Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2003. / Includes bibliographical references. Also available in electronic version. Access restricted to campus users.

Thesis (Ph. D.)--Lehigh University, 2003. / Includes bibliographical references and vita.

Raman spectroscopy is a promising technique because it contains abundant vibrational chemical information. However, Raman spectroscopy is restricted by its small scattering cross section, and many techniques have been developed to amplify Raman scattering intensity. In this dissertation, I study two of these techniques, coherent Raman scattering and surface enhanced Raman scattering and discuss their properties. In the first part of my dissertation, I investigate two coherent Raman processes, coherent anti-Stokes Raman scattering (CARS) and stimulated Raman scattering (SRS). In CARS project, I mainly focus on the molecular resonance effect on detection sensitivity, and I find the detection sensitivity can be pushed into 10 [micromolar] with the assistance of molecular resonance. Also, I am able to retrieve background-free Raman spectra from nonresonant signals. For SRS, we develop a new SRS system by applying spectral focusing mechanism technique. We examine the feasibility and sensitivity of our SRS system. The SRS spectra of standards obtained from our system is consistent with literature, and the sensitivity of our system can achieve 10 times above shot-noise limit. In second part of this dissertation, I study surface enhanced Raman scattering (SERS) and related plasmonic effects. I synthesize different shapes of nanoparticles, including nanorod, nanodimer structure with gap and pyramids by template method, and study how electric field enhancement effects correlate to SERS by two photon luminescence (TPL). Also, I build an optical system to study optical image, spectra and particle morphology together. I find that SERS intensity distribution is inhomogeneous and closely related to nanoparticle shape and polarization direction. However, TPL and SERS are not completely correlated, and I believe different relaxation pathways of TPL and SERS and coupling of LSPR and local fields at different frequencies cause unclear correlation between them. / text

A multiple-pass cell is developed and applied to enhance the Raman signal from methane-air flames for temperature measurements. Stable operation of the cell was demonstrated and studied in two alignment modes. In the ring mode, the beams are focused into a ring of ~ 3 mm diameter at the center of the cell, and spectra were recorded at low dispersion (0.26 nm/pixel). Temperature is calculated from the ratio of the intensity of Stokes to anti-Stokes signal from nitrogen. Temperature is also inferred from the shapes of the Stokes and anti-Stokes peaks in the spectrum. The uncertainty in the value of flame temperature in these measurements was ±50 K. The signal gain from 100 passes is a factor of 83. Signal to noise ratio (SNR) improved by a factor of 9.3 in room temperature air with an even higher factor in flames. The improvement in SNR depends on the acquisition time and is best for short acquisition times. In the two point mode, multi passing is achieved simultaneously with high spatial resolution as the laser is focused at two small regions separated by ~ 2 mm at the center of the cell. The probe regions are 300 [mu]m × 200 [mu]m. The vast improvement in the spatial resolution is achieved at the cost of a reduced number of passes and signal gain. The two point mode is operated with 25 passes at each point with a signal gain factor of ~20; the SNR gain depends on the data acquisition time. Spectra were recorded at high dispersion (~0.03 nm/pixel). Temperature is inferred from curve fitting to the high resolution Stokes spectrum of nitrogen in methane-air flames. The curve fit is based on very detailed simulation of Raman spectrum of nitrogen. The final model includes the angular dependence of Raman scattering, electrical and mechanical anharmonicity in the polarizability matrix elements, and the presence of a rare isotope of nitrogen in air. The uncertainty in the value of temperature in the least noisy data is ±9 K. The sources of uncertainty in temperature and their contribution to the total uncertainty are also identified. / text

