Browsing by Subject "LSPR"
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Item Comparative Performance Analysis of the Algorithms for Detecting Periodically Expressed Genes(2012-10-19) Agyepong, KwadwoThus far, a plethora of analysis on genome-wide gene expression microarray experiments on the cell cycle have been reported. Time series data from these experiments include gene expression profiles that might be periodically expressed. However, the numbers and actual genes that are periodically expressed have not been reported with consistency, analysis on similar experiments reports disparate numbers of genes that are periodically expressed with scant overlap. This work ultimately compares the performance of five spectral estimation schemes in their ability to recover periodically expressed genes profiles. Lomb-Scargle (LS), Capon, Missing-Data Amplitude and Phase Estimation (MAPES), Real Value Iterative Adaptive Approach (RIAA) and Lomb-Scargle Periodogram Regression (LSPR) are rigorously studied and pitted against each other in various simulated testing conditions. Results obtained using synthetic and microarray data reveals that RIAA is an efficient and robust method for the detection of periodically expressed genes in short time series data that might be characterized with noisy and irregularly sampled data points.Item Localized surface plasmon resonance spectroscopy of gold and silver nanoparticles and plasmon enhanced fluorescence(2011-12) Vokac, Elizabeth Anne; Willets, Katherine A.; Brodbelt, Jennifer S.This thesis presents spectroscopic studies of metallic nanoparticle localized surface plasmons and plasmon enhanced fluorescence. We investigated the dielectric sensitivity of silver nanoprisms to an external electric field and gold nanorods to the formation of a self-assembled surface monolayer. Dark field microscopy was used to image plasmonic scattering from single nanoparticles, and a liquid crystal tunable filter was used to construct corresponding spectra. The plasmon resonances of silver nanoprisms displayed both reversible red shifts and irreversible blue shifts along with drastic intensity changes upon exposure to an applied bias. The plasmon resonances of gold nanorods showed sensitivity to the presence of alkanethiol molecules adhered to the particle surface by a moderate red shift. An increase in the effective external dielectric caused a shift toward longer wavelengths. We imaged plasmon enhanced fluorescence in order to optimize experimental parameters for a developing project that can characterize nanoparticle structure on sub-wavelength dimensions. Preliminary controls were performed to account for the effect of O₂ plasma treatment, solvent and alkanethiol monolayer formation on surface plasmon resonances. We found that O₂ plasma treatment for different time intervals did not result in a plasmon shift compared to untreated nanoparticles exposed to N₂; however when exposed to solvent the surface plasmons of the treated particles shifted five times as far toward the red. Interestingly, the solvent effect only resulted in a plasmon shift when the particles were N₂ dried after solvent incubation. Gold nanorods incubated in ethanol showed no wavelength maximum shift in pure solvent over time, but shifted moderately to the red after incubation in a solution of alkanethiol molecules. Conditions for the plasmon enhanced fluorescence study were optimized using a dye conjugate of the same alkanethiol molecule used previously by formation from solution in a monolayer on the gold nanorod surface. The appropriate synthesis for dye functionalization, molecular concentrations, solvents and optical settings were determined.