This dissertation covers a broad range of research topics all towards the ultimate goal establishing of a novel type of biosensor in which the biocompatible membrane structure reconstituted with functional transmembrane proteins is utilized as the sensing element. It focuses on 1) examining the activity of a model transmembrane protein, bovine rhodopsin (Rho) when reconstituted into stabilized lipid membranes and 2) the instrumentation of a novel type of optical spectroscopy, plasmon waveguide resonance (PWR), which is a surface sensitive technique and its application in sensing biological events.Lipid membrane play crucial roles in cell function. Their biophysical properties affect the activity of a large amount of transmembrane receptors. They are great candidates for biosensing/ biomedical coating. However, the intrinsic instability of natural or fluid membranes prevents them to be used in a device. Studies have been done to show indirect evidence that the activity of Rho maybe maintained in polymerized membrane composed of bis-SorbPC lipids. The activity of Rho reconstituted into vesicular membranes comprised of various lipids was studied by a more direct technique, UV-Vis. It was found Rho activity was maintained to 66% of that in natural Egg PC lipid in the mixture of Egg PC:(poly)bis-SorbPC (1:1 mol:mol) as opposed to minimal values in 100 % (poly)lipids.A new type of spectral PWR was developed. The working concept, technical characterization and comparisons with similar techniques were discussed and compared in this work. A modified version of angular PWR in which lipid bilayers were formed by vesicle fusion was also developed. This method excludes possible effects from a high boiling point organic solvent on either the lipid bilayer itself or the membrane proteins associated with it. A calculating program NphaseAll for PWR was developed to do predictions of waveguide properties can be made to provide guidance for waveguide design. Theoretical calculations were done for PWR and experimental results were compared with the theoretical predictions.PWR was used to detect the formation of a biological lipid membrane, the association of alpha synuclein with membranes and the binding activity of human melanarcortin to its ligands in fluid and polymerized/dried membranes.

Patterned arrays of metallic nanostructures are commonly used in photonics, electronics, as well as functional materials and biotechnology because of their unique electronic and optical properties. Although great effort has been devoted to the development of nano-patterning techniques in the past decades, there are still existing challenges for nano-fabrication to achieve fine resolution and complex features over macroscopic areas in a reasonable time period. Herein, we devise two versatile patterning strategies, namely indentation colloidal lithography (ICL) and oblique colloidal lithography (OCL), for the stepwise patterning of planar substrates with numerous complex and unique designs. Those strategies combine colloidal self-assembly, imprint molding in conjunction with capillary force lithography and reactive ion etching, all of which are simple and straightforward. Hexagonal arrays of symmetric and nonconcentric gold features are fabricated on glass substrates with highly controllable geometric parameters. The width, size and asymmetry of each surface structure could be tuned down to the ~10 nm level while the scale of the patterned area could exceed 1 cm^(2). Moreover, our technique also leads to the ability to develop an enormous variety of patterns through stepwise amplification of feature types. In particular, some of the features are fabricated for the first time, including target-triangle, hexagram, hexagram-dot and triangle-dot. Distinctive surface plasmon resonance (SPR) properties, such as higher order surface plasmon modes and Fano resonances are both observed from our patterns, which would be highly desired forthe study of plasmonic coupling. In addition, we have demonstrated a surface orientation dependent Raman selectivity on two nano-structures for the first time. Molecular vibrations with opposite symmetries can be selectively enhanced on different substrates. As a demonstration, this property is applied to the odd-even effect of n-alkanethiol self-assembly monolayers (SAMs) on the gold surface. The alternative alternation of the intensity ratios of two vibration pairs have been shown by surface enhanced Raman spectroscopy (SERS) as a function of the number of carbon atoms. The results obtained exhibit high sensitivity and excellent agreement with previous publications.

