The ionization of xenon Rydberg atoms at metallic surfaces is examined. The data show that, when the effects of stray electric "patch" fields present on the surface are taken into account, ionization is well described by a simple over-the-barrier model. The patch fields are determined from direct measurements of the potential variations across the target surfaces using Kelvin probe force microscopy. Monte Carlo techniques are used to model the atom-surface interaction. The results confirm the important role that patch fields can play during Rydberg atom-surface interactions and suggest that such interactions can provide a sensitive probe of stray fields at surfaces. To demonstrate this, measurements of the threshold conditions required to observe ions resulting from surface ionization are used to estimate how large such stray fields can be. The data show that the stray fields can be sizable, as large as ∼ 10 3 V · cm -1 100 nm from the surface and ∼ 10 V · cm -1 500 nm from the surface, and illustrate the potential of Rydberg atoms for detecting and characterizing surface electric fields. Methods to enhance the surface ionization signal using electrode arrays patterned on a surface are investigated. Simulations show that bias voltages applied to a series of parallel wires comprised of two interleaved comb-shaped electrodes can have a dramatic impact on ion collection efficiency. It is suggested that such a surface can be used to efficiently collect low- n Rydberg atoms ( n [Special characters omitted.] 10). Significant progress towards fabrication of a functioning surface of 1 μm wide wires with 1 μm spacing is documented.

We establish several new results about the ( n )-solvable filtration, [Special characters omitted.] , of the string link concordance group [Special characters omitted.] . We first establish a relationship between ( n )-solvability of a link and its Milnor's μ-invariants. We study the effects of the Bing doubling operator on ( n )-solvability. Using this results, we show that the "other half" of the filtration, namely [Special characters omitted.] , is nontrivial and contains an infinite cyclic subgroup for links with sufficiently many components. We will also show that links modulo (1)-solvability is a nonabelian group. Lastly, we prove that the Grope filtration, [Special characters omitted.] of [Special characters omitted.] is not the same as the ( n )-solvable filtration.

Peroxisomes compartmentalize a variety of important metabolic reactions including fatty acid β-oxidation and the related process of IBA β-oxidation. Peroxisomal proteins are encoded by nuclear genes and must be post-translationally imported. A dynamic import process is vital for proper matrix protein localization and is dependent on the family of peroxin (PEX) proteins. The delivery and peroxisomal import of cargo from a loaded receptor, PEX5 or PEX7, is carried out by the early-acting peroxins, including PEX13 and PEX14, and receptor recycling is carried out by the late-acting peroxins, including PEX4 and PEX6. In this thesis, I describe the use of double mutant analysis to differentiate early-acting and late-acting pex mutants by phenotypic and molecular analysis. I found that double mutants made with two early-acting or two late-acting pex mutants showed enhanced phenotypes in β-oxidation and import defects. In contrast, defects of double mutants made with a weak early-acting mutant and a late-acting mutant were suppressed. Additionally, I found that receptor localization is central to proper peroxisomal function. My results suggest that when the receptor is not removed from the peroxisome, stabilized peroxisomal pores may be formed, perhaps impairing peroxisomal function due to leaching of peroxisomal contents. Together my data suggest that balance between import and receptor recycling is fundamental for peroxisomal function. In humans, peroxisomal biogenesis disorders are most often caused by defects in late-acting peroxins. Peroxisomal defects occur in plants and humans as a result of the same lesions in PEX proteins. The understanding of how these late-acting defects can be ameliorated in plants, may inspire new approaches to human therapeutics.

The terahertz (THz) frequency range. 0.1 - 20 THz, exists between the microwave and infrared ranges and contains abundant information on the dynamics of charge and spin carriers in condensed matter systems. Since its advent two decades ago, THz spectroscopy has been extensively used to study a wide range of solid state materials, including typical semiconductors, conducting polymers, insulators, superconductors, and artificially grown structures such as quantum wells. In these systems, electronic and photonic events tend to occur on the time scale of tens to hundreds of femtoseconds, which results in many important excitations, resonances and dynamical phenomena in the THz frequency range. In this dissertation work, we have developed a typical THz time-domain spectroscopy (TDS) system to investigate the THz dynamics of quantum-confined electrons in two important types of carbon nanomaterial: single-walled carbon nanotubes (SWNTs) and graphene. Polarization dependent THz transmission measurements were conducted on a highly-aligned SWNT film on a sapphire substrate, revealing extremely high anisotropy: virtually no attenuation was observed when the polarization of the THz beam was perpendicular to the nanotube axis, while the THz beam was strongly absorbed when its polarization was parallel to the tube axis. From the measured absorption anisotropy, we calculated the reduced linear dichrosim to be 3, corresponding to a nematic order parameter of 1. These observations are a direct result of the one-dimensional nature of conduction electrons in the nanotubes and at the same time, demonstrate that any misalignment of nanotubes in the film mast have characteristic length scales much smaller than the wavelengths used in these experiments (1.5 mm - 150 μm). Based on this work, an ideal THz linear polarizer built with parallel stacks of such aligned SWNT films was synthesized, exhibiting a degree of polarization of 99.9% throughout the frequency range 0.2 - 2.2 THz and a high extinction ratio of 10 -3 (or 30 dB). The THz complex conductivity of the thin SWNT film was extracted through a proper model directly from the TDS data without Kramers-Kronig analysis. Both real and imaginary parts of the conductivity showed a non-Drude frequency dependence, indicating the presence of plasmon-dipole resonance at higher frequencies. Finally, the optical conductivity of large-area. graphene grown from solid state carbon source was studied in a wide spectral range (7 cm -1 - 9500 cm -1 ) using THz-TDS and Fourier transform infrared spectroscopy. We observed that the Fermi level E f of graphene could be tuned by both electrical gating and thermal annealing. The optical conductivity measured at different carrier concentrations exhibited Drude-like frequency dependence, and different 2 E f onsets in the spectrum were probed as well.

New electrochemical storage and conversion materials hold promise as important additions to the world's energy supply, and the growing ability to control both sequestration and transfer of charge and matter via functionally responsive materials promises to transform the field. Already, new understanding of the role played by nano-scale morphology of materials in transport function has contributed to considerable material improvements, with functional polymers possessing specific chemistry and morphology playing a key role in the future of electrochemical material applications. However, many challenges to optimizing properties still exist due to incomplete descriptions of transport. In this work, fluorescence spectroscopy and single molecule spectroscopy experimental techniques and analysis are developed and employed to reveal details of the mechanisms underpinning ion transport in structurally ordered polyelectrolyte polymer-brush membranes. The studies reveal the existence and nature of heterogeneous transport mechanisms in these polymer films, and provide a description of the dynamic association of molecular ions with the brush. It is also shown that it is possible to tune charged ion transport characteristics in the thin films by controlling the solvent pH, with an effective switching of ion transport rates in these brushes past a threshold pH value. Additionally, Monte Carlo models designed to model molecular scale interactions that give rise to experimental observables are developed to provide additional insight into the physical nature of transport processes in these materials. These models provide additional support for the conclusions of the experimental work.

A poly-leucine transmembrane domain library was randomized at positions corresponding to contact surfaces for a right-handed crossing of two helices to determine the significance of small residues, GxxxG motifs, and hydrogen bonding residues in driving helix-helix interactions within membranes. About 10000 sequences, which include the interfaces of tightly interacting biological transmembrane domains, were subjected to increasing selection strength in the membrane interaction assay TOXCAT and surviving clones were sequenced to identify single site and pairwise amino acid trends. Statistical analysis identified a central glycine to be essential to strong dimerization. The next strongest statistical preference was for a phenylalanine three positions before the key glycine. Secondary to these residues, polar histidine and asparagine residues are also favored in strongly dimerizing sequences, but not to the exclusion of hydrophobic leucine and isoleucine. The analysis identifies novel pairwise combinations that contribute to or are excluded from strong dimerization, the most striking of which is that the biologically important GxxxGxxxG/A pattern is under-represented in the most strongly associating BNIP3-like transmembrane dimers. The variety of residue combinations that support strong dimerization indicates that not only key 'motif' residues, but also the residues that flank them, are important for strong dimerization. Because favorable pairwise combinations of flanking residues occur between both proximal positions and residues separated by two or more turns of helix, the complexity of how sequence context influences motif-driven dimerization is very high.

This thesis compared anionic polyelectrolyte wrapping stabilization with poly(sodium 4-stryene-sulfonate), (PSS), polyelectrolyte and methoxy (polyethylene glycol)-thiol (mPEG (5000) -SH) strategies. From this data the critical gold nanorod (GNR) and cetyl-trimethylammonium bromide (CTAB) concentration ratio needed for GNR stabilization was determined using optical and chemical extraction methods. This was followed by functionalization with a heterobifunctional Polyethylene glycol (PEG) linker, such as a-thio-w-carboxy poly(ethylene glycol) termed t-PEG-c and carbodiimide chemistries for antibody linkage with Immunoglobulin G (IgG), and epidermal growth factor receptor (EGFR) based Human Epidermal growth factor Receptor 2 (Her2), and Cetuximab (C225) antibodies, for in vitro cancer cell targeting. Confocal, two-photon luminescence (TPL), and dark scattering microscopy, and fluorescence, zeta potential, and Nanoparticle Enzyme-linked immunosorbent assay (ELISA) were used to monitor changes to the GNR surface. An untreatable form of bladder cancer was then studied using the t-GNR-PEG-c-Ab bioconjugates with C225 antibody, which housed a glyceraldehyde-3-phosphate (GAPDH), Fluorescein isothiocyanate (FITC) labeled siRNA, termed GAPDH-siRNA-FITC, which was included within a Luciferase based plasmid. A salt based electrostatic heating method was used to trap the GAPDH-siRNA-FITC from the PEG layer by activating the PEG polymer pour point, while a laser based heating system was used for in vitro release inside cancer cells. The down regulation of the GAPDH gene was targeted by the siRNA. as GAPDH has been shown to be up-regulated in many cancers and down-regulated by chemotherapeutic drugs. Cell culture, and subsequent imaging by transmission electron microscopy (TEM), TPL and confocal microscopy were used to view the internalized conjugates, and reverse transcriptase polymerase chain reaction (RT-PCR) were used to determine if the release of the GAPDH-siRNA caused a reduction in the expression of GAPDH-mRNA. Plasmonic gene silencing of the gene by the GAPDH-siRNA was then compared to a lipid based Dharmafect control in terms of transfection ability. RT-PCR results evidenced gene silencing of the plasmonic-GAPDH-siRNA vector when compared to the Dharmafect control. Silencing likely resulted from the zwitterionic charges of the plasmonic vector and the encapsulated GAPDH-siRNA, which yielded near neutral charge tendencies. This differs significantly from the Dharmafect lipid vector, which is cationic in nature. Endosomal release of the plasmonic vector is further enhanced by the laser excitation of the GNR at the longitudinal surface plasmon resonance (LSPR), which allows for the endosomal release of the GAPDH-siRNA through pore formation leading to cytoplasmic transport and subsequent gene silencing. Near neutral charges were welcomed in this plasmonic gene therapy study as they tend to favor endosomal release, pore formation, and transport.

Recent advances in the self-assembly of highly organized structures of organic semiconducting molecules by controlled non-covalent interactions has opened avenues for creating materials with unique optical and electrical properties. The main focus of this thesis lies in the synthesis and self-assembly of n-type perylene based organic semiconducting molecules into highly organized materials. Perylene based molecules used in this study are perylene diimide (PTCDI, two side-chains), perylene mono imide (m-PTCI, one side-chain), perylene tetracarboxylic acid (PTCA, no side-chain) and tetra-alkali metal salts of PTCA (M 4 -PTCA, no side-chain), which are synthesized from the parent perylene tetracarboxylic dianhydride (PTCDA). The self-assembly of these molecules have been performed using solution processing methods (dispersion, phase-transfer, and phase-transfer at high temperature) by taking advantage of the changes in solubility of the molecules, wherein the molecular interactions are maximized to favorably allow for the formation of highly organized structures. Dimension control (1D, 2D and 3D structures) of self-assembly has been obtained for different perylene based molecules by appropriate design of the molecule followed by controlling the conditions of assembly. In case of PTCDI, a new solution processing method phase-transfer at high temperature (2L-HT) allowed for the controlled formation of extremely long and fluorescent 1D structure. For the m-PTCI molecules the organization by the 2L-HT method was found to result in highly organized, single-crystalline, fluorescent 2D sheets. In the case of perylene based molecules with no side-chains two different methods have been developed for the realization of organized 1D nanostructures. The first method utilizes the chemical conversion of a highly soluble PTCA into 1D nanofibers of the parent insoluble perylene tetracarboxylic anhydride. The second method utilizes the assembly of tetra potassium salt of PTCA (K 4 -PTCA) into 1D nanostructures. Furthermore, it has been demonstrated that these 1D nanostructures can be chemically converted to two different chemical species, both of which still retain the 1D morphological characteristic, though with changes in the size. Various functional self-assembled structures developed in this thesis opens up new avenues to explore structure-property-function relationships and their use in applications such as sensors, electronics and opto-electronic devices.

