer des dispersions photoniques à la demande. En effet, le contrôle des propriétés spectro-spatiales est primordiale à la réalisation de composants photoniques efficients. Par exemple l'établissement d'un régime d'émission laser dans un cristal photonique membranaire passe par un contrôle minutieux des propriétés temporelles de la résonance (fort facteur de qualité) mais aussi spatiales (fort ralentissement de la lumière) afin de pouvoir générer des densités d'états photoniques suffisamment importantes. Ainsi, de nombreuses stratégies de contrôle ont été mises en place durant les années 2000, permettant l'établissement d'un régime laser dans des structures diverses. Néanmoins, si les méthodes de fabrication et la maîtrise dans la conception de ces structures se sont améliorées au fil de leur développement, ces dispositifs restent difficilement compétitifs face à d'autres technologies. Démontrer la versatilité de ces structures par l'ajout de fonctionnalités tels que le \emph{beam steering} ou d'autres capacités serait alors une véritable plus-value. Récemment, de nouvelles stratégies de contrôle de la lumière ont émergé. Ces stratégies se basent sur une approche totalement différente des procédés de contrôle habituels. Ainsi, on peut citer les nouveaux phénomènes de localisation de la lumière basés sur des procédés inédits de découplage de la lumière du continuum radiatif, ou des dispersions en cône de Dirac qui pourraient permettre la réalisation de composants originaux tels que des lasers mono-modes à grande surface active. Ces nouveaux phénomènes permettent d'envisager d'autres approches pour la réalisation de lasers à cristaux photoniques et pourraient apporter les nouvelles fonctionnalités recherchées. Parallèlement, l'utilisation de membranes photoniques multi-modes reste encore peu répandue dans la littérature. L'utilisation conjointe de modes d'ordres différents offre pourtant des possibilités supplémentaires dans le contrôle des propriétés de propagation de la lumière dans les cristaux photoniques membranaires. Ce contrôle supplémentaire peut se traduire par des capacités de ralentissement de la lumière accrues ou par la réalisation de dispersions plus exotiques. Le but de cette thèse est alors de mettre en place les briques conceptuelles nécessaires à la génération de ces dispersions particulières. Pour cela, un modèle théorique permettant d'appréhender les dynamiques de couplage opérant dans les cristaux photoniques membranaires étudiés est mis en place. Ce modèle est ensuite confronté aux résultats de simulation ainsi qu'aux caractérisations optiques des structures fabriquées. En parallèle, une étude prospective des applications possibles est menée pour chacune des dispersions générées. / Work carried out in this thesis is part of the overall work done at INL on optical resonators based on photonic crystals for the design of passive as well as active components integrated on silicon chips. These works especially focus on spectral properties and propagation control of guided modes and resonances settled in photonic crystal slabs. They rely partly on the guided nature of these modes as well as their symmetry properties to generate on-demand photonic dispersions. Indeed, control of the spectro-spatial properties is overriding for the design of efficient photonic components. For instance, obtaining a laser effect with a photonic crystal requires a precise control of both spectral properties (high quality factor) and spatial ones (high light slow-down) so that large photonic densities of states are achieved. Thereby, numerous strategies of control have been developed during the 2000s, allowing a laser effect to occur with various structures. Nonetheless, despite both manufacture and design qualities have been improved, these components still remain hardly competitive compared to other technologies. Demonstrating the versatility of these structures by achieving novel functionalities like beam steering or other capacities would be a real betterment. Recently, new strategies to control light using photonic crystals have been discovered. These strategies are based on completely new phenomena. For instance, new possibilities to localize light based on novel light decoupling processes from the continuum have arisen and Dirac cone dispersions could allow the formation of monomode larger-area photonic crystal lasers. These new phenomena enabled to consider new approaches to design photonic crystal laser that could lead to the novel functionalities sought. In parallel, the use of multimode photonic membranes still remains uncommon in the literature. The use of several guided orders gives additional possibilities to the control of light propagation within photonic crystal membrane thought. This additional control can lead to improved slowing-down capabilities or exotic dispersion generation. The goal of this thesis is to set up the fundamental blocks on which these particular dispersions are based on. In this purpose, a theoretical model allowing apprehending the coupling dynamic occurring in photonic crystal membranes is established. Then, this model is compared to simulation results and experimental characterizations of the manufactured structures.

