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.

Cancer is a major health problem in the world today. Almost all cancers have a significantly better chance for therapy and recovery if detected at their early stage. The capability to perform disease diagnosis at an early stage requires high-resolution imaging that can visualise the physiological and morphological changes at a cellular level. However, resolving powers of current medical imaging systems are limited to sub-millimeter sizes. Furthermore, the majority of cancers are associated with morphological and functional alterations of cells in epithelial tissue, currently assessed by invasive and time-consuming biopsy. Optical imaging enables visualisations of tissue microstructures at the level of histology in non-invasive means. Optical imaging is suitable for detecting neoplastic changes with sub-cellular resolution in vivo without the need for biopsy. Nonlinear optical microscopy based on multi-photon absorption and higher harmonic generation has provided spectacular sights into visualisation of cellular events within live tissue due to advantages of an inherent sectioning ability, the relatively deep optical penetration, and the direct visualisation of intrinsic indicators. Two-photon excited uorescence (TPEF) from intrinsic cell components and second harmonic from asymmetric supermolecular structures can provide complementary information regarding functionalities and morphologies in tissue environments, thus enabling premalignant diagnosis by detecting the very earliest changes in cellular structures. During the past sixteen years, nonlinear optical microscopy has evolved from a photonic novelty to a well-established laboratory tool. At present, in vivo imaging and long-term bedside studies by use of nonlinear optical microscopy have been limited due to the fact that the lack of the compact nonlinear optical instrument/imaging technique forces the performance of nonlinear optical microscopy with bulk optics on the bench top. Rapid developments of fibre-optics components in terms of growing functionalities and decreasing sizes provide enormous opportunities for innovation in nonlinear optical microscopy. Fibre-based nonlinear optical endoscopy will be the soul instrumentation to permit the cellular imaging within hollow tissue tracts or solid organs that are inaccessible with a conventional optical microscope. Lots of efforts have been made for development of miniaturised nonlinear optical microscopy. However, there are major challenges remaining to create a nonlinear optical endoscope applicable within internal cavities of a body. First, an excitation laser beam with an ultrashort pulse width should be delivered eciently to a remote place where ecient collection of faint nonlinear optical signals from biological samples is required. Second, laser-scanning mechanisms adopted in such a miniaturised instrumentation should permit size reduction to a millimeter scale and enable fast scanning rates for monitoring biological processes. Finally, the design of a nonlinear optical endoscope based on micro-optics must maintain great exibility and compact size to be incorporated into endoscopes to image internal organs. Although there are obvious diculties, development of fibre-optic nonlinear optical microscopy/endoscopy would be indispensible to innovate conventional nonlinear optical microscopy, and therefore make a significant impact on medical diagnosis. The work conducted in this thesis demonstrates the new capability of nonlinear optical endoscopy based on a single-mode fibre (SMF) coupler or a double-clad photonic crystal fibre (PCF), a microelectromechanical system (MEMS) mirror, and a gradientindex (GRIN) lens. The feasibility of all-fibre nonlinear optical endoscopy is also demonstrated by the further integration of a double-clad PCF coupler. The thesis concentrates on the following key areas in order to exploit and understand the new imaging modality. It has been known from the previous studies that an SMF coupler is suitable for twoii photon excitation by transmitting near infrared illumination and collecting uorescence at visible wavelength as well. Although second harmonic generation (SHG) wavelength is farther away from the designed wavelength of the fibre coupler than that of normal TPEF, it is demonstrated in this thesis that both SHG and TPEF signals can be collected simultaneously and eciently through an SMF coupler with axial resolution of 1.8 um and 2.1 um, respectively. The fibre coupler shows a unique feature of linear polarisation preservation along the birefringent axis over the near infrared and the visible wavelength regions. Therefore, SHG polarisation anisotropy can be potentially extracted for probing the orientation of structural proteins in tissue. Furthermore, this thesis shows the characterisation of nonlinear optical microscopy based on the separation distance of an SMF coupler and a GRIN lens. Consequently, the collection of nonlinear signals has been optimised after the investigation of the intrinsic trade-off between signal level and axial resolution. These phenomena have been theoretically explored in this thesis through formalisation and numerical analysis of the three-dimensional (3D) coherent transfer function for a SHG microscope based on an SMF coupler. It has been discovered that a fibreoptic SHG microscope exhibits the same spatial frequency passband as that of a fibreoptic reection-mode non-uorescence microscope. When the numerical aperture of the fibre is much larger than the convergent angle of the illumination on the fibre aperture, the performance of fibre-optic SHG microscopy behaves as confocal SHG microscopy. Furthermore, it has been shown in both analysis and experiments that axial resolution in fibre-optic SHG microscopy is dependent on the normalised fibre spot size parameters. For a given illumination wavelength, axial resolution has an improvement of approximately 7% compared with TPEF microscopy using an SMF coupler. Although an SMF enables the delivery of a high quality laser beam and an enhanced sectioning capability, the low numerical aperture and the finite core size of an SMF give rise to a restricted sensitivity of a nonlinear optical microscope system. The key innovation demonstrated in this thesis is a significant signal enhancement of a nonlinear optical endoscope by use of a double-clad PCF. This thesis has characterised properties of our custom-designed double-clad PCF in order to construct a 3D nonlinear optical microscope. It has been shown that both the TPEF and SHG signal levels in a PCF-based system that has an optical sectioning property for 3D imaging can be significantly improved by two orders of magnitude in comparison with those in an SMF-based microscope. Furthermore, in contrast with the system using an SMF, simultaneous optimisations of axial resolution and signal level can be obtained by use of double-clad PCFs. More importantly, using a MEMS mirror as the scanning unit and a GRIN lens to produce a fast scanning focal spot, the concept of nonlinear optical endoscopy based on a double-clad PCF, a MEMS mirror and a GRIN lens has been experimentally demonstrated. The ability of the nonlinear optical endoscope to perform high-resolution 3D imaging in deep tissue has also been shown. A novel three-port double-clad PCF coupler has been developed in this thesis to achieve self-alignment and further replace bulk optics for an all-fibre endoscopic system. The double-clad PCF coupler exhibits the property of splitting the laser power as well as the separation of a near infrared single-mode beam from a visible multimode beam, showing advantages for compact nonlinear optical microscopy that cannot be achieved from an SMF coupler. A compact nonlinear optical microscope based on the doubleclad PCF coupler has been constructed in conjunction with a GRIN lens, demonstrating high-resolution 3D TPEF and SHG images with the axial resolution of approximately 10 m. Such a PCF coupler can be useful not only for a fibre-optic nonlinear optical probe but also for double-clad fibre lasers and amplifiers. The work presented in this thesis has led to the possibility of a new imaging device to complement current non-invasive imaging techniques and optical biopsy for cancer detection if an ultrashort-pulsed fibre laser is integrated and the commercialisation of the system is achieved. This technology will enable in vivo visualisations of functional and morphological changes of tissue at the microscopic level rather than direct observations with a traditional instrument at the macroscopic level. One can anticipate the progress in bre-optic nonlinear optical imaging that will propel imaging applications that require both miniaturisation and great functionality.