Single-walled carbon nanotubes (SWNTs) are one of the leading candidate materials to realize novel nanoscale photonic devices. In order to assess their performance characteristics as optoelectronic materials, it is crucial to examine their optical properties in highly non-equilibrium situations such as high magnetic fields, low temperatures, and under high photoexcitation. Therefore, we present our latest result on the magnetic susceptibility anisotropy of metallic carbon nanotubes due to the Aharonov-Bohm effect. Here, we performed magnetic linear dichroism on a metallic-enriched HiPco SWNT sample utilizing a 35 T Hybrid Magnet to measure absorption with light polarization both perpendicular and parallel to the magnetic field. By relating these values with the nematic order parameter for alignment, we found that the metallic carbon nanotubes do not follow a strict diameter dependence across the 7 chiralities present in our sample. In addition to the studying the absorption properties exhibited at high magnetic field, we performed temperature-dependent (300 K to 11 K) photoluminescence (PL) on HiPco SWNTs embedded in an ι -carrageenan matrix utilizing intense fs pulses from a wavelength-tunable optical parametric amplifier. We found that for each temperature the PL intensity saturates as a function of pump fluence and the saturation intensity increases from 300 K to a moderate temperature around 100-150 K. Within the framework of diffusion-limited exciton-exciton annihilation (EEA), we successfully estimated the density of 1D excitons in SWNTs as a function of temperature and chirality. These results coupled with our results of magnetic brightening, or an increase in PL intensity as a function of magnetic flux through each SWNT due to the Aharonov-Bohm effect, yield great promise that in the presence of a high magnetic field the density of excitons can be further increased.

Plasmonics is a successful new field of science and technology that exploits the exclusive optical properties of metallic nanostructures to manipulate and concentrate light at nano-meter length scales. When light hits the surface of gold or silver nanoparticles it can excite collective oscillations of the conduction electrons called surface plasmons. This surface plasmon undergoes two damping processes; it can decay into photon and reemit the plasmon energy as scattered energy or decay into electron-hole pair with the excitation energy equal to the energy of the plasmon resonance, known as absorption. This high energy electron subsequently undergoes into the carrier multiplication and eventually scatters into the electrons with lower energy. We used Finite-Difference Time-Domain (FDTD) and Finite-Element Method (Comsol) to design nanoscale structures to act as nanoantenna for light harvesting and consequently manipulating radiative and absorption properties of them for Sensing and Photovoltaic applications. To manipulate near and far field we designed our structures in a way that the bright and dark plasmon modes overlap and couple to each other. This process is called Fano resonance and introduces a transparency window in the far-field spectra. At the same time it increases the near-field enhancement. We applied the changes in near-field and far-field to SERS (Surface Enhanced Raman Spectroscopy) and LSPR (Localized Surface plasmon Resonance) shift for sensing purposes. We modeled Fano resonances with classical harmonic oscillator and reproduced the same feature with a simple equation of motion. We used this model to replicate scattering spectra from different geometries and explain the cathodoluminescence results obtained from nanoscale gold clusters structure. All of these nanoantenna optical properties and applications are due to the reemission ability of the plasmon energy to the vacuum and confining optical field, but the plasmon energy can decay into a high energy carrier rather than radiation. Photons coupled into metallic nanoantenna excite resonant plasmons, which can decay into energetic, hot electrons injected over a potential barrier at the nanoantenna-semiconductor interface, resulting in a photocurrent. We design a device which the range of its potential applications is extremely diverse. As silicon based detector capable of detecting sub-band gap photons, this device could be used in photovoltaic devices to harvest solar energy. Plasmon generated hot electrons can be used in photocatalytic dissociation of H2 molecules at the room temperature as well. The hot electrons in their higher energy states can populate the antibonding orbital of H2 molecules adsorbed on the metal surface and thus trigger the H2 molecule dissociation. The goal is to demonstrate the high efficiency of metallic photocatalytic systems by detecting the formation of HD molecules from the individual dissociation of two isotopes, H2 and D2. At the end we introduce lightning rod effect in metallic nanostructures and investigated the relation between the geometry properties of micrometer rod antennas and the electromagnetic field enhancement induced due to the lightning rod effect. At long wavelength, metals behave like perfect equipotential conductors and all the field enhancement results from the drop of potentials across the junctions between individual nanoparticles. This phenomenon is called lightning rod effect. By designing proper geometry we were able to utilize this effect to obtain enough electromagnetic enhancements in MIR region of spectrum to observe SEIRA signals from few hemoglobin molecules. Our simulation shows that the field enhancement obtained from this antenna does not depend sensitively on wavelength which is another advantage for SEIRA spectroscopy. We offered an analytical model to explore the coupling between the hemoglobin molecules and the Efield. We used this model to study the location effect of the molecule on the reflection signal. This technique allows us to detect the vibrational mode of molecules such as Hemoglobin in the real time and study their changes when the molecules are exposed to different environmental circumstances.