In this research, two major experiments, including the self-assembly of silica spheres, were performed by using a physical confinement method with an attractive capillary force. The silica spheres were dragged and aggregated as results of the evaporation of the solvent. In the first experiment, silica spheres were assembled into the two-dimensional pattered substrate, constructed by the photo-resist film formed under a lithography process. Several patterned substrates could work as a physical trap during the flow of the silica spheres. The ordered arrangement of the silica spheres was controlled by the concentration and the size of the silica spheres, the thickness of the photo-resist film, and the titled angle of the substrate. In our conditions, the silica spheres could orderly arrange in larger area of the substrate. In the second experiment, a surface-enhanced Raman scattering (SERS) enhancement was observed from a chain of silica spheres with silver nanoparticles, which worked as a excitation source to provid a strong local electromagnetic fields exciting the crystal violet (CV) dye coated on the silica spheres. We found that the CV molecules has a strong SERS intensity due to the refraction and reflection of the incident light within the silica spheres. When the silica spheres were linearly arranged, longer length of the chained silica spheres would lead to a maximum value of the SERS intensity.

The first part of this study is focused on numerical studies of light scattering from a single microscopic particle using the Discrete Dipole Approximation (DDA) method. The conventional DDA formalism is generalized to two cases: (a) inelastic light scattering from a dielectric particle and (b) light scattering from a particle with magnetic permeability u /= 1. The first generalization is applied to simulations of Raman scattering from bioaerosol particles, and the second generalization is applied to confi rmation of irregular invisibility cloaks made from metamaterials. In the second part, radiative transfer in a coupled atmosphere-ocean system is solved to study the asymptotic nature of the polarized light in deep oceans. The rate at which the radiance and the polarization approach their asymptotic forms in an ideal homogeneous water body are studied. Effects of the single scattering albedo and the volume scattering function are studied. A more realistic water body with vertical pro files for oceanic optical properties determined by a Case 1 water model is then assumed to study the e ffects of wavelength, Raman scattering, and surface waves. Simulated Raman scattering patterns computed from the generalized DDA formalism are found to be sensitive to the distribution of Raman active molecules in the host particle. Therefore one can infer how the Raman active molecules are distributed from a measured Raman scattering pattern. Material properties of invisibility cloaks with a few irregular geometries are given, and field distributions in the vicinity of the cloaked particles computed from the generalized DDA formalism con rm that the designated material properties lead to invisibility. The radiative transfer model calculation in deep oceans suggest that the underwater radiance approaches its asymptotic form more quickly than the polarization does. Therefore, a vector radiative transfer solution is necessary for asymptotic light field studies. For a typical homogeneous water body whose scattering property is characterized by the Petzold phase function, a single scattering albedo of w0 > 0:8 is required in order that the asymptotic regime can be reached before there are too few photons to be detected.

Nowadays plasmonics is rapidly developing areas from fundamental studies to more application driven research. This dissertation contains three different research topics on plasmonics. In the first research topic, by modulating the zone width of a plasmonic zone plate, we demonstrate that a beam focused by a proposed plasmonic zone plate lens can be achieved with higher intensity and smaller spot size than the diffraction-limited conventional zone plate lens. This sub-diffraction focusing capability is attributed to extraordinary optical transmission, which is explained by the complex propagation constant in the zone regions afforded by higher refractive index dielectric layer and surface plasmons. On the other hand, the resulted diffraction efficiency of this device is relatively low. By introducing a metal/dielectric multilayered zone plate, we present higher field enhancement at the focal point. This higher field enhancement originates not only from surface plasmon polaritons-assisted diffraction process along the propagation direction of the incident light (longitude mode), but also from multiple scattering and coupling of surface plasmons along the metal/dielectric interface (transverse mode). In the second research topic, we suggest a novel concept of SERS-active substrate applications. The surface-enhanced Raman scattering enhancement factor supported by gap surface plasmon polaritons is introduced. Due to higher effective refractive index induced by gap surface plasmon polaritons in the spacer region between two metal plates, incident light tends to localize itself mostly in the medium with higher refractive index than its adjacent ones and thereby the lights can confine with larger field enhancement. In the last research topic, we offer a simple structure in which a gold dipole antenna is formed on the SiC substrate. Surface phonon polaritons, counterparts of surface plasmon polaritons in the mid-infrared frequencies, are developed. Due to the synergistic action between the conventional dipole antenna coupling and the resonant excitation of surface phonon polaritons, strong field enhancement in the gap region of dipole antenna is attained. Most of research topics above are expected to find promising applications such as maskless nanolithography, high resolution scanning optical microscopy, optical data storage, optical antenna, SERS-active substrate, bio-molecular sensing and highly sensitive photo-detectors.

Quantum coherence and interference(QCI) effects have been studied for decades and are widely exploited in many areas. For media with QCI effect, the optical properties can change drastically, which leads to many interesting effects, such as coherent population trapping, electromagnetically induced transparency(EIT), lasing without population inversion(LWI) and so on. We have theoretically studied the pulsed regime of EIT. In particular, simulations of propagation of gaussian and 0 - pi co-propagating laser pulses in a medium consisting of 3-level Lambda-atoms have been performed. It has been found that, even at the two-photon resonance, the length of propagation for the 0 - pi pulses is much smaller than that for the Gaussian probe pulses. We explained such a behavior using the dark and bright basis and the dressed state basis. Some possible applications are discussed. We also investigated the collision-induced coherence of two decay channels along two optical transitions. Quantum interference will suppress the spontaneous emission. The degree of this suppression is measured by the branch ratio of these two transitions. Our preliminary calculations show that a significant decrease of the branching ratio with increase of electron densities is reproduced in the theory. We have developed a new variant of Raman spectroscopy with shaped femtosecond pulses. It has several advantages to be applied in multiscatterd media. It is based on change of the spectra of femtopulses due to Raman scattering (stimulated or coherent). The technique can be used for a broad range of applications from atomic and molecular optical and IR spectroscopy to spore detection and tissue microscopy. Finally, we have shown that Fano interference in the decay channels of three levels system can lead to considerably different absorption and emission profiles. We found that a coherence can be built up in the ground state doublet whose strength depends on a coupling parameter that arises from Fano interference. This can in principle lead to breaking of the detail balance between the absorption and emission processes in atomic systems.

We study in this thesis work the spectroscopic and thermodynamic quantities of some substances such as ammonium halides (NH4Cl, NH4I), ferroelectric crystals of tris-sarcosine calcium chloride (TSCC), tris-sarcosine calcium bromide (TSCB), organic compounds of carbon tetrachloride (CCl4) and s-triazine (C3N3H3) close to the phase transitions. Various physical and chemical properties of those materials have been measured near the critical points and have been reported in the literature. In this study, the spectroscopic parameters of the frequency shifts, intensity and bandwidths are calculated as functions of temperature or pressure near the phase transitions in ammonium halides using the experimental data from the literature. The spectroscopic parameters are related to the crystal volume and the specific heat in these compounds. The thermodynamic quantities of the specific heat, thermal expansion and the isothermal compressibility are also calculated in the solid and liquid phases of carbon tetrachloride using the experimental data. In another part of this thesis work, we analyze the temperature dependence of the spontaneous polarization and the dielectric susceptibility at fixed pressures for TSCC and TSCB by using the experimental data from the literature. The temperature dependence of the damping constant for the s-triazine is also calculated here close to the I-II transition. We use the theoretical models on the basis of the observations in the literature to calculate the critical behaviour of these physical quantities and we compare the results with the observed data. Various experimental studies in the literature give us the opportunity to find the proper way of fitting the calculated and observed results. This study gives us the chance of a better understanding of the critical behavior of the studied materials by verifying the values of some critical exponents and the types of transitions as expected by different theoretical models.

