Thesis (Ph. D.)--Auburn University, 2008. / Abstract. Vita. The following patent resulted from the dissertation research: Davis, V., Simonian, A.L., Nepal, D., Balasubramanian, S, "Preparation of Precisely Controlled Thin Film Nanocomposites of Carbon Nanotubes and Biomaterials", U.S. Provisional Patent Application No. 61/000,938, filed on 30 October 2007. The following peer-reviewed publications resulted from the dissertation research: Dhriti Nepal, Shankar Balasubramanian, Aleksandr Simonian, and Virginia Davis, "Mechanically Strong Antibacterial Thin Film Based on Single-Walled Carbon Nanotubes Armored with Biopolymers", Nano Letters ASAP article, May 2008 (# equal contribution) -- Shankar Balasubramanian, Iryna B. Sorokulova, Vitaly J. Vodyanoy, and Aleksandr L. Simonian, "Lytic Phage as a Specific and Selective Probe For Detection of Staphylococcus Aureus: A Surface Plasmon Resonance Spectroscopic Study", Biosensors and Bioelectronics, 2007, 22, 948-955 -- Shankar Balasubramanian, Alexander Revzin, Aleksandr Simonian, "Electrochemical Desorption of Proteins from Gold Electrode Surface", Electroanalysis, 2006, 18, 1885-1892 (Invited article) -- Vishwaprakash Nanduri, Shankar Balasubramanian, Srinivas Sista, Vitaly J. Vodyanoy, and Aleksandr L. Simonian, "Highly Sensitive Phage-based Biosensor for the Detection of ß-galactosidase", Analytica Chimica Acta, 2007, 589, 166- 172 -- H. Luckarift, Shankar Balasubramanian, S. Paliwal, G. Johnson and A. Simonian, "Enzyme-Encapsulated Silica Monolayers For Rapid Functionalization of a Gold Surface", Colloids and Surfaces B: Biointerfaces, 2007, 58, 28-33 (Invited article) -- Dong Wei, Omar Oyarzabal, Tung-Shi Huang, Shankar Balasubramanian, Srinivas Sista, Aleksandr Simonian, "Development of Surface Plasmon Resonance Biosensor For The Identification of Campylobacter jejuni", Journal of Microbiological Methods, 2007, 69, 78-85. The following conferences presentations resulted from the dissertation research: Covalent Immobilization of Organophosphorus Hydrolase on Carbon Nanotubes for Biosensor Applications, accepted for oral presentation at 12th International Meeting on Chemical Sensors, Jul. 13-16, 2008, Columbus, OH -- Electrochemical characteristics of SWNT-biopolymer nanocomposites, accepted for 213th meeting of The Electrochemical Society, May 18-23, 2008, Phoenix, AR -- Mechanically Robust Antibacterial Thin Films Composed of Single-Walled Carbon Nanotubes and Biopolymers, 2008 AIChE Spring National Meeting, Apr. 6-10, New Orleans, LA -- Production and characterization of protein and DNA based single wall carbon nanocomposites by layer-by-layer assembly, MRS Fall Meeting, Nov. 26-30, 2007, Boston, MA -- Gold surface modified with enzyme-encapsulated silica monolayers for biosensor application, The 58th Southeast Regional Meeting of the American Chemical Society, Nov. 1-4, 2006, Augusta, GA -- Electrochemical modulation of biological interfaces, 209th meeting of The Electrochemical Society, May 7-12, 2006, Denver, CO -- SPR based biosensor using lytic phage as a specific and selective probe for staphylococcus aureus detection, 57th Pittsburgh Conference on Analytical Chemistry and Applied Spectroscopy, Mar. 12-17, 2006, Orlando, FL -- Specific & selective detection of staphylococcus aureus by lytic phage using SPR biosensor, 57th Southeast / 61st Southwest Joint Regional Meeting of the American Chemical Society, Nov. 1-4, 2005, Memphis, TN -- Prevention of non-specific binding as a way to increase sensitivity of SPR-based sensors, 206th meeting of The Electrochemical Society, October 3-8, 2004, Honolulu, HI. Includes bibliographical references.

Gold nanoparticles are excellent candidates for all the biomedical applications due to their size and shape dependent optical and physiological properties. In this study, gold nanoparticles were synthesized chemically for bio-application. It was observed that the size and shape of gold nanoparticles depend strongly on the concentration of chemical solution, type of reducing agent used in the reaction, temperature of the solution and stabilizing agent for reaction. Transmission electron microscopy (TEM) has been used extensively to determine the size and shape of the gold nanoparticles. Optical properties of the size and shape selected nanoparticles were studied using UV-vis spectrophotometer in absorption mode. The chemically synthesized gold nanoparticles were observed to show excellent absorption property which is reflected by the presence of the characteristic surface plasmon resonance (SPR) band peak. The SPR peak was found to be predominantly dependent on the size of nanoparticles. We have observed a strong red shift with increasing the size of gold nanoparticles. The position of the SPR peak was also observed to change with shape of gold nanostructures. Synthesis and characterization of the composites of gold nanoparticles and Poly (Oanisidine) (POAS) have been carried out in this thesis. Gold-POAS materials system was characterized using UV-vis spectroscopy, TEM, Fourier Transform Infrared Spectroscopy. The chemically synthesized gold nanoparticles were successfully utilized for the study of Respiratory Syncycial Virus (RSV) interaction. Gold nanoparticles were found to inhibit the RSV infection. The electrochemical behavior of gold nanoparticles was studied and their potentials for biosensing applications were tested. Cyclic voltaammetry was performed for the detection of dopamine and ascorbic acid using gold nanoparticles of different sizes. Interaction of gold nanoparticles with Bovine Serum Albumin (BSA) has been studied via absorption spectroscopy and TEM measurements. The absorption spectra of the GNP-BSA show remarkable shift in SPR band peak towards high wavelength. Catalytic properties of the gold nanoparticles were studied by using them as a catalytic activator for the gas sensing applications.