Thesis advisor: Krzysztof Kempa / Though nature provides a plethora of materials to work with, their properties are very much restricted, forcing severe limitations on the devices that are built from them. A huge portion of current technology stands to be significantly advanced and even revolutionized by the emergence of a new class of “configurable” materials. This class, generally referred to as metamaterials, has become more feasible than ever due to advancements in nanotechnology and fabrication techniques. Notable among nature’s limitations is an ever-positive index of refraction. This barrier has only recently been broken, and the known paths to negative refraction are few and limited. This paper introduces two distinct three-dimensional crystals capable of all-angle negative refraction. One uses the familiar photonic band, while the other is the first of its kind to rely on polaritonic waves. Their mode structures are examined and a set of parameters are chosen at which a negative effective index of refraction can be harnessed for unrestricted sub-wavelength lensing, demonstrated via numerical simulation. This work is expected to enable experimental observation of polaritonic negative refraction and sub-wavelength lensing at microwave frequencies. / Thesis (BS) — Boston College, 2009. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: College Honors Program. / Discipline: Physics.

This thesis presents the development of photonic tools towards the realisation of an optical intensity waveform synthesiser and of an attosecond pulse synthesiser based on the generation and Fourier synthesis of a continuous-wave coherent spectral comb spanning more than 3 octaves (UV to mid-IR) by use of a gas-filled hollow core photonic crystal fibre (HC-PCF).

This thesis introduces the linear and nonlinear properties of photonic crystal fibre (PCF), describes the fabrication and characterisation of different PCFs, and demonstrates their applications to supercontinuum (SC) generation and single-photon sources. The linear properties of PCF include endlessly single-mode transmission, highly controllable dispersion and birefringence. These unique properties have made PCFs the best media to demonstrate all kinds of nonlinear effects such as self-phase modulation (SPM), cross-phase modulation (XPM), Raman effects, four-wave mixing and modulation instability (FWM and MI), and soliton effects. The combination of these nonlinear effects has led to impressive spectral broadening known as SC generation in PCFs. The intrinsic correlation of signal and idler photons from FWM has brought PCF to the application of single-photon generation. Four projects about SC generation were demonstrated. The first was visible continuum generation in a monolithic PCF device, which gave a compact, bright (-20 dBm/nm), flat and single-mode visible continuum source extending to short wavelength at 400 nm. The second was polarised SC generation in a highly bire-fringent PCF. A well linearly polarised continuum source spanning 450-1750 nm was achieved with >99% power kept in a single linear polarisation. This polarised continuum source was then applied to tuneable visible/UV generation in a BIBO crystal. The third was residual pump peak removal for SC generation in PCFs. The fourth was to design an all-fibre dual-wavelength pumping for spectrally localised continuum generation. Two projects about photon pair generation using FWM were then demonstrated. One was an all-fibre photon pair source designed in the telecom band for quantum communication. This source achieved >50% heralding efficiency which is the highest in fibre photon pair sources reported so far. Another one was to design birefringent PCFs for naturally narrow band photon pair generation in the Si SPAD high detection efficiency range. 0.122 nm bandwidth signal photons at 596.8 nm were generated through cross polarisation phase matched FWM in a weakly birefringent PCF pumped by a picosecond Ti:Sapphire laser at 705 nm in the normal dispersion regime.

This thesis presents the development of photonic microcells for use as the host for coherent optics phenomena and related applications. A photonic microcell consists of a length of hollow-core photonic crystal fibre (HC-PCF) with a gas-filled core that is spliced to conventional optical fibre at either end to seal the gas within the fibre. Towards the goal of demonstrating and assessing the coherence properties of quantum optical effects in photonic microcells, the fabrication of two types of HC-PCF is presented. The established photonic bandgap HC-PCF offers extremely low transmission loss of ~10 dB/km over kilometre distances. However, the fibre has a limited transmission bandwidth of ~50 THz and exhibits modal coupling unfavourable for many applications. Work is presented on the tailoring of this fibre by control and shaping of the core-surround in order to improve its modal properties. A second type of HC-PCF is based on a large-pitch lattice, whose guidance relies on a new mechanism. This fibre exhibits a much improved bandwidth (>1000 THz) and has a relatively higher but still practical loss of ~1 dB/m. The development of photonic microcells at microbar pressure level and with low optical insertion loss is shown, an important step in the improvement of the technology for coherent optics applications which will take advantage of the extreme gas-laser interaction efficiency achieved in HC-PCF. Finally, quantum optical effects are demonstrated in HC-PCF and photonic microcells loaded with both the molecular gas acetylene and atomic vapour rubidium. The observation of electromagnetically induced transparency (EIT) in acetylene-filled HC-PCF represents the first such observation in a molecular gas, while the use of a photonic microcell allows a comparison of many experimental configurations to explore the coherence properties of coherent optical systems in the core of a HC-PCF. Furthermore, EIT is observed unambiguously in a rubidium loaded HC-PCF for the first time, and the anti-relaxation effects of a polymer coating demonstrated in this configuration.

In this thesis we study elliptic PDEs and PDE systems with e-pcriodic coeffi- cients, for small E, using the theory of two-scale homogenisation. We study a class of PDEs of partially degenerating type: PDEs with coefficients that are not uniformly elliptic with respect to E, and become degenerate in the limit E -t O. We review a recently developed theory of homogenisation for a general class of partially degenerating PDEs via the theory of two-scale convergence, and study two such problems from physics. The first problem arises from the study of a linear elastic composite with periodically dispersed inclusions that are isotropic and (soft' in shear: the shear modulus is of order E2. By passing to the two- scale limit as E -t 0 we find the homogenised limit equations to be a genuinely two-scale system in terms of both the macroscopic variable x and the micro- scopic variable y. We discover that the corresponding two-scale limit solutions must satisfy the incompressibility condition in y and therefore the composite only undergoes microscopic deformations when a (microscopically rotational' force is applied. We analyse the corresponding limit spectral problem and find that, due to the y-incompressibility, the spectral problem is an uncoupled two-scale prob- lem in terms of x and y. This gives a simple representation of the two-scale limit spectrum. We prove the spectral compactness result that states: the spectrum of the original operator converges to the spectrum of the limit operator in the sense of Hausdorff. The second problem we study is the propagation of electro- magnetic waves down a photonic fibre with a periodic cross section. We seek solutions to Maxwell's equations, propagating down the waveguide with wave number k E2-close to some (critical' value. In this setting, Maxwell's equations are reformulated as a partially degenerating PDE system with z-periodic coeffi- cients. Using the theory of homogenisation we pass to the limit as E -t 0 to find a non-standard two-scale homogenised limit and prove that the spectral compact- ness result holds. We finally prove that there exist gaps in the limit spectrum for two particular examples: a one-dimensionally periodic 'multilayer ' photonic crystal and a two-dimensionally periodic two-phase photonic crystal with the in- clusion phase consisting of arbitrarily small circles. Therefore, we prove that these photonic fibres have photonic band gaps for certain k.

