The behaviour of surface plasmon polaritons (SPPs) in nanoscale geometries is studied using numerical methods supported by theory and experiment. First, we derive the behaviour of SPPs at graded metal-dielectric interfaces, including dispersion relations, field profiles, propagation velocities, losses, and cutoff wavelength. Numerical simulations show excellent agreement with analytic solutions. In the second part of the thesis we design hybrid vanadium dioxide-plasmonic based absorption switches. The switches are designed and optimized using optical, electrical and thermal simulations. 5 $\mu$m switch designs have extinction ratios exceeding 30 dB and require powers of 10 mW. A switch is fabricated based on the proposed design. A 7 $\mu$m experimental switch reaches 16.4 dB of extinction and requires 64 mW of power, making it one of the most efficient optical switches ever demonstrated in terms of extinction and power consumption. Numerical simulations predict experimental results with a high degree of accuracy.

The behaviour of surface plasmon polaritons (SPPs) in nanoscale geometries is studied using numerical methods supported by theory and experiment. First, we derive the behaviour of SPPs at graded metal-dielectric interfaces, including dispersion relations, field profiles, propagation velocities, losses, and cutoff wavelength. Numerical simulations show excellent agreement with analytic solutions. In the second part of the thesis we design hybrid vanadium dioxide-plasmonic based absorption switches. The switches are designed and optimized using optical, electrical and thermal simulations. 5 $\mu$m switch designs have extinction ratios exceeding 30 dB and require powers of 10 mW. A switch is fabricated based on the proposed design. A 7 $\mu$m experimental switch reaches 16.4 dB of extinction and requires 64 mW of power, making it one of the most efficient optical switches ever demonstrated in terms of extinction and power consumption. Numerical simulations predict experimental results with a high degree of accuracy.

Angiotensinogen is a blood protein that plays a critical role in the regulation of blood pressure in the body. This protein exists in two forms, oxidised and reduced, determined by the presence or absence of a disulfide bridge between Cys 18 and Cys 138. The ratio of oxidised to reduced angiotensinogen is 60:40 in the blood of healthy individuals - an equilibrium that is disrupted in women who develop pre-eclampsia, leading to a higher proportion of oxidised angiotensinogen in the blood. Pre-eclampsia, one of the leading causes of premature births, is a severe and potentially fatal pregnancy condition characterised by the sudden onset of symptoms such as high blood pressure and proteinuria typically during the third trimester. This condition is responsible for an estimated 550,000 deaths globally each year, and with no available treatment or cure other than early delivery of the child, there is a desperate need for a reliable and predictive diagnostic test for this condition. Can we use angiotensinogen as a biomarker for the early diagnosis of pre-eclampsia? Being able to distinguish between reduced and oxidised angiotensinogen and determine the relative amounts of each in blood samples would be of a huge diagnostic value for this condition. This thesis outlines the expression and purification of recombinant human angiotensinogen in Escherichia coli, and the development of an antibody-based SPR assay for angiotensinogen that was subsequently used to probe whether reduced and oxidised angiotensinogen can be distinguished experimentally. The assay developed was sensitive and reproducible, and demonstrated that the reduced and oxidised forms can be distinguished experimentally. The antibody bound the two forms with differential affinity, due to differences in both the association and dissociation rates of the two forms with the monoclonal antibody. Finally, in an attempt to further elucidate the differences between the two redox states of angiotensinogen, molecular dynamic simulations were carried out on angiotensinogen in the presence or absence of the disulfide bond between Cys 18 and Cys 138. These simulations revealed some quite striking differences in the dynamics between the two forms. Reduced angiotensinogen was found to be more dynamic in regions critical for binding to renin, providing a possible explanation for the reported differential affinity that renin displays for the two forms.1 Thus, reduced and oxidised angiotensinogen show some quite distinct differences and can be distinguished in an SPR-based assay, highlighting their potential for use as a biomarker in a diagnostic bioassay.

Polymer waveguides present a potentially low cost alternative to electronics in communication systems. Polymers offer relatively straightforward and economical fabrication when compared to conventional materials. In this study, a fabrication process for Bragg gratings in polymer waveguides was developed. Waveguides were designed using finite-element analysis, patterned via e-beam lithography, and a detailed fabrication method was developed. Surface-Plasmon Resonance (SPR) is a widely accepted method for biological and chemical sensing. Measurement of bulk refractive index changes and specific surface binding is a crucial part in any biosensing. Design and fabrication of a novel self-referencing SPR sensor is described and its functionality is tested.