Food poisoning is mainly caused by pathogenic microorganisms and is now a severe problem worldwide. Therefore, rapid and sensitive methods are required to detect foodborne pathogens. A locally isolated bacterium, Bacillus licheniformis B38 was selected for this study. The spores of B. licheniformis B38 were induced by Schaeffer’s sporulation medium containing KCl, MgSO4.7H2O, Ca(NO3)4, MnCl2 and FeSO4. Schaeffer-Fulton endospore staining was used to differentiate spores and vegetative cells, where spores were stained green and vegetative cells were stained red. In order to separate the spores from the cells, a two-phase system was used to obtain pure spore suspension for following experiments. Spore coat proteins were extracted by SDS-8 M urea sample buffer and visualized by two different types of coomassie brilliant blue staining solutions. One of the staining solutions was more suitable for gel elution by diffusion. An ~10 kDa spore coat protein was selected for protein purification. Based on the given results, the protein purification by liquid chromatography was less convincing than using gel elution by diffusion technique. The two hypothetical protein sequences, P06552 and P45693, from the ~10 kDa spore coat protein were identified. In the preliminary study of B. licheniformis B38 spores detection by surface plasmon resonance, several binding parameters were studied. Dot blot was done to verify the reaction between the Bacillus spores polyclonal antibody against the B. licheniformis B38 spore coat protein. The most promising result was the binding of 0.1 mg/mL polyclonal antibody (analyte) to the 0.2 mg/mL spore coat protein at pH 2 (ligand) which showed 5.74 RU. The differences between a dot blot and a SPR detection techniques are described.

Thermophotovoltaic (TPV) devices, also known as (nano-TPVs) are energy-conversion systems which generate electric current from thermal radiation energy by a heat source. Although their conversion efficiency is limited in the far field by the Schockley-Queisser limit, in near field the heat flux transferred to a TPV cell can be significantly enchanced due to the contribution of evanescent waves, in particular supporting a surface mode. Unfortunately, spectral mismatch between the emitter and the TPV cell spectrum limits the TPV conversion efficiency. Photons with energy lower than the TPV cell bandgap may not be able to create electron-hole pairs because mobile carriers start diffusing and drifting between conductance and valence band, and try to exceed the upper limit of the band. This destroys the thermal equilibrium of the semiconductor and results in excess heat. Also, for high energy photons, the difference between the photon's energy and the bandgap energy is lost in Joule heating. Thus, quasimonochromatic, narrow-band and coherent emitters at a frequency near the energy bandgap of the converter is an ideal source to achieve high conversion efficiency. Nano-TPV device consisting of tungsten thermal emitter, maintained at 1200K, and the cell made of GaInAsSb are considered; thermal management system is reviewed assuming a constant heat flux boundary due to heat generation by the cell with a fluid temperature fixed at 293K. Tungsten thermal selective emitters are designed, characterized and optimized based on two-dimensional (2D) tungsten PhC by controlling periodic triangular grooves such that channel plasmon polaritons (CPPs) are coupled efficiently into these grooves to excite a localized groove modes which are well-matched to the GaInAsSb cell external quantum efficiency (EQE). The results show that power output and the 2D TE normal efficiency of the system are predicted to be 0.82x10⁴ W/m² and 43.8%, respectively. This leads to a promising device for many different sectors such as military, space and semiconductor industry. / text

Optical whispering-gallery mode (WGM) cavities, which exhibit extraordinary spatial and temporal confinement of light, are one of the leading transducers for examining molecular recognition at low particle counts. With the advent of hybrid photonic-plasmonic and increasingly sophisticated forms of these resonators, the importance of supporting numerical methods has correspondingly become evident. In response, we adopt a full-vector finite difference approximation in order to solve for WGM's in terms of their field distributions, resonant wavelengths, and quality factors in the context of naturally discontinuous permittivity structure. A segmented Taylor series and alignment/rotation operator are utilized at such singularities in conjunction with arbitrarily spaced grid points. Simulations for microtoroids, with and without dielectric nanobeads, and plasmonic microdisks are demonstrated for short computation times and shown to be in agreement with data in the literature. Constricted surface plasmon polariton (SPP) WGM's are also featured within this document. The module of this thesis is devised as a keystone for composite WGM models that may guide experiments in the field. / Graduate

Small molecules interacting with DNA is an emerging theme in scientific research due to its specificity and minimal side-effect. Moreover, a large amount of research has been done on finding compounds that can stabilize G-quadruplex DNA, a non-canonical secondary DNA structure, to inhibit cancerous cell proliferation. G-quadruplex DNA is found in the guanine-rich region of the chromosome that has an important role in protecting chromosomes from unwinding, participate in gene expression, contribute in the control replication of cells and more. In this research, rationally designed, synthetic cyanine dye derivatives, which were tested under physiologically relevant conditions, were found to selectively bind to G-quadruplex over duplex DNA and are favored to one structure over another. The interactions were observed using UV-Vