Thesis (M.S.)--West Virginia University, 2000. / Title from document title page. Document formatted into pages; contains xi, 81 p. : ill. (some col.). Vita. Includes abstract. Includes bibliographical references.

Thesis (Ph. D.)--University of Idaho, 2005. / Also available online in PDF format Abstract. "October 2005." Includes bibliographical references.

Thesis (Ph. D.)--University of Washington, 2006. / Vita. Includes bibliographical references (leaves 185-203).

Thesis (M.Sc.Eng.) / Sepsis is a serious medical condition in which a person becomes infected with bacteria in his or her bloodstream. The symptoms of sepsis are a result of the immune system’s interaction with the infecting agent. Currently, to diagnose a patient with sepsis, a blood sample must be collected and cultured for 24-48 hours before the infection can be confirmed. In the meantime, a broad-scope antibiotic is administered which may or may not be effective in treating the patient. If the antibiotic is ineffective, a different antibiotic must be chosen. When the results of the blood culture are available, a narrow scope antibiotic, appropriate to treat the infection is administered. However, sepsis has a mortality rate of 18-30% depending on the infecting agent and the treatment is highly time sensitive. Within 24 hours, the syndrome may progress to septic shock and mortality rates reach 50%. Therefore, it is important to quickly and correctly identify the infecting agent and provide immediate targeted treatment. Surface Enhanced Raman Spectroscopy (SERS) can be used to quickly identify and distinguish between different bacterial strains; however it requires higher bacterial concentrations than are present in the blood during the early stages of sepsis. A microfluidic evaporator chip has been developed to concentrate bacteria samples from 4μl to 100nl; the chip has been evaluated for concentration efficiency on Escherichia coli and methicillin-sensitive Staphylococcus aureus. Various blocking methods using bovine serum albumin (BSA) have been tested to reduce bacterial adhesion to the chip and have improved bacterial recovery to around 70% for both strains tested. Ongoing tests are being performed to improve bacterial recovery and sample purity for identification. / 2031-01-01

The rational combination of dielectric and metallic nano particles brings novel optical properties to conventional subwavelength structures. This thesis introduces the optoplasmonic geometries demonstrating versatile ability in both far and near field modification within nano scale. Template-assisted self-assembly approaches are applied creating nano entities with titanium dioxide and gold nano spheres. A top-bottom mono hybrid unit and interdigitated array are developed. With the examination of the elastic and inelastic response of these hybrid materials, physical models are simulated to depict the scenario of varied geometry and combination of nano particles. In contrast to solely metal or dielectric particle arrays, this type of artificial material not only enhances the near electric field intensity within the metal nano cluster hot spots, but also expands the overall volume of enhanced electric field. Further study reveals that the additional enhancement and redistribution of near field are derived from the coupling between the nano gold cluster plasmon resonance and the in-plane diffractive mode of the dielectric array. The redirected emission profile of the fluorescent dyes within the hybrid array is explored.

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Fresh foods, including meats and produce are the fastest growing market in the supermarket and the class of foods most likely to cause a bacterial foodborne illness. As the rate of consumption of perishable products increases, rapid detection of pathogens within the food supply becomes a critical issue. Current methods used for the detection of bacteria that cause food-borne illnesses are time consuming, expensive and often require selective enrichment. In this study we adapted a separation technique originally developed for PCR to extract bacteria from ground beef using β-cyclodextrin (β-CD) and milk protein coated activated carbon (MP-CAC) as filtration agents. The recovered bacteria were bound to a gold slide via a 3-mercaptophenylboronic acid (3-MPBA) sandwich assay and detected with Surface Enhanced Raman Spectroscopy (SERS). The 3-MPBA sandwich assay used with the separation technique allowed detection of Salmonella enterica Enteritidis (BAA-1045), separated from a ground beef matrix, as low as 1x102 CFU/g. Detection at this level was accomplished in less than 8 hours, significantly faster than plate count or enrichment methods that require multiple days. Previously, SERS has been used to detect bacteria within simple matrices; this is the first study to have utilized SERS bacterial detection in a ground beef.

