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.

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.

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.

In recent years, there has been rapid development in processing of quantum information using quantum states of light. The focus is now turning towards developing real-world implementations of technologies such as all-optical quantum computing and cryptography. The ability to consistently create and control the required single photon states of light is crucial for successful operation. Therefore, high performance single photon sources are very much in demand. The most common approach of generating the required nonclassical states of light is through spontaneous photon pair generation in a nonlinear medium. One photon in the pair is detected to "herald" the presence of the remaining single photon. For many applications the photons are required to be in pure indistinguishable states. However, photon pairs generated in this manner typically suffer from spectral correlations, which can lead to the production of mixed, distinguishable states. Additionally, these sources are probabilistic in nature, which fundamentally limits the number of photons that can be delivered simultaneously by independent sources and hence the scalability of these future technologies. One route to deterministic operation is by actively multiplexing several independent sources together to increase the probability of delivering a single photon from the system. This thesis presents the development and analysis of a multiplexing scheme of heralded single photons in high-purity indistinguishable states within an integrated optical fibre system. The spectral correlations present between the two photons in the pair were minimised by spectrally engineering each photonic crystal fibre source. A novel, in-fibre, broadband filtering scheme was implemented using photonic bandgap fibres. In total, two sources were multiplexed using a fast optical switch, yielding an 86% increase in the heralded count rate from the system.

Microscopy techniques have been developed and refined over multiple decades, but innovation around single photon modalities has slowed. The advancement of the utility of information acquired, and minimum resolution available is seemingly reaching an asymptote. The fusion of light microscopy and well-studied nonlinear processes has broken through this barrier and enabled the collection of vast amounts of additional information beyond the topographical information relayed by traditional microscopes. Through nonlinear imaging modalities, chemical information can also be extracted from tissue. Nonlinear microscopy also can beat the resolution limit caused by diffraction, and offers up three-dimensional capabilities. The power of nonlinear imaging has been demonstrated by countless research groups, solidifying it as a major player in biomedical imaging. The value of a nonlinear imaging system could be enhanced if a reduction in size would permit the insertion into bodily cavities, as has been demonstrated by linear imaging endoscopes. The miniaturization of single photon imaging devices has led to significant advancements in diagnostics and treatment in the medical field. Much more information can be extracted from a patient if the tissue can be imaged in vivo, a capability that traditional, bulky, table top microscopes cannot offer. The development of new technologies in optics has enabled the miniaturization of many critical components of standard microscopes. It is possible to combine nonlinear techniques with these miniaturized elements into a portable, hand held microscope that can be applied to various facets of the biomedical field. The research demonstrated in this thesis is based on the selection, testing and assembly of several miniaturized optical components for use as a nonlinear imaging device. This thesis is the first demonstration of a fibre delivered, microelectromechanical systems mirror with miniaturized optics housed in a portable, hand held package. Specifically, it is designed for coherent anti-Stokes Raman scattering, second harmonic generation, and two-photon excitation fluorescence imaging. Depending on the modality being exploited, different chemical information can be extracted from the sample being imaged. This miniaturized microscope can be applied to diagnostics and treatments of spinal cord diseases and injuries, atherosclerosis research, cancer tumour identification and a plethora of other biomedical applications. The device that will be revealed in the upcoming text is validated by demonstrating all designed-for nonlinear modalities, and later will be used to perform serialized imaging of myelin of a single specimen over time.

Cette thèse décrit la conception et la réalisation d'une plateforme expérimentale pour le refroidissement par laser et le guidage d’atomes de Rb dans les fibres à cristal photonique à cœur creux (HC-PCF). Cette plateforme a pour but de fournir un système polyvalent pour explorer le refroidissement par laser à l’intérieur des fibres avec l'objectif à plus long terme de réaliser une fibre optique constituée d’un cœur rempli d’atomes froids (micro-cellule photonique). La plateforme a été conçue pour héberger plusieurs expériences sur le guidage d'atomes froids et thermiques ainsi que la spectroscopie dans les HC-PCFs pour répondre à plusieurs questions ouvertes liées par exemple à l'effet de la surface interne des HC-PCFs sur la structure énergétique des atomes ainsi que le piégeage et le refroidissement des atomes. La plateforme comprend une chambre spécifique à vide ultra-élevée (UHV) et un ensemble de lasers pour le refroidissement et le guidage des atomes à l'intérieur du HC-PCF hautement adapté. La chambre UHV a été conçue pour accueillir plusieurs HC-PCFs et deux pièges magnéto-optiques (MOT). Les HC-PCFs ont été conçus et fabriqués avec différents diamètres de cœur, contenu modal et post-traités avec des matériaux différents pour la surface interne du cœur. Par exemple, les diamètres du cœur varient de ~ 30 μm à ~ 80 μm traités avec une couche d'aluminosilicate ou une couche de PDMS afin de fournir un grand espace de paramètres pour évaluer l'effet de la surface sur les atomes confinés dans les fibres. Ainsi, le système a été construit et caractérisé. Le laser de refroidissement/repompage a été stabilisé en fréquence, avec une variance d'Allan de σ(τ)=3,8×10^(-11)/√τ. Avec ce système nous avons généré un MOT avec les deux isotopes du Rb, avec une température de refroidissement faible de l’ordre de 7 μK. La plateforme est maintenant opérationnelle pour entreprendre le premier guidage atomique et explorer la faisabilité du refroidissement des atomes à l'intérieur des HC-PCFs. / This thesis reports on the design and fabrication of an experimental platform for in-fibre laser cooling of Rb and atom optics. By in-fibre laser cooling, we mean the long term aim of laser cooling thermal Rb atoms of a Photonic MicroCell (PMC), and subsequently developing what would be cold-atom photonic crystal fibre (PCF). The platform was designed to harbor several experiments on cold and thermal atom guidance and in-fibre spectroscopy so to address several open questions related for example to the effect of the core inner-wall surface on the atom energy structure and on selective fibre mode excitation for atom trapping and cooling. The completed platform comprises a specific and large ultra-high vacuum (UHV) chamber and a set of lasers for both atom cooling and atom guiding inside highly tailored hollow-core PCF (HC-PCF). The UHV chamber was designed to accommodate several HC-PCFs and two magneto-optical traps (MOT). The HC-PCF were designed, fabricated and post-processed to exhibit different core diameter, modal content and core inner surface material. For example, the mode field diameters range from ~30 µm to ~80 µm for the fundamental Gaussian-like core mode, and the surface materials include pure silica, a layer of Aluminosilicate or a layer of PDMS so to provide a large parameter space in assessing the effect of surface on the fibre-confined atoms. The system has been constructed and characterized. The cooling/repumping laser was frequency-stabilized, with measured Allan variance deviation of σ(τ)=3.8×10^(-11)/√τ. With the system we generated MOT with both isotopes of the Rb atom, with a cooling temperature as low as 7 µK. The platform is now operational to undertake the first atom guidance and explore the feasibility of atom cooling inside a HC-PCF.

The real-time detection of trace species is key to a wide range of applications such as on-line chemical process analysis, medical diagnostics, identification of environmentally toxic species and atmospheric pollutant sensing. There is a growing demand for suitable techniques that are not only sensitive, but also simple to operate, fast and versatile. Most currently available techniques, such as spectrophotometry, are neither sensitive enough nor fast enough for kinetic studies, whilst other techniques are too complex to be operated by the non-specialist. This thesis presents two techniques that have been developed for and applied to liquid-phase analysis, with supercontinuum (SC) radiation used for liquid-phase absorption for the first time. Firstly, supercontinuum cavity enhanced absorption spectroscopy (SC-CEAS) was used for the kinetic measurement of chemical species in the liquid phase using a linear optical cavity. This technique is simple to implement, robust and achieves a sensitivity of 9.1 × 10−7 cm−1 Hz−1/2 at a wavelength of 550nm for dye species dissolved in water. SC-CEAS is not calibration-free and for this purpose a second technique, a time-resolved variant called broadband cavity ring-down spectroscopy (BB-CRDS), was successfully developed. Use of a novel single-photon avalanche diode (SPAD) array enabled the simultaneous detection of ring-down events at multiple spectral positions for BB-CRDS measurements. The performance of both techniques is demonstrated through a number of applications that included the monitoring of an oscillating (Belousov-Zhabotinsky) reaction, detection of commercially important photoluminescent metal complexes (europium(III)) at trace level concentration, and the analysis of biomedical species (whole and lysed blood) and proteins (amyloids). Absorption spectra covering the entire visible wavelength range can be acquired in fractions of a second using sample volumes measuring only 1.0mL. Most alternative devices capable of achieving similar sensitivity have, up until now, been restricted to single wavelength measurements. This has limited speed and number of species that can be measured at once. The work presented here exemplifies the potential of these techniques as analytical tools for research scientists, healthcare practitioners and process engineers alike.

Microscopy techniques have been developed and refined over multiple decades, but innovation around single photon modalities has slowed. The advancement of the utility of information acquired, and minimum resolution available is seemingly reaching an asymptote. The fusion of light microscopy and well-studied nonlinear processes has broken through this barrier and enabled the collection of vast amounts of additional information beyond the topographical information relayed by traditional microscopes. Through nonlinear imaging modalities, chemical information can also be extracted from tissue. Nonlinear microscopy also can beat the resolution limit caused by diffraction, and offers up three-dimensional capabilities. The power of nonlinear imaging has been demonstrated by countless research groups, solidifying it as a major player in biomedical imaging. The value of a nonlinear imaging system could be enhanced if a reduction in size would permit the insertion into bodily cavities, as has been demonstrated by linear imaging endoscopes. The miniaturization of single photon imaging devices has led to significant advancements in diagnostics and treatment in the medical field. Much more information can be extracted from a patient if the tissue can be imaged in vivo, a capability that traditional, bulky, table top microscopes cannot offer. The development of new technologies in optics has enabled the miniaturization of many critical components of standard microscopes. It is possible to combine nonlinear techniques with these miniaturized elements into a portable, hand held microscope that can be applied to various facets of the biomedical field. The research demonstrated in this thesis is based on the selection, testing and assembly of several miniaturized optical components for use as a nonlinear imaging device. This thesis is the first demonstration of a fibre delivered, microelectromechanical systems mirror with miniaturized optics housed in a portable, hand held package. Specifically, it is designed for coherent anti-Stokes Raman scattering, second harmonic generation, and two-photon excitation fluorescence imaging. Depending on the modality being exploited, different chemical information can be extracted from the sample being imaged. This miniaturized microscope can be applied to diagnostics and treatments of spinal cord diseases and injuries, atherosclerosis research, cancer tumour identification and a plethora of other biomedical applications. The device that will be revealed in the upcoming text is validated by demonstrating all designed-for nonlinear modalities, and later will be used to perform serialized imaging of myelin of a single specimen over time.