Thesis (Ph. D.)--University of Canterbury, 2008. / Typescript (photocopy). "January, 2008." Includes bibliographical references (p. 179-206). Also available via the World Wide Web.

Thesis (Ph. D.)--Ohio State University, 2008. / Title from first page of PDF file. Includes vita. Includes bibliographical references (p. 110-118).

archives@tulane.edu / G protein-coupled receptors (GPCRs) are the largest family of proteins in humans and are expressed widely throughout the body. GPCRs consist of seven-transmembrane helices that bind extracellular ligands to initiate intracellular downstream signaling via interaction with G proteins, and function in many short and long-term responses in the body, including taste, immune function, and sugar sensing. Extracellular binding and the coupled downstream signaling pathway means that GPCRs are ideal drug targets for many diseases, making them of great interest to the pharmaceutical industry. Some GPCRs have been crystallized in an effort to better elucidate the structure-function relationship to aid in the design of novel therapeutics. The adenosine A2A receptor (A2AR) is a GPCR that has been crystallized bound to agonist, antagonist, and G protein. Although these crystal structures are informative in regards to A2AR structure when associated with binding partners, all current crystal structures truncate nearly 100 amino acids of the C-terminus. As a crystallization strategy, this truncation makes sense considering the C-terminus is long and unstructured. However, truncating roughly 25% of the protein, as well as making other point mutations calls into question the authenticity of the crystal structures in reflecting functional receptor and thus their potential value for therapeutic design. Beyond structural studies, biophysical characterization of drug binding to receptors in vitro to predict efficacy in vivo has shifted away from measures of affinity and selectivity and towards determination of kinetic rates. Kinetic rate constants in combination with affinity and drug residence time are thought to be better predictors of drug behavior in vivo. For these reasons, this thesis focuses on experiments to characterize A2AR kinetic rate constants. Previously, our lab showed that truncating the A2AR C-terminus reduced downstream cAMP signaling in mammalian cells, although where the effect on the signaling pathway occurred was not determined. Here, we report that truncation of the C-terminus ablates receptor association to Gαs, the first step in signaling. In this work, A2AR ligand binding kinetics, stability, and association to Gαs are characterized to better delineate the importance of interactions between receptor and stimuli in a way that is impactful to drug design. / 1 / Kirsten Swonger Koretz

In this work, we investigated nano-metal plasmonic coupling between dissimilar metals. We measured the optical transmission of nano-Ag coupled to other nano-metals using glass and Si substrates respectively. The reflected colors shifted from yellow to violet were obtained through the plasmonic coupling with nearest-neighbor nano-metals such as aluminum, magnesium, and ytterbium nano-metals. They were deposited randomly next to the nano-Ag. The metal size is from 8 to 15 nanometers. The results show that the colors changing is essentially due to plasmonic coupling between nano-Ag and another the nano-metals e.g. nano-Al The coupling caused a red shift in plasmonic resonance frequency, thus, changing the reflection color. The resonance shift agrees well with the simulation result using COMSOL. The inter-particle distance and particle size dependency of the optical spectra correspond to surface plasmon resonance extinction peaks for isolated nano-Ag and coupled with those neighboring nano- metals. Due to plasmonic coupling between nanoparticles in small space can create new resonances; red shifts as the interparticle distance reduce. Wavelengths are tuned by the extent of the interparticles interactions which relate to the particles size, interparticles distance and the similarity of nano metals. Using different nano metals to fabricate thin films can change the plasmonic resonance frequency which makes the reflected colours become multihued. When we look into the effect of the nano-particle size, and the distance between nano-particles, we discovered that larger nano-particle size has larger distance between the particles, and since the plasmonic coupling is a function of Inverse Square of the distance between particles. Therefore, smaller nano-particles have the strongest plasmonic coupling. Al produced the smallest nano-particle therefore it has the shortest distance between nano-Al and nano-Ag. Since the size of the particles can be controlled during deposition, the color changing of nano-Ag can be well defined. Thus tunable color changing devices can be fabricated

An electrochemical detection method based on long range surface plasmon waveguides is proposed and demonstrated in this integrated article thesis. This dissertation uses CYTOP gold (Au) waveguides supporting long range surface plasmon polaritons (LRSPPs) in conjunction with grating couplers as well as Au waveguides embedded on a one-dimensional photonic crystal (1DPC) supporting Bloch LRSPPs integrated grating couplers. Grating couplers for Au stripe waveguides embedded in Cytop are demonstrated and analyzed. Grating couplers are used in a broadside coupling scheme where a laser beam incident on a stripe of Au on Cytop. The use of gratings for excitation of LRSPPs simplifies optical alignment and does not require high-quality input and output edge facets. Over a broad operating wavelength range, optical experiments are performed to demonstrate coupling loss and determine the efficiency of grating coupling using both a cleaved bow-tie PM fiber and a lensed PM fiber. The coupling loss and grating coupling efficiency of both types of fibers are also calculated numerically. Fluoropolymers with refractive indices close to water, such as CYTOP, are widely used to make waveguide biosensors today. Due to its low glass transition temperature, CYTOP presents limitations to fabrication processes. A truncated 1D photonic crystal may replace a low-index polymer cladding such as CYTOP to support Bloch LRSPPs within the bandgap of the 1DPC over limited wavenumbers and wavelength range. As a result of the high sensitivity of Au stripe Bloch LRSPP waveguide biosensors and their compatibility with high levels of integration, microelectrode systems that can be integrated with such optical biosensors are examined. A chip bearing a Au LRSPP waveguide that can also function as a working electrode (WE), a Pt counter electrode (CE), and Pt/Cu electrical contact pads, is used to demonstrate the electrochemical performance of LRSPPs waveguides. The cyclic voltammetry measurements were performed at different scan rates and concentrations of potassium ferricyanide as the redox species on Au LRSPPs waveguides. By fitting our experimental data to the Randles-Sevcik equation, we find the diffusion coefficient of potassium ferricyanide. The results from CV measurements obtained from chips are compared with commercial macroscopic electrodes. The CV measurements are also compared with theoretical results computed using the Butler-Volmer equation to determine the rate constant of the redox species at zero potential. A waveguide containing a stripe of Au that propagates infrared surface plasmon polaritons (SPPs), acting simultaneously as an electrode in a three-electrode electrochemical cell is also examined. Under SPP excitation, cyclic voltammetry was measured as a function of incident optical power and wavelength (1350 nm). In oxidation and reduction reactions, energetic electrons are separated from energetic holes. Under SPP excitation, redox current densities increase by 10×. With the SPP power, the oxidation, reduction, and equilibrium potentials drop by as much as 2× and separate in correlation with the photon energy. According to electrochemical impedance spectroscopy, charge transfer resistance dropped by almost 2× under SPP excitation. During SPP excitation, the temperature of the working electrode is monitored in situ and independent control experiments are performed to isolate thermal effects. Measurements of chronoamperometry with SPPs modulated at 600 Hz yield a rapid current response modulated at the same frequency, ruling out thermally enhanced mass transport. The observation is attributed to the opening of optically controlled non-equilibrium redox channels associated with the energetic carrier transfer to the redox species. During CV and chronoamperometry measurements, convolutional voltammetry is performed by monitoring the SPP output power versus the applied voltage. Using both experimental and theoretical methods, we demonstrate that the SPP output power is proportional to the electrochemical current convolution. A SPP voltammogram confirms that signal changes are mainly caused by differences in refractive index between reduced and oxidized forms of redox species. In addition, we demonstrate that energetic carriers resulted from SPP absorption significantly improved electrochemical sensitivity. As a complementary electrochemical technique, convolutional voltammetry is useful since the signal is related directly to the concentration of electroactive species on the working electrode (WE) and independent of the scan rate. As a probe of electrochemistry taking place in waveguides, surface plasmon polaritons (SPPs) propagating along one are sensitive. In such a waveguide, the optical output power is proportional to the time convolution of the electrochemical current density, eliminating the need to calculate the latter a posteriori via numerical integration. It is demonstrated that a waveguide WE provide an optical response that can be experimentally validated by chronoamperometry and cyclic voltammetry measurements under SPP excitation for a few potassium ferricyanide (redox species) concentrations in potassium nitrate (electrolyte) and various scan rates. Cyclic voltammetry measurements taken under increasing SPP power produce a regime where SPPs no longer act solely as the probe, but also act as a pump, producing energetic electrons and holes via their absorption in the WE. The energetic carriers enhance (10×) redox current densities as well as the convolution signal measured directly as the optical output power over time.

During the COVID-19 outbreak, PCR tests were widely used for large-scale testing and screening. Yet, this technique requires bulky and time-consuming procedures to prepare the samples collected from the patients before their analysis by well-trained experts with expensive and specific equipment. PCR is therefore not competitive as a technique of detection for a widespread and rapid use in point-of-care sites. Thus, the COVID-19 pandemic highlighted the need for cheap and easy-to-implement biosensors. Surface plasmon resonance based sensors were suggested as a promising alternative in recent years. Indeed, they enable real-time and label-free detection of a wide range of analytes. That explains their widespread use in various fields of applications such as pharmacology, toxicology, food safety, and diagnosis. This thesis proposes and demonstrates a new plasmonic configuration of detection, which can address challenges posed by point-of-care settings. The gratings used as transducers in this configuration were fabricated based on laser interference lithography combined with a nanoimprinting process. The responses of these nanostructures interrogated by a p-polarized light beam result in a transfer of energy between two diffracted orders over an angular scan. This optical phenomenon termed as “optical switch”, was theoretically and experimentally investigated and optimized. The principle of detection based on this specific configuration was demonstrated for the detection of small variations in the bulk refractive index with solutions comprised of different ratios of de-ionized water and glycerol. A limit of detection in the range of 10−6 RIU was achieved. In addition, preliminary bio-assays obtained by combining this configuration with a functionalization are presented and demonstrate the selectivity and the potential of this new plasmonic configuration for biosensing applications. This thesis work paves the way for the use of the optical switch configuration as a biosensor aligned with low-cost manufacturing and relevant for diagnosing in point-of-care sites.

No description available.

The Microelectronics Group has been researching sensors useful for detecting and quantifying events in biological molecular chemistry, for example, binding events. Our previous research has been based primarily on quartz resonators. This thesis describes the results of our initial research of Surface Plasmon Resonance (SPR) based technology. This study contains the design and implementation of a fully functional SPR biosensor with detailed disclosure of monolayer construction, digital hardware interfaces and software algorithms for process the SPR sensors output. An antibody monolayer was constructed on the biosensor surface with the goal of setting the strengths, weaknesses and limitation of measuring molecular events with SPR technology. We documented several characteristics of molecular chemistry that directly effect any measurements made using Surface Plasmon Resonance technology including pH, free ions, viscosity and temperature. Furthermore, the component used in our study introduced additional limitations due to wide variations amongst parts, the constraint of a liquid medium and the large surface area used for molecular interrogation. We have identified viable applications for this sensor by either eliminating or compensating for the factors that affect the measured results. This research has been published at the inaugural IEEE sensors conference and to our knowledge is the first time a biosensor has been constructed by attaching a sensor to a PDA and performing all signal processing, waveform analysis and display in the PDAs core processor.

Over the past few years, surface plasmon photodetectors have been of renewed interest. This is due to their unique double functionality of combining an SPP waveguide structure with a photodetection structure. This thesis investigates the performance of a Schottky nano-photodetector integrated into a finite width metal stripe which is covered by air on top and supported by silicon at the bottom, supporting the propagation of bound SPP modes. Properties of surface plasmons, including the sub-wavelength confinement, were exploited to increase the efficiency of the detector. The detector performance was explored via applying end-fire coupling to the fundamental supported mode, then the results were used to calculate the devices responsivity, dark current, minimum detectable power, and photocurrent for various metal lengths. End fire coupling to a Schottky mode supported by a nano-structured metal was done for what is believed to be the first time.

Different types of plasmonic nanostructures are proposed and examined experimentally and theoretically, with a view towards sensing applications. First, a self-assembly approach was developed to create arrays of well-ordered glass-supported gold nanoparticles (AuNPs) with controllable particle size and inter-particle spacing. Then, a periodic array of gold nano-disks (AuNDs) supported by a Bragg reflector was proposed and examined in a search for Fano resonances in its optical response. Arrays of heptamer-arranged nanoholes (HNH) in a thin gold film were also proposed and explored theoretically and experimentally, revealing a very rich spectrum of resonances, several exhibiting a Fano lineshape. A commercial implementation of the vectorial finite element method (FEM) was used to model our plasmonic structures. Taking advantage of the periodic nature of the structures, a unit cell containing a single element was modelled. The transmittance, reflectance or absorbance spectra were computed, and the associated electromagnetic fields were obtained by solving the vector wave equations for the electromagnetic field vectors throughout the structures, subject to the applicable boundary conditions, and the applied source fields. The sensing performance of the structures, based on the bulk sensitivity, surface sensitivity and figure of merit (FOM) was calculated. First, a novel bottom-up fabrication approach was applied (by our collaborators) to form a periodic array of AuNPs with controllable size over large areas on SiO2 substrates. In this method, self-assembly of block copolymer micelles loaded with metal precursors was combined with a seeding growth route to create ordered AuNPs of desired size. It was shown that this new fabrication method offers a new approach to tune the AuNP size and edge-to-edge inter-particle spacing while preserving the AuNP ordering. The optical characteristics of the AuNP arrays, such as their size, interparticle spacing, localized surface plasmon resonance (LSPR) wavelength, and bulk sensitivity, were examined, numerically and experimentally. This proposed novel fabrication method is applicable for low-cost mass-production of large-area arrays of high-quality AuNPs on a substrate for sensing applications. Then, we proposed and examined the formation of Fano resonances in a plasmonic-dielectric system consisting of uncoupled gold nano-disk (AuND) arrays on a quarter-wave dielectric stack. The mechanism behind the creation of Fano resonances was explained based on the coherent interference between the reflection of the Bragg stack and the LSPPs of the AuNDs. Fano parameters were obtained by fitting the computational data to the Fano formula. The bulk sensitivities and figure of merit of the Fano resonances were calculated. This plasmonic structure supports Fano resonances with a linewidth around 9 nm which is much narrower than the individual AuND LSPP bandwidth ( 80 nm) and the Bragg stack bandwidth ( 100 nm). Supporting Fano resonances with such a narrow linewidth, the structure has a great potential to be used for sensing applications. Also, this metallic-dielectric nanostructure requires no near-field coupling between AuNDs to generate the Fano resonances. So, the AuNDs can be located far enough from each other to simplify the potential fabrication process. The optical properties of HNH arrays on an SiO2 substrate were investigated, numerically and experimentally. Helium focused ion beam (HeFIB) milling was applied (by Dr. Choloong Hahn) to fabricate well-ordered and well-defined arrays of HNHs. Transmittance spectra of the structures were obtained as the optical response, which exhibits several Fano resonances. Then, the mechanism behind the formation of the Fano resonances was explained, and the sensing performance of the structure was inspected by measuring the bulk sensitivities. This array of nanohole cluster is exciting because it supports propagating SPPs and LSPPs, and also Wood’s anomaly waves, which makes the optical response very rich in excitations and spectral features. Also, as a periodic array of sub-wavelength metallic nanoholes, the system produces extraordinary optical transmission - highly enhanced transmission through (otherwise) opaque metallic films at specific wavelengths, facilitating measurement acquisition in transmission.