Surface plasmon waves are TM polarized charge density waves that propagate at the interface of two media with real dielectric constants of opposite sign (i.e. liquid dielectric and certain metals). Surface plasmon resonance (SPR) sensors use these waves to detect refractive index changes adjacent to the metal layer. Refractive index changes arise from the binding of an analyte (e.g. a target molecule, protein, or bacterium) to the functionalized metal layer or from interfering effects such as changes in solution index. Standard, single channel SPR sensors cannot differentiate these two effects as their design allows only one mode to be coupled. This novel self-referencing technique employs two surface plasmon modes to simultaneously measure surface binding and solution refractive index. Dual surface plasmon modes are achieved by matching the refractive indices on either side of the metal film. The two modes generated - symmetric, long-range surface plasmon (LRSP) and anti-symmetric, short-range surface plasmon (SRSP) - have different field profiles and hence assist in differentiating solution refractive index changes from surface layer formation. Amorphous Teflon, with a refractive index close to water, is chosen as the buffer layer and gold is chosen as the metal layer. Magnesium fluoride, with a higher index than Teflon, is used as the buffer layer when using ethanol as the base solution. The sensor operation was optimized through simulations to yield higher sensitivity, lower reflectivity and resonances within the spectrometers range. Optimization results showed good performance over a wide range for Teflon, MgF2 and gold thicknesses which helped in the fabrication of the sensor. Demonstration of self-referencing operation was done through two different sets of experiments: (1) formation of an alkanethiol self-assembled monolayer on gold in the presence of ethanol and methanol solutions having different refractive indices and (2) streptavidin-biotin binding with solutions of different NaCl concentration and thus different refractive indices. In both these experiments, the resonance wavelengths were accurately predicted, reflectivity varied by 10-15% and sensitivity by 25% from that of the simulated values.

Surface plasmon resonance (SPR) sensors are advantageous to other techniques of sensing chemical binding, offering quantitative, real-time, label-free results. Previous work has demonstrated the effectiveness of using dual-mode SPR sensors to differentiate between surface and background effects, making the sensors more robust to dynamic environments. This work demonstrates a technique that improves upon a previously optimized planar film dual-mode SPR sensor’s LOD by introducing a periodic array of subwavelength nano-gaps throughout the plasmon supporting material. First, general figures of merit for a sensor having an arbitrary number of modes are studied. Next, the mode effective index dispersion and magnetic field profiles of the two strongly bound modes found using a gap width of 20nm are analyzed. Qualitative analysis of the results demonstrates how such a design can enable better LODs in terms of each figure of merit. By optimizing a nano-gap enhanced sensor containing 20nm gaps, it is quantitatively demonstrated that the resulting modes improve upon almost every figure of merit, especially with respect to the orthogonality and magnitude of the sensitivity vectors, resulting in LODs approximately a factor of five less than the optimal planar design.

Surface plasmons are bound TM polarized electromagnetic waves that propagate along the interface of two materials with real dielectric constants of opposite signs. Surface plasmon resonance (SPR) sensors make use of the surface plasmon waves to detect refractive index changes occurring near this interface. For sensing purposes, this interface typically consists of a metal layer, usually gold or silver, and a liquid dielectric. SPR sensors usually measure the shift in resonance wavelength or resonance angle due to index changes adjacent to the metal layer. However this restricts the limit of detection (LOD), as the regions of low slope (intensity vs. wavelength or angle) in the SPR curve contain little information about the resonance. This work presents the technique of tunable laser interrogation of SPR sensors. A semiconductor laser with a typical lasing wavelength of 650nm was used. A 45nm gold layer sputtered on a BK7 glass substrate served as the sensor. The laser wavelength is tuned to always operate in the region of highest slope by using a custom-designed LabVIEW program. It is shown that the sensitivity is maximized and LOD is minimized by operating around the region of high slope on the SPR curve.

This thesis is focused on nanofabrication and its application in plasmonic chemical and bio- sensors. The contribution thus is the development of novel nanofabrication techniques and nano- structures for the sensors based on surface plasmon (SP). Part I (Chapter 1-3) is about novel nanofabrication techniques, especially nanoimprint lithography (NIL) and electron beam lithography (EBL). For NIL, the four major aspects of NIL were discussed, including the resist, mold, imprint process and equipment for NIL. Combined with NIL and soft lithography, hybrid nanoimprint-soft lithography was investigated. To overcome the difficulty of mold fabrication, a more robust solution of mold fabrication through a sacrificial poly(dimethyl glutarimide) (PMGI) master mold was designed in this work. Based on this method, the mold was fabricated without structure distortion, and pattern replication with sub-10 nm resolution was demonstrated. For EBL, several aspects were discussed to improve the performance of EBL, including the resist, development, and exposure condition. The charging effect to the pattern distortion was studied systemically for the electron beam exposure in large area with high current (>nA). Tilted periodic nanostructure was achieved by electron beam scanning on tilted sample with dynamic focus mode. EBL on irregular surface was realized by the exposure on evaporated polystyrene. Part II (Chapter 4-6) is the application in surface plasmonic chemical and bio-sensors. The first type of sensors is surface enhanced Raman scattering (SERS) sensor based on localized SP. Bowtie-shape nano-antenna structures of sub-10 nm gap were fabricated with the breakthrough of EBL resolution to 3 nm by exposing resist on Si3N4 membrane. By controlling the gap size during lithography, the surface plasmon enhancement was tuned accurately. High sensitivity of Au bowties antenna with sub-10 nm gap was achieved at low concentration of the target molecule (10^-7 mM, 1,2-di(4-pyridyl)ethylene in ethanol solution) and high enhancement of 10^7 resulting from the corresponding bowtie structure. The second type of sensors is extraordinary optical transmission (EOT) sensor based on propagating SP. The process of double liftoff was developed for the fabrication of nano-hole arrays on 100 nm-thick Au film utilizing EBL. This technique is versatile for the fabrication of many kinds of high-aspect-ratio noble metal structures. Additionally, annealing method was employed in this work to improve the smoothness of Au film. It was found that the RMS roughness of the deposited film was reduced by 72 % and the sensitivity was increased by 32 nm/RIU as a result of annealing. It was also found that the optical transmission intensity of the annealed NHA of similar hole diameter was increased more than twice which is due to the smaller absorption/scattering of the incident light and surface waves from the Au film surface. Besides the double liftoff process, several techniques were developed for EOT structures, including electroplating, imprint method, and deposition on membrane.