published_or_final_version / Physics / Doctoral / Doctor of Philosophy

This study was conducted to investigate the biofilm formation by using advanced microscopic and high-throughput sequencing techniques. The major tasks were (1) to quantitatively evaluate the initial bacterial attachment processes by Atomic Force Microscopy (AFM); (2) to characterize the chemical variation during biofilm formation by Raman microscopy; (3) to analyze the microbial structure and functions in the wastewater and drinking water biofilms by metagenomic analysis. To determine the lateral detachment force for bacteria, a quantitative method using contact mode of AFM was developed. The established method had good repeatability and sensitivity to various bacteria and substrata, and was applied to evaluate the roles of bacterial surface polymers in Phase I and II attachment, i.e. lipopolysaccharides, type 1 fimbria and capsular colanic acid. The results indicated lipopolysaccharides largely enhanced Phases I and II attachment. Fimbriae increased Phase I attachment but not significantly influence the adhesion strength in Phase II. Moreover, colanic acid had negative effect on attachment in both of Phases I and II. Surface-enhanced Raman scattering was applied to evaluate the chemical components in the biofilm matrix at different growth phases, including initial attached bacteria, colonies and mature biofilm. Three model bacteria, including Escherichia coli, Pseudomonas putida, and Bacillus subtilis, were used to cultivate biofilms. The results showed that the content of carbohydrates, proteins, and nucleic acids in biofilm matrix increased significantly along with the biofilm growth of three bacteria judging from the intensities and appearance probabilities of related marker peaks in the spectra. The content of lipids, however, only increased in the Gram-negative biofilms. Moreover, metagenomic data, coupled with PCR-based 454 pyrosequencing reads, were generated for activated sludge and biofilm from a full-scale hybrid reactor to study the microbial taxonomic and functional differences/connections between activated sludge and biofilm. The results showed that the dominant bacteria co-existed in two samples. Global functions in activated sludge and biofilm metagenomes showed quite similar pattern, revealing the limited differences of overall functions existed in two samples. For nitrogen removal, the diversity and abundance of nitrifiers and denitrifiers in biofilm did not surpass that in activated sludge. Whilst, higher abundances of nitrification and denitrification genes were indeed found in biofilm, suggesting the increased nitrogen removal by applying biofilm might be attributed to removal efficiency rather than biomass accumulation of nitrogen removal bacteria. To investigate the bacterial structure and functions of drinking water biofilm, PCR-based 454 pyrosequencing of 16S rRNA gene and Illumina metagenomic data were generated and analyzed. Significant differences of bacterial diversity and taxonomic structure were found between biofilms formed on stainless steel and plastics. Moreover, ecological succession could be obviously observed during biofilm formation. The metabolic network analysis for drinking water biofilm constructed for the first time. Moreover, the occurrence and abundance of specific genes involving in the bacterial pathway of glutathione metabolism and production/degradation of extracellular polymeric substances were also evaluated. / published_or_final_version / Civil Engineering / Doctoral / Doctor of Philosophy

Fungal species perform many important roles in biotechnology and recycling and act as agents of disease and decay. Surface-enhanced Raman scattering (SERS) has attracted significant attention as an analytical method for chemical and biological identification. For SERS experiments, it is essential to generate gold nanoparticles (AuNPs) with proper sizes and shapes. Raman and SERS imaging of fungi via in vivo synthesis of AuNPs were used to explore cellular components of Aspergillus nidulans (A. nidulans) cell. Critical parameters including pH, temperature and metal concentration affect the sizes and shapes of the NPs. For better control of NP formation (size, shape and location), pre-formed NP were incubated with A. nidulans colonies. Aspergillus nidulans outer hyphal walls were coated with NPs. Raman and SERS imaging of fungal walls revealed that proteins, carbohydrates and lipids are the main constituents of fungal cell wall. / October 2014

Polythiophenes have shown potential as inexpensive organic semiconductors because of their charge mobility properties. Small changes in structures can change the electronic and optical properties. Because oligothiophenes demonstrate the same electronic properties, have better solubility, and are easier to purify without defects, oligothiophenes are used as models for the polythiophenes. X-ray diffraction is an accepted method for studying the structure and arrangement of atoms in oligothiophenes; however, XRD requires crystalline solids for analysis. Obtaining suitable crystals can be difficult. In this paper, two crystallization techniques, vapor diffusion and zone sublimation, and the results are discussed. Raman spectroscopy, a type of vibrational spectroscopy, will give information about the structure of a molecule and can act as the molecular fingerprint of the molecule. Raman spectroscopy does not require crystalline solids and provides a relatively fast analysis. If the Willets lab can characterize the oligothiophenes by Raman spectroscopy, demonstrate distinguishable spectra for the different morphologies, and correlate this to the X-ray diffraction data, Raman spectroscopy will be an easier and faster means for analyzing the oligothiophenes. / text

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published_or_final_version / abstract / toc / Chemistry / Doctoral / Doctor of Philosophy