Raman spectroscopy is an extremely versatile technique with molecular sensitivity and fingerprint specificity. However, the translation of this tool into a deployable technology has been stymied by irreproducibility in sample preparation and the lack of complex data analysis tools. In this dissertation, a droplet microfluidic platform was prototyped to address both sample-to-sample variation and to introduce a level of quantitation to surface enhanced Raman spectroscopy (SERS). Shifting the SERS workflow from a cell-to-cell mapping routine to the mapping of tens to hundreds of cells demanded the development of an automated processing tool to perform basic SERS analyses such as baseline correction, peak feature selection, and SERS map generation. The analysis tool was subsequently expanded for use with a multitude of diverse SERS applications. Specifically, a two-dimensional SERS assay for the detection of sialic acid residues on the cell membrane was translated into a live cell assay by utilizing a droplet microfluidic device. Combining single-cell encapsulation with a chamber array to hold and immobilize droplets allowed for the interrogation of hundreds of droplets. Our novel application of computer vision algorithms to SERS maps revealed that sialic sugars on cancer cell membranes are found in small clusters, or islands, and that these islands typically occupy less than 30% of the cell surface area. Employing an opportunistic mindset for the application of the data processing platform, a number of smaller projects were pursued. Biodegradable aliphatic-aromatic copolyesters with varying aromatic content were characterized using Raman spectroscopy and principal component analysis (PCA). The six different samples could successfully be distinguished from one another and the tool was able to identify spectral feature changes resulting from an increasing number of aryl esters. Uniquely, PCA was performed on the 3,125 spectra collected from each sample to investigate point-to-point heterogeneities. A third set of projects evaluated the ability of the data processing tool to calculate spectral ratios in an automated fashion and were exploited for use with nano-pH probes and Rayleigh hot-spot normalization. / Ph. D.

Metallic nanoparticles (NPs) are exploited for their ability to interact with organic compounds and to increase significantly the fluorescence intensity and the photostability of many fluorescent dye molecules. Metal enhanced fluorescence (MEF) is therefore widely investigated for biosensing applications. When used in immunoassays, silver island films (SIFs) could augment the fluorescence intensity of fluorescein by a factor of seventeen; SIFs were also able to double or triple the emission intensity of cyanine dyes which are commonly used in (deoxyribonucleic acid) DNA microarrays. The emission intensity of indocyanine green — widely used as a contrast agent in medical imaging — was about twenty times higher in the proximity of SIFs. This enhancement phenomenon — due to the surface plasmon polaritons associated with the metallic NPs — can be explained by energy transfer from the metal NPs to the fluorescent dye molecules or by a modified local electromagnetic field experienced by the fluorophores in the vicinity of metal surfaces. Our research focused on the optical characterization of colloidal gold-silver alloy NPs containing different ratios of gold and silver (Au_1.00-Ag_0.00, Au_0.75-Ag_0.25, Au_0.50-Ag_0.50, and Au_0.25-Ag_0.75), as well as their interaction with three fluorophores: rose bengal, rhodamine B, and fluorescein sodium. Depending upon the dye quantum yield and its concentration in solution, enhancement or quenching of fluorescence was obtained. Thus, a three to five times increase in fluorescence intensity was observed in a 2.0 mM solution of rose bengal with all nanoalloys, a slight enhancement of fluorescence (1.2 – 1.6 times) was noticed in a 0.13 mM solution of rhodamine B with all four types of NPs, and fluorescence quenching occurred in all the fluorescein-NP solutions regardless of the dye concentration. / Master of Science

Title: Optical Responses of Biomolecules on Regular Metal Plasmonic Nanostructures Author: Martin Šubr Department: Institute of Physics of Charles University Supervisor of the doctoral thesis: prof. RNDr. Marek Procházka, Dr., Institute of Physics of Charles University Abstract: Adsorption of molecules on metal plasmonic nanostructures leads to significant enhancement of many optical processes, such as Raman scattering (surface-enhanced Raman scattering - SERS) or fluorescence (surface-enhanced fluorescence - SEF). Two groups of substrates were tested within this thesis: (i) Silver nanorods prepared by oblique angle vapor deposition, and (ii) silver and gold nanoislands growing on magnetron-sputtered polytetrafluoroethylene film. Step-by- step optimization process was performed on the nanoislands in order to obtain optimum SERS sensitivity and reproducibility. Detailed SERS intensity profiles were obtained using gradient nanostructures with the localized surface plasmon resonance (LSPR) condition varying across the sample and three different excitation wavelengths. It was also found that spectral position and height of the LSPR band can be controlled simultaneously using mixed gold/silver nanoislands. Detailed investigation of polarization- and angular- dependences of anisotropic silver nanorods was...