Surface plasmon-polaritons are optical surface waves formed through the interaction of photons with free electrons at the surface of metals. They offer interesting applications in a broad range of scientific fields such as physics, chemistry, biology, and material science. However, many of such applications face limitations imposed by the high propagation losses of these waves at visible and near-infrared wavelengths, which result mainly from power dissipation in the metal. In principle, the propagation losses of surface plasmon-polaritons can be compensated through optical amplification. The objective of this thesis is to provide deeper insights on the physics of surface plasmon-polariton amplification and spontaneous emission in surface plasmon-polariton amplifiers through theoretical and experimental vehicles applied (but not necessarily restricted) to a particular plasmonic mode termed long-range surface plasmon-polariton. On the theoretical side, the objective is approached by developing a realistic theoretical model to describe the small-signal amplification of surface plasmon-polaritons in planar structures incorporating dipolar gain media such as organic dye molecules, rare-earth ions, and quantum dots. This model takes into account the inhomogeneous gain distribution formed near the metal surface due to a non-uniform excitation of dipoles and due to a position-dependent excited-state dipole lifetime that results from near-field interactions between the excited dipoles and the metal. Also, a theoretical model to describe the amplified spontaneous emission of surface plasmon-polaritons supported by planar metallic structures is developed. This model takes into account the different energy decay channels into which an exited dipole located in the vicinity of the metal can relax. The validity of this model is confirmed through experimentation. On the experimental side, the objective is approached by providing a direct experimental demonstration of complete loss compensation in a plasmonic waveguide. The experiments are conducted using the long-range surface plasmon-polariton supported by a symmetric thin gold waveguide incorporating optically pumped organic dye molecules in solution as the gain medium. Also, an experimental study of spontaneous emission in a long-range surface plasmon-polariton amplifier is presented. It is shown that this amplifier benefits from a low spontaneous emission into the amplified mode, which leads to an optical amplifier with low noise characteristics. The experimental setup and techniques are explained in detail.

Protein-protein and protein-molecule interactions are complicated phenomena due to the tendency of proteins to change shape and function in response to their environment. Protein aggregation whether onto surfaces or in solution, can pose numerous problems in industry. Surface plasmon resonance (SPR) devices and quartz crystal microbalances (QCM) are two real-time, label free methods that can be used to detect the interactions between molecules on surfaces. These devices often employ self-assembled monolayers (SAMs) to produce specific surfaces for studying protein-protein interactions. The objective of this work was to develop methodologies utilizing SPR to better understand protein-protein and protein-molecule interactions with possible applications in the food and separation industrial sectors. A very well characterized whey protein, β-lactoglobulin (BLG), is used in numerous applications in the food industry. BLG can undergo different types of self-aggregation due changes in external environment factors such as buffer strength, pH or temperature. In this work, a hydrophilic SAM was developed and used to study the interaction and non-specific adsorption of BLG and palmitic acid (PA), a molecule which is known to bind to BLG. It was found that PA tended to reduce BLG conformational changes once on the surface, resulting in a decrease in its surface adhesion. Fluorescent excitation emission matrices (EEM’s) using a novel fluorescence probe technique were utilized to detect protein on the surface as well as conformational changes on the surface of the sensor, although the extent these changes could not be quantified. Another whey protein, α-lactoglobulin (AL), was utilized as a surrogate protein to study the adsorption of colloidal/particulate and protein matter (CPP) extracted from filtration studies of river water. A large fraction of natural organic matter (NOM), the major foulant in membrane based water filtration, is CPP and protein. Understanding the interactions between these components is essential in abating NOM membrane fouling. Several SPR methods were investigated in order to verify the interactions. A mixture of AL and CPP particles in solution prevented the non-specific adsorption of AL to the SAM surface. This change in association was then detected through SPR. Fluorescent EEM’s of the sensor surface verified that CPP and AL bound to the surface. This finding has fundamental significance in the interpretation of NOM-based membrane fouling. To better understand the mechanisms behind non-specific adsorption, a mechanistic mathematical model was developed to describe the adsorption of BLGs onto the hydrophilic SAM. The resulting model performed well in terms of predicting adsorption based on SPR data. The model incorporated the monomer-dimer equilibrium of BLG in solution, highlighting the impact of protein aggregation on non-specific adsorption mechanisms. For future studies, improvement in fluorescent FOP surface scan methodology would help identify different protein/molecules and conformations on the surface.