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The work presented in this dissertation suggests novel design of chemical plasmonic sensors which have been developed based on Localized Surface Plasmon Resonance (LSPR), and Surface-enhanced Raman scattering (SERS) phenomena. The goal of the study is to understand the SERS phenomena for 3D hybrid (organic/inorganic) templates and to design of the templates for trace-level detection of selected chemical analytes relevant to liquid explosives and hazardous chemicals. The key design criteria for the development of the SERS templates are utilizing selective polymeric nanocoatings within cylindrical nanopores for promoting selective adsorption of chemical analyte molecules, maximizing specific surface area, and optimizing concentration of hot spots with efficient light interaction inside nanochannels. The organic/inorganic hybrid templates are optimized through a comprehensive understanding of the LSPR properties of the gold nanoparticles, gold nanorods, interaction of light with highly porous alumina template, and the choice of physical and chemical attributes of the selective coating. Furthermore, novel method to assemble silver nanoparticles in 3D as the active SERS-active substrate has been demonstrated by uniform, in situ growth of silver nanoparticles from electroless deposited silver seeds excluding any adhesive polymer layer on template. This approach can be the optimal for SERS sensing applications because it is not necessary to separate the Raman bands of the polyelectrolyte binding layer from those of the desired analyte. The fabrication method is an efficient, simple and fast way to assemble nanoparticles into 3D nanostructures. Addressable Raman markers from silver nanowire crossbars with silver nanoparticles are also introduced and studied. Assembly of silver nanowire crossbar structure is achieved by simple, double-step capillary transfer lithography. The on/off SERS properties can be observed on silver nanowire crossbars with silver nanoparticles depending on the exact location and orientation of decorated silver nanoparticles nearby silver nanowire crossbars. As an alternative approach for the template-assisted nanostructure design, porous alumina membrane (PAM) can be utilized as a sacrificial template for the fabrication of the nanotube structure. The study seeks to investigate the design aspects of polymeric/inorganic hybrid nanotube structures with plasmonic properties, which can be dynamically tuned by external stimuli such as pH. This research suggests several different organic/inorganic nanostructure assemblies by various template-assisted techniques. The polymeric/inorganic hybrid nanostructures including SERS property, pH responsive characteristics, and large surface area will enable us to understand and design the novel chemical plasmonic sensors.

DNA is packaged into the nucleus of a mammalian cell as a nucleoprotein complex called chromatin. Changes in chromatin structure occur during processes that are critical to an understanding of mammalian cell biology such as cell division. Existing fixed-cell techniques have provided insight into chromatin organization in the mammalian nucleus. In addition, fluorescence microscopy techniques have allowed us to study changes in chromatin structure in living cells. However, most of these fluorescence techniques cannot be used for tissue imaging or long-term imaging due to photobleaching. In this thesis, we demonstrate that a label-free technique called Stimulated Raman Scattering (SRS) microscopy can be used to solve these problems and study chromatin structure in living mammalian cells both in culture and in tissue. SRS is a vibrational microscopy technique that takes advantage of intrinsic contrast arising from specific chemical bonds in a molecule. Nucleic acids have specifc phosphate and CH vibrations that can be used to determine their cellular distributions. Imaging at specific phosphate peaks using fingerprint SRS microscopy allows the detection of polytene chromosomes in Drosophila salivary gland cells and condensed chromatin in metaphase mammalian cells. In addition, we develop a technique called multicolor SRS microscopy, in which we image at several wavelengths across the CH vibrational band, and then use linear combination to simultaneously determine the nucleic acid, lipid and protein distributions in living mammalian cells. This technique achieves greater contrast than imaging at the phosphate vibrational peak due to the stronger SRS signal in the high wavenumber CH band and so allows us to determine chromatin structure in interphase mammalian cells. This technique also allows long-term imaging of living mammalian cells and the imaging of tissue such as mouse skin. The technique is used to monitor mammalian cell division in culture and paves the way for similar studies in living tissue. This technique will provide insight into cell division, differentiation and apoptosis during development and in disease models such as cancer.

Metallic nanostructures that employ localized surface plasmon resonances to capture or radiate electromagnetic waves at optical frequencies are termed "plasmonic optical antennas". These structures enhance light-matter interactions in an efficient manner, enabling unique linear and nonlinear optical applications. One such application is surface-enhanced Raman scattering (SERS), which employs plasmonic antennas to enhance Raman cross-section of molecules by orders of magnitude. SERS has attracted a significant amount of research attention since it enables molecules to be identified through their characteristic vibrational spectra, even at the single molecule level. / Engineering and Applied Sciences