This thesis explores the generation and the coherence properties of Raman frequency combs that are initiated from vacuum fluctuations using hydrogen-filled hollow-core photonic crystal fibre (HC-PCF). The motivation is to explore a novel route for generating attosecond pulses and waveform synthesis. To this end, work has been undertaken in the design and fabrication of HC-PCF, in the generation of Raman comb with a compact set-up and finally in an experimental demonstration of the mutual coherence between the comb spectral components. Here, the well-established photonic bandgap (PBG) HC-PCF is further developed. Surface mode spectral positions are controlled by chemical etching technique, and a single piece of fibre with two robust bandgaps is fabricated. Furthermore, the second established class of HC-PCF; namely large-pitch Kagome-lattice HC-PCF, has experienced challenging developments. This led to the fabrication of a hypocycloid-core seven-cell Kagome HC-PCF with comparable attenuation value to that of PBG HC-PCF while offering much larger bandwidth. Using the fabricated HC-PCF, different Raman frequency comb systems are developed. In addition to the previously-generated multi-octave Raman frequency comb from a large 1064 nm Nd:YAG Q-switch laser, several more compact version of Raman comb sources have been developed, including one whose lines lay in the visible and UV for applications in forensics and biomedicine. The Raman frequency comb generated inside a length of hydrogen-filled HC-PCF is further investigated by studying the coherence of the Raman lines. Despite of vacuum-fluctuation-initiation, it is demonstrated that the comb has self- and mutualcoherence properties within each single shot, bringing thus the possibility of generating attosecond pulses with non-classical properties.

The primary research aim in this thesis is to demonstrate the versatility of porous silicon based nanomaterials for biomaterial and photonic applications. In chapter 2 of this thesis, the suitability of porous silicon as a biomaterial was investigated by performing different surface modifications on the porous silicon films and evaluating biocompatibility of these surfaces in vitro. The porous silicon surfaces were characteriszed by means of atomic force microscopy (AFM), scanning electron microscopy (SEM), diffuse reflectance infrared spectroscopy (DRIFT) and interferometric reflectance spectroscopy (IRS). Cell attachment and growth was studied using fluorescence microscopy and cell viability assays. Both fabrication of the porous silicon films and subsequent surface modifications were demonstrated. Polyethylene glycol functionalised porous silicon prevented cell attachment, whilst collagen or fetal bovine serum coating encouraged cell attachment. Surface modifications were also performed on porous silicon films with different pore sizes and the influence of pore size and surface modification on primary hepatocyte growth was recorded over a course of 2 weeks by means of laser scanning confocal microscopy (LSCM), toxicity and metabolic assays. On collagen-coated surfaces with average pore sizes of 30 nm, multilayer cells stacks were formed. This stacking behaviour was not observed on samples with smaller pore sizes (10 nm), or in the absence of collagen. Hepatocytes remained viable and functional (judging by a metabolic assay) for 6 days, after which they generally underwent apoptosis. Collagen-coated porous silicon films showed later onset of apoptosis than porous silicon films not coated with collagen or collagen-coated flat silicon.. In chapter 3 of this thesis, the nitrogen laser of a laser desorption/ionization (LDI) mass spectrometer was used to selectively ablate regions on porous silicon films that had been functionalised with a non-fouling polyethylene oxide layer, affording a microscale patterning of the surface. Surface characterization was performed by means of AFM, SEM, LDI mass spectrometry, DRIFT and IRS. This approach allowed the confinement of mammalian cell attachment exclusively on the laser-ablated regions. By using the more intense and focussed laser of a microdissection microscope, trenches in a porous silicon film were produced of up to 50 micron depth, which allowed the construction of cell multilayers within these trenches, mimicking the organization of liver cords in vivo. Fluorescent staining and LSCM was used to study cell multilayer organization. To gain a better understanding of how surface topography influences cell attachment and behaviour, porous silicon films were fabricated containing a gradient of pore sizes by means of asymmetric anodisation (chapter 4). These gradients allowed the investigation of the effect of subtle changes of pore size on cell behaviour on a single sample. Analysis by means of LSCM and SEM showed that pore size can dictate cell size and area as well as cell density. In addition, a region of pore size where cell attachment and proliferation was strongly discouraged was also identified. This information can prove to be useful for designing non-biofouling surface topographies. Using the same asymmetric anodisation setup, photonic mirrors gradients were produced and overlaid over one another to produce multidirectional lateral photonic mirror gradients that display a series of roving spectral features (photonic stop-bands) from each gradient layer (chapter 4). These multidirectional photonic gradients have the potential to serve as optical barcodes or contributing to the development of graded refractive index devices such as lenses for high quality image relay and graded-index optical fibers.