Surface plasmon is a collective oscillation behavior of electrons in metal nanoparticle induced by the excitation of incident light, which can create an enhanced localized electric field near the surface of metal nanoparticle. To date, metal nanoparticle surface plasmon resonances have been extensively studied in the photoluminescence domain; little work however was devoted to electroluminescent and photovoltaic research. In this thesis, as a fundamental study we firstly investigated surface plasmon enhanced europium complex luminescence and obtained an improved understanding of the importance of optical spacer in metal enhanced fluorescence phenomenon. Under this guideline, we incorporated metal NPs into organic light emitting diodes (OLED) and organic solar cells, by means of thermal evaporation and wet chemistry. Metal nanoparticles are demonstrated to enhance the efficiency of both OLEDs and solar cells only under tailored device architecture. The surface plasmon enhanced local electric field plays an important and comprehensive role in enhancing device performance. In Alq3 based OLED we observed increased charge carrier injection by depositing Ag nanoparticles underneath the Al cathode; in Ir(ppy)3 based OLED we gained enhanced luminous efficiency via doping silica functionalized Ag nanoparticles into emitting layer; in P3HT based organic polymer solar cell we noticed an increased polymer absorption by incorporating Ag nanoparticles over the active layer. On the other hand, adverse effects such as metal nanoparticle induced charge carrier recombination and light extinction are also observed. The study of surface plasmon effects in organic optoelectronic devices reveals interesting surface plasmon features and permits to optimize optoelectronic devices from a novel point of view. / Thesis (Ph.D, Chemistry) -- Queen's University, 2012-01-05 17:22:40.074

A novel surface plasmon resonance sensor is fabricated to evaluate its use in biochemical sensing. The sensor can differentiate between bulk refractive index changes and surface binding reactions of interest. There has been a great interest in developing sensors to differentiate biological or chemical agents from interfering effects, but they still remain in research phase. In this work, a prism coupler is used to simultaneously excite both long and short range surface plasmon modes of the sensor. The differing sensitivities of the long and short range modes allow one to distinguish surface binding reactions of interest from refractive index fluctuations. In this thesis, we have demonstrated the sensors self referencing capability by detecting the formation of an octadecanethiol self assembled monolayer while varying solution refractive index.

Integrated optics present a potentially low cost and higher performance alternative to electronics in optical communication systems. Surface plasmon waveguides (SPWGs) offer a new approach for manipulating light in integrated optical chips. SPWGs provide several advantages over dielectric waveguides. In this study, a fabrication process for SPWGs is developed. SPWGs are fabricated with various lengths and bend radii to allow for study of absorption and bending losses in the waveguides at telecommunications wavelengths (~1550nm). Finite-element method models of straight, bent, and optically coupled waveguides are developed and analyzed.

This thesis report works on optically characterizing waveguide based biosensors consisting of thin, narrow Au stripes embedded in CYTOP. The devices were examined using an ever evolving and improving interrogation setup, variations of which are described in detail in this document. A number of changes were made to the setup configuration in order to reduce noise levels and increase efficiency and accuracy of acquired measurements. Waveguides of varying configurations (straight waveguides and Mach-Zehnder Interferometers with etched and cladded channels) are described and optically characterized. The characterization results of these devices are presented in this thesis. Bulk index measurements are carried out in order to determine a suitable bio-sensing solution with a refractive index matched to that of CYTOP. Step index measurements clearly distinguishing the introduction of sensing solutions of refractive indices varying from one another, are made available. Preliminary bio-sensing experiments involving detection of change in refractive index of sensing fluid as well as adlayer thickness with the introduction of analytes binding to the waveguide surface that has been functionalized with antibodies, using both straight and cladded waveguides with single mode outputs are studied.

As the developments in nanoscale fabrication and characterization technology, the investigation and applications of light in metal nanostructures have been becoming one of the most focused research areas. Metal materials allow to couple the incident light energy into electromagnetic waves propagating on the metal surface under certain configurations, which is called surface plasmon (SP). This feature tremendously expanded the application possibility of metals in optical regime, such as extraordinary transmission (EOT), near-field optics and surface enhanced spectroscopies. In this talk, various metal structures will be demonstrated which could control SP’s propagation, resonance andlocal field enhancement. A number of SP applications are benefited – the plasmonic bragg reflector (PBR), the frequency sensitive plasmonic microcavity, the subwavelength metallic taper, the long range surface plasmon (LRSP) waveguide and surface enhanced Raman spectroscopy (SERS). Especially for SERS, long-term effort was devoted into it to achieve the single molecule detection limit. / Graduate

Heat shock protein 70 (HSP70) is an important health related biomarker, being implicated as an early stage cancer marker and as an indicator of cardiac health. It also has important implications in wildlife environmental monitoring, as its levels can be affected by food deprivation, elevated temperatures, and pollution. Therefore, the use of HSP70 as a biomarker is highly desirable, yet the current methods of quantifying HSP70 are time consuming, expensive, and require dedicated labs. In order to facilitate widespread use of the HSP70 biomarker, a quantification tool that can be used at the point-of-care is needed. This implies the development of a simple and inexpensive HSP70 biosensing technique that is highly sensitive and selective. Therefore, in this work a label-free HSP70 biosensor has been designed based on the optical properties of gold nanoparticles (NPs). Gold NPs exhibit a large absorbance peak in the visible spectrum due to localized surface plasmon resonance (LSPR). The peak position is dependent on the local refractive index, which can be employed as a biosensor by selectively capturing the target analyte to the NP surface. To design an LSPR HSP70 sensor, optical and fluidic simulations were developed to determine optimal NP geometries and microchannel dimensions. The results showed optimal response when using 100nmx5nm gold nanotriangles inside of a 100μmx100μm microchannel. Simulations of the sensor performance showed HSP70 detection from 0.92-4000ng/ml with a resolution of 1.1ng/ml, all of which satisfied the design requirements. An LSPR sensor was experimentally tested at the benchtop scale to prove the concept. Gold NPs were fabricated by electron beam lithography and enclosed in a polymer flow cell. For initial testing of the LSPR sensor, the NPs were functionalized with biotin for selective capture of streptavidin. Streptavidin was detected in real time over the range 55-500,000ng/ml. The use of bovine serum albumin (BSA) was shown to be necessary to block non-specific binding sites to ensure a streptavidin-specific response. The LSPR sensor was then demonstrated to detect salmon HSP70 at 4600ng/ml using its synthetic antibody. Overall, these results demonstrate that LSPR can be used to realize an HSP70 biosensor suitable for point-of-care applications.

The study and applications of surface plasmon polaritons (SP) – also known as plasmonics – has attracted the interest of a wide range of researchers in various fields such as biology, physics, and engineering. Unfortunately, the large propagation losses of the SP severely limit the usefulness of plasmonics for many practical applications. In this dissertation a new wave guiding mechanism is proposed in order to address the large propagation losses of the plasmonic guides. Possible applications of this guiding scheme are also investigated. The proposed hybrid plasmonic waveguide (HPWG) consists of a metal layer separated from a high index slab by a low index spacer. A detailed analysis is carried out to clarify the wave guiding mechanism and it is established that the mode guided by the HPWG results from the coupling of a SP mode and a dielectric waveguide mode. A two dimensional HPWG is proposed and the effects of various parameters on the HPWG performance are analyzed in detail. This structure offers the possibility of integrating plasmonic devices on a silicon platform. The proposed waveguide supports two different modes: a hybrid TM mode and a conventional TE mode. The hybrid TM mode is concentrated in the low index layer, whereas the conventional TE mode is concentrated in the high index region. This polarization diversity is used to design a TM- and a TE-pass polarizer and a polarization independent coupler on a silicon-on-insulator (SOI) platform. Moreover, the performance of a HPWG bend is investigated and is compared with plasmonic waveguide bends. The proposed devices are very compact and outperform previously reported designs. The application of HPWG for biosensing is also explored. By utilizing the polarization diversity, the HPWG biosensor can overcome some of the limitations of plasmonic sensors. For example, unlike plasmonic sensors, the HPWG biosensor can remove the interfering bulk and surface effects.

Strongly localised plasmons in metallic nano-structures offer exciting characteristics for guiding and focusing light on the nano-scale, opening the way for the development of new types of sensors, circuitry and improved resolution of optical microscopy. The work presented in this thesis focuses on two major areas of plasmonics research - nano-focusing structures and nano-sized waveguides. Nano-focusing structures focus light to an area smaller than the wavelength and will find applications in sensing, efficiently coupling light to nano-scale devices, as well as improving the resolution of near field microscopy. In the past the majority of nano-focusing structures have been nano-scale cones or tips, which are capable of focusing light to a spot of nano-scale area whilst enhancing the light field. The alternatives are triangular nano-focusing structures which have received far less attention, and only one type of triangular nano-focusing structure is known – a sharp V-groove in a metal substrate. This structure focuses light to a strip of nano-scale width, which may lead to new applications in microscopy and sensing. The difficulty with implementing the V-groove is that the structure is not robust and is quite difficult to fabricate. This thesis aims to develop new triangular nano-focusing devices which will overcome these difficulties, whilst still producing an intense light source on the nano-scale. The two proposed structures presented in this thesis are a metallic wedge submerged in uniform dielectric and a tapered metal film lying on a dielectric substrate, the latter being the easier to fabricate and the more structurally sound and robust. The investigation is performed using the approximation of continuous electrodynamics, the geometrical optics approximation and the zero-plane method. The second aim of this thesis is to investigate plasmonic waveguides and couplers for the development of nano-optical circuitry, more compact photonic devices and sensors. The research will attempt to fill the gaps in the current knowledge of the V-groove waveguide, which consists of a sharp triangular groove in a metal substrate, and the gap plasmon waveguide, which consists of a rectangular slot in a thin metal film. The majority of this work will be performed using the author’s in house finite-difference time-domain algorithm and FEMLAB as well as the effective medium method and geometric optics approximation. The V-groove may be used as either a nano-focusing or waveguiding device. As a waveguide the V-groove is one of the most promising plasmonic waveguides in the optical regime. However, there exist quite a number of gaps in the current knowledge of V-groove waveguides which this thesis will attempt to fill. In particular, the effect of rounded groove tip on plasmon propagation has been assessed for the V-groove. The investigation of rounded groove tip is important, as due to modern fabrication processes it’s not possibly to produce an infinitely sharp groove, and the existing literature has not considered the impact of this problem. The thesis will also investigate the impacts of the inclusion of dielectric filling in the groove on plasmon propagation parameters. This research will be important for optimising the propagation characteristics of the mode for certain applications, but it may also lead to easier methods of fabricating the V-groove device and prevent oxidation of the metal film. The gap plasmon waveguide is easier to fabricate than the V-groove, and is a new type of sub-wavelength waveguide which displays many advantages over other types of plasmon waveguides, including ease of fabrication, almost 100% transmission around sharp bends, sub-wavelength localisation and long propagation distances of the guided mode, etc. This waveguide may prove invaluable in the development of compact photonic devices. In the past the modes supported by this structure were not thoroughly analysed and the possibility of using this structure to develop sub-wavelength couplers for sensing and nano-optical circuits was not considered in detail. This thesis aims to resolve these issues. In conclusion, the results of this thesis will lead to a better understanding of Vgroove and gap plasmon waveguide devices for the development of nano-optical circuits, compact photonic devices and sensors. This thesis also proposes two new nano-focusing structures which are easier to fabricate than the V-groove structure and will lead to applications in sensing, coupling light efficiently into nano-scale devices and improving the resolution of near-field microscopy.