Doctor of Philosophy

dissertationPlasmonics relates to the interaction between electromagnetic radiation and conduction electrons at metallic interfaces or in metallic nanostructures. Surface plasmons are collective electron oscillations at a metal surface, which can be manipulated by shape, texture and material composition. Plasmonic applications cover a broad spectrum from visible to near infrared, including biosensing, nanolithography, spectroscopy, optoelectronics, photovoltaics and so on. However, there remains a gap in this activity in the ultraviolet (UV, < 400 nm), where significant opportunity exists for both fundamental and application research. Motivating factors in the study of UV Plasmonics are the direct access to biomolecular resonances and native fluorescence, resonant Raman scattering interactions, and the potential for exerting control over photochemical reactions. This dissertation aims to fill in the gap of Plasmonics in the UV with efforts of design, fabrication and characterization of aluminium (Al) and magnesium (Mg) nanostructures for the application of label-free bimolecular detection via native UV fluorescence. The first contribution of this dissertation addresses the design of Al nanostructures in the context of UV fluorescence enhancement. A design method that combines analytical analysis with numerical simulation has been developed. Performance of three canonical plasmonic structures - the dipole antenna, bullseye nanoaperture and nanoaperture array - has been compared. The optimal geometrical parameters have been determined. A novel design of a compound bullseye structure has been proposed and numerically analyzed for the purpose of compensating for the large Stokes shift typical of UV fluorescence. Second, UV lifetime modification of diffusing molecules by Al nanoapertures has been experimentally demonstrated for the first time. Lifetime reductions of ∼3.5× have been observed for the high quantum yield (QY) laser dye p-terphenyl in a 60 nm diameter aperture with 50 nm undercut. Furthermore, quantum-yield-dependence of lifetime reduction has been experimentally demonstrated for the first time. Lifetime reduction as a function of aperture size and native quantum yield has been accurately predicted by simulation. Simulation further predicts greater net fluorescence enhancement for tryptophan compared to p-terphenyl. In order to increase fluorescence enhancement, the "poor" molecules and structures with proper undercuts are required. Third, UV lifetime modification by Mg nanoapertures has been experimentally demonstrated for the first time. Lifetime reductions of ∼13× have been observed for the laser dye p-terphenyl with high QY in a 50 nm diameter aperture with 125 nm undercut. In addition, extraordinary optical transmission of Mg nanohole arrays in the UV has been measured for the first time. By using Al as a reference, the feasibility of applying Mg in the UV plasmonic applications has been evaluated both numerically and experimentally. Finally, this work has established a methodology for the study of plasmonic enhancement of UV fluorescence, including design method, thin-film characterization, nanofabrication with focus ion beam milling, and fluorescence measurement. It has paved the way for more extensive research on UV fluorescence enhancement

Optical antenna design for fluorescence enhancement in the ultraviolet

pre-printThrough rational design, we compare the performance of three plasmonic antenna structures for UV fluorescence enhancement. Among the antenna performance metrics considered are the local increase in excitation intensity and the increase in quantum efficiency, the product of which represents the net fluorescence enhancement.With realistic structures in aluminum, we predict that greater than 100× net enhancement can be obtained

OsTIR1 and OsAFB2 Downregulation via OsmiR393 Overexpression Leads to More Tillers, Early Flowering and Less Tolerance to Salt and Drought in Rice

The microRNA miR393 has been shown to play a role in plant development and in the stress response by targeting mRNAs that code for the auxin receptors in Arabidopsis. In this study, we verified that two rice auxin receptor gene homologs (OsTIR1 and OsAFB2) could be targeted by OsmiR393 (Os for Oryza sativa). Two new phenotypes (increased tillers and early flowering) and two previously observed phenotypes (reduced tolerance to salt and drought and hyposensitivity to auxin) were observed in the OsmiR393-overexpressing rice plants. The OsmiR393-overexpressing rice demonstrated hyposensitivity to synthetic auxin-analog treatments. These data indicated that the phenotypes of OsmiR393-overexpressing rice may be caused through hyposensitivity to the auxin signal by reduced expression of two auxin receptor genes (OsTIR1 and OsAFB2). The expression of an auxin transporter (OsAUX1) and a tillering inhibitor (OsTB1) were downregulated by overexpression of OsmiR393, which suggested that a gene chain from OsmiR393 to rice tillering may be from OsTIR1 and OsAFB2 to OsAUX1, which affected the transportation of auxin, then to OsTB1, which finally controlled tillering. The positive phenotypes (increased tillers and early flowering) and negative phenotypes (reduced tolerance to salt and hyposensitivity to auxin) of OsmiR393-overexpressing rice present a dilemma for molecular breeding

Silver-Catalyzed Radical Transformation of Aliphatic Carboxylic Acids to Oxime Ethers

Oximes and oxime ethers are privileged building blocks and can be conveniently converted to ketones, amines, hydroxylamines, and nitriles. We describe the catalytic decarboxylation of aliphatic carboxylic acids to oxime ethers. With AgNO₃ as the catalyst, valuable oxime ethers bearing various substituents could be easily obtained. The broad substrate scope, easy accessibility of aliphatic carboxylic acids, and mild reaction conditions make this strategy immediately applicable to the synthesis, late-stage functionalization, and modification of biologically active compounds. Experimental studies show the reaction undergoes a radical process

Improving the Retrieval of Crop Canopy Chlorophyll Content Using Vegetation Index Combinations

Estimates of crop canopy chlorophyll content (CCC) can be used to monitor vegetation productivity, manage crop resources, and control disease and pests. However, making these estimates using conventional ground-based methods is time-consuming and resource-intensive when deployed over large areas. Although vegetation indices (VIs), derived from satellite sensor data, have been used to estimate CCC, they suffer from problems related to spectral saturation, soil background, and canopy structure. A new method was, therefore, proposed for combining the Medium Resolution Imaging Spectrometer (MERIS) terrestrial chlorophyll index (MTCI) and LAI-related vegetation indices (LAI-VIs) to increase the accuracy of CCC estimates for wheat and soybeans. The PROSAIL-D canopy reflectance model was used to simulate canopy spectra that were resampled to match the spectral response functions of the MERIS carried on the ENVISAT satellite. Combinations of the MTCI and LAI-VIs were then used to estimate CCC via univariate linear regression, binary linear regression and random forest regression. The accuracy using the field spectra and MERIS data was determined based on field CCC measurements. All the MTCI and LAI-VI combinations for the selected regression techniques resulted in more accurate estimates of CCC than the use of the MTCI alone (field spectra data for soybeans and wheat: R2 = 0.62 and RMSE = 77.10 μg cm−2; MERIS satellite data for soybeans: R2 = 0.24 and RMSE = 136.54 μg cm−2). The random forest regression resulted in better accuracy than the other two linear regression models. The combination resulting in the best accuracy was the MTCI and MTVI2 and random forest regression, with R2 = 0.65 and RMSE = 37.76 μg cm−2 (field spectra data) and R2 = 0.78 and RMSE = 47.96 μg cm−2 (MERIS satellite data). Combining the MTCI and a LAI-VI represents a further step towards improving the accuracy of estimation CCC based on multispectral satellite sensor data

A planar metallic collimator based on controlling surface plasmons&apos;s phase

Abstract We present numerical study of the optical transmission of a metal film perforated by slits array with different spacing. A planar metallic collimator with phase retardation controlled by the slits space is designed. The analysis results show this structure with appropriate space between the slits can collimate or deflect the transmitted beam, which is attributed to phase retardation of surface plasmons propagating from one slit to the other. The numerical analysis results demonstrate a useful deflecting or collimating function of a planar metallic film in the applied fields of optical storage, optical coupler, nano-optics

UV Fluorescence Lifetime Modification by Aluminum Nanoapertures

We report excited-state lifetime modification of diffusing molecules by Al nanoapertures in the UV. Lifetime reductions of ∼3.5× have been observed for the high quantum yield laser dye <i>p</i>-terphenyl in a 60 nm diameter aperture. The lifetime reduction is smaller for the low quantum yield molecule tryptophan, for which a maximum reduction of ∼1.7 is observed. Lifetime reduction as a function of aperture size and native quantum yield is accurately predicted by simulation. Simulation further predicts greater net fluorescence enhancement for tryptophan compared to <i>p</i>-terphenyl, which is consistent with the expectation that low quantum yield emitters experience greater enhancement in the effective quantum yield

Genome-wide detection of predicted non-coding RNAs related to the adhesion process in Vibrio alginolyticus using high-throughput sequencing

The ability to adhere to fish mucus can be affected by environmental conditions and is considered to be a key virulence factor of Vibrio alginolyticus. However, the molecular mechanism underlying this ability is unclear. Our previous study showed that stress conditions such as exposure to Cu, Pb, Hg and low pH were capable of reducing the adhesion ability of V. alginolyticus. Non-coding RNAs (ncRNAs) play a crucial role in the intricate regulation of bacterial gene expression, thereby affecting bacterial pathogenicity. Therefore, we hypothesized that ncRNAs played a key role in the V. Alginolyticus adhesion process. To validate this, we combined high throughput sequencing with computational techniques to detect ncRNA dynamics in the stressed samples. The expression of randomly selected novel ncRNAs was confirmed by QPCR. Among the significantly changed ncRNAs, 30 ncRNAs were up-regulated and 2 ncRNAs were down-regulated by all stress treatments. The QPCR results reinforced the reliability of the sequencing data. Target prediction and KEGG pathway analysis indicated that these ncRNAs were closely related to pathways associated with in vitro adhesion. Our results indicated that the chemical stress-induced reduction in the adhesion ability of V. alginolyticus might be due to the perturbation of ncRNA expression. Our findings provide important information for further functional characterization of ncRNAs during the adhesion process of V. alginolyticus