This dissertation describes the development of a new method for increasing the resolution of the current protein microarray technology, down to the single molecule detection level. By using a technique called size-dependent self-assembly, different proteins can be bound to different sized fluorescent nanostructures, and then located on a patterned silicon substrate based on the sized pattern which is closest to the size of the bead diameter.The protein nanoarray was used to detect antibody-antigen binding, specifically anti-mouse IgG binding to mouse IgG. The protein nanoarray is designed with the goal of analyzing rare proteins. However, common proteins, such as IgG, are used in the initial testing of the array functionality. Mouse IgG, representing rare proteins, is conjugated to fluorescent beads and the beads are immobilized on a patterned silicon surface. Then anti-mouse IgG binds to the mouse IgG on the immobilized beads. The binding of the antibody, anti-mouse IgG, to the antigen, mouse IgG is determined by fluorescent signal attenuation.The first objective was to bind charged nanoparticles, conjugated with proteins, to an oppositely charged silicon substrate. Binding of negatively charged gold nanoparticles (AuNP), conjugated with mouse IgG, to a positively charged silicon surface was successful.The second objective was to demonstrate the method of size-dependent self-assembly at the nanometer scale (<100 >nm). Different-sized, carboxylated, fluorescent beads and AuNP, which were conjugated with proteins, were serially added to a patterned polymethyl methacrylate (PMMA) coated silicon surface. Size-dependent self-assembly was successfully demonstrated, down to the nanometer scale.The final objective was to obtain a signal from antibody-antigen binding within the protein array. Conjugated fluorescent beads were bound to e-beam patterns and signal attenuation was measured when the antibodies bound to the conjugated beads. The size-dependent self-assembly is a valuable new method that can be used for the detection and quantification of proteins.

Arrays of nanotubes/rods made of appropriate materials can yield unique radiative properties, such as large absorption and optical anisotropy, with broad applications from high-efficiency emitters and absorbers for energy conversion to the polarization conversion via anisotropic responses. The objective of this dissertation is to investigate the radiative properties of arrays formed by aligned carbon nanotubes (CNTs) and silver nanorods (AgNRs). The CNT arrays used in the present study consist of multi-walled CNTs synthesized vertically on silicon substrates using thermal chemical vapor deposition. Their close-to-unity absorptance is demonstrated by measuring the directional-hemispherical reflectance in the visible and near-infrared spectral ranges using an integrating sphere. The bidirectional reflectance distribution function and angle-resolved reflectance were measured at the 635-nm wavelength. The results demonstrate that high-absorptance CNT arrays may be diffusely or specularly reflecting and have important applications in radiometry. Theoretical modeling based on the effective medium theory (EMT) and reflectivity of an anisotropic medium are developed to explain the high absorption and polarization dependence. The effective optical constants of the CNT array for both ordinary and extraordinary polarizations are quantitatively determined by fitting the angle-resolved reflectance. The AgNR arrays used in the present study were fabricated using oblique angle deposition, which results in inclined Ag nanorods that can be modeled as an effective homogenous and optically anisotropic thin film. The spectral and directional radiative properties of AgNRs grown on different substrates, including a glass slab with a silver film, and compact disc gratings, were characterized at the 635-nm and 977-nm wavelengths for different polarizations. The results are analyzed based on the EMT, rigorous coupled-wave analysis, and anisotropic thin-film optics. The results of this dissertation help gain a better understanding of radiative properties of anisotropic nanostructures for potential applications in high-efficiency energy conversion, radiometric devices, and optical systems.