<p>This thesis concerns some experimental and theoretical issues in fiber optics. In particular, properties and devices based on photonic crystal fibers (PCFs) are investigated.</p><p>The work can be grouped into three parts. In the first part we use sound to control light in PCFs. The lowest order flexural acoustic mode of various PCFs is excited using an acoustic horn. The acoustic wave acts as a traveling long-period grating. This is utilized to couple light from the lowest order to the first higher order optical modes of the PCFs. Factors affecting the acoustooptic coupling bandwidth are also investigated. In particular, the effect of axial variations in acoustooptic phase-mismatch coefficient are studied.</p><p>In the second part of the thesis we use an electric field to control transmission properties of PCFs. Tunable photonic bandgap guidance is obtained by filling the holes of an initially index-guiding PCF with a nematic liquid crystal and applying an electric field. The electric field introduces a polarization-dependent change of transmission properties above a certain threshold field. By turning the applied field on/off, an electrically tunable optical switch is demonstrated.</p><p>The third part consists of two theoretical works. In the first work, we use relativistic causality, i.e. that signals cannot propagate faster than the vacuum velocity of light, to show that Kramers-Kronig relations exist for waveguides, even when material absorption is negligible in the frequency range of interest. It turns out that evanescent modes enter into the Kramers-Kronig relations as an effective loss term. The Kramers-Kronig relations are particularly simple in weakly guiding waveguides as the evanescent modes of these waveguides can be approximated by the evanescent modes of free space. In the second work we investigate dispersion properties of planar Bragg waveguides with advanced cladding structures. It is pointed out that Bragg waveguides with chirped claddings do not give dispersion characteristics significantly different from Bragg waveguides with periodic claddings.</p>

<p>This Licentiate presents the main results of theoretical study of light propagation in photonic structures, namely lasing disk microcavities and photonic crystals. In the first two papers (Paper I and Paper II) we present the developed novel scattering matrix technique dedicated to calculation of resonant states in 2D disk microcavities with the imperfect surface or/and inhomogeneous refractive index. The results demonstrate that the imperfect surface of a cavity has the strongest impact on the quality factor of lasing modes.</p><p>The generalization of the scattering-matrix technique to the quantum-mecha- nical case has been made in Paper III. That generalization has allowed us to treat a realistic potential of quantum-corrals (which can be considered as nanoscale analogues of optical cavities) and to obtain a good agreement with experimental observations.</p><p>Papers IV and V address the novel effective Green's function technique for studying propagation of light in photonic crystals. Using this technique we have analyzed characteristics of surface modes and proposed several novel surface-state-based devices for lasing/sensing, waveguiding and light feeding applications.</p> / Report code: LIU-TEK-LIC 2006:5

Photonic properties depend on both dielectric contrast in a microscopic composite and the arrangement of the microstructural components. No theory exists for direct prediction of photonic properties, and so progress relies on numerical methods combined with insight into manufacturable composite architectures. We present a discussion of effective photonic crystal production techniques and several numerical methods to predict dispersion relations of hypothetical but fabricable structures. / Singapore-MIT Alliance (SMA)

Lately, there has been an increasing interest in studying the propagation of electromagnetic waves in periodic dielectric structures (photonic crystals). Like the electron propagation in semiconductors, these structures are represented by band diagrams in which gaps can be found where the electromagnetic propagation is forbidden. Much effort is dedicated to find structures that can prohibit the propagation of light in all directions. This effect could lead to light localization. / Singapore-MIT Alliance (SMA)

Colloidal self assembly is an efficient method for making 3-D ordered nanostructures suitable for materials such as photonic crystals and macroscopic solids for catalysis and sensor applications. Colloidal crystals grown by convective methods exhibit defects on two different scales. Macro defects such as cracks and void bands originate from the dynamics of meniscus motion during colloidal crystal growth while micro defects like vacancies, dislocation and stacking faults are indigenous to the colloidal crystalline structure. This paper analyses the crystallography and energetics of the microscopic defects from the point of view of classical thermodynamics and discusses the strategy for the control of the macroscopic defects through optimization of the liquid-vapor interface. / Singapore-MIT Alliance (SMA)

Advanced optical technologies profoundly impact countless aspects of modern life. At the heart of these technologies is the manipulation of light using optical materials. Currently, optical technologies are created using naturally occurring materials. However, a new and exciting approach is to use nanomaterials for technology development. Nanomaterials are artificially constructed material systems with precisely engineered nanostructures. Many technological revolutions await the development of new nanoscale fabrication methods that must provide the ability to control, enhance, and engineer the optical properties of these artificial constructs. This thesis responds to the challenges of nanofabrication by examining glancing angle deposition (GLAD) and improving its optical-nanomaterial fabrication capabilities. GLAD is a bottom-up nanotechnology fabrication method, recognized for its flexibility and precision. The GLAD technique provides the ability to controllably fabricate high-surface-area porous materials, to create structurally induced optical-anisotropy in isotropic materials, and to tailor the refractive index of a single material. These three advantages allow GLAD to assemble optical nanomaterials into a range of complex one-dimensional photonic crystals (PCs). This thesis improves upon previous GLAD optical results in a number of important areas. Multiple optical measurement and modeling techniques were developed for GLAD-fabricated TiO2 nanomaterials. The successful characterization of these nanomaterials was extended to engineer PC structures with great precision and a superior degree of control. The high surface area of basic PC structures was exploited to fabricate an optimized colourimetric sensor with excellent performance. This colourimetric sensor required no power source and no read-out system other than the human eye, making it a highly attractive sensing approach. Incorporating engineered defects into GLAD-fabricated PCs established a new level of design sophistication. Several PC defect structures were examined in detail, including spacing layers and index profile phase-shifts. Remarkable control over defect properties was achieved and intriguing polarization-sensitive optical effects were investigated in anisotropic defect layers. The success of these results demonstrates the precision and flexibilty of the GLAD technique in fabricating optical nanomaterials and advanced photonic devices. / Micro-Electro-Mechanical Systems (MEMS) and Nanosystems

This thesis investigates technologies directed towards developing photonic crystal display devices. A switching technology based on dye electrophoretic motion within a 1D porous photonic crystal was developed. Dissociated absorbing dye species were moved through the assembled device and reflectance was controllably altered by up to 0.4. Refinement of fabrication techniques yielded a slow switching device, whose time-resolved reflectance data was analyzed. A wavelength dependence of the device switching speed was observed. This phenomenon was described by modelling where bandgap effects match observation. These devices may be improved by employing a 3D photonic crystal. We developed a nanoimprint lithography technique for seeding films deposited by GLAD for the fabrication of 3D square spiral photonic crystals. Parameters for patterning a precisely defined mould pattern using electron beam lithography were established. A large area diamond:1 square spiral photonic crystal was fabricated on the nanoimprinted seeds, and it exhibited a visible wavelength bandgap. / Micro-Electro-Mechanical Systems (MEMS) and Nanosystems

The thesis explores preparation and properties of bismuthiron garnet (BIG) films and the incorporation of BIG films intoone-dimensional magneto-optical photonic crystals (MOPCs). Films were prepared by pulsed laser deposition. Weinvestigated or measured crystallinity, morphology,film-substrate interface, cracks, roughness, composition,magnetic coercivity, refractive index and extinctioncoefficient, and magneto-optical Faraday rotation (FR) andellipticity. The investigations were partly performed onselected samples, and partly on two series of films ondifferent substrates and of different thicknesses. BIG filmswere successfully tested for the application of magneto-opticalvisualization. The effect of annealing in oxygen atmosphere wasalso investigated - very careful annealing can increase FR byup to 20%. A smaller number of the above mentionedinvestigations were carried out on yttrium iron garnet (YIG)films as well. Periodical BIG-YIG multilayers with up to 25 single layerswere designed and prepared with the purpose to enhance FR at aselected wavelength. A central BIG layer was introduced asdefect layer into the MOPC structure and generated resonancesin optical transmittance and FR at a chosen design wavelength.In a 17- layer structure, at the wavelength of 748 nm, FR wasincreased from -2.6 deg/µm to -6.3 deg/µmat a smallreduction in transmittance from 69% to 58% as compared to asingle-layer BIG film of equivalent thickness. In contrast tothick BIG films, the MOPCs did not crack. We were first toreport preparation of all-garnet MOPCs and second toexperimentally demonstrate the MOPC principle inmagneto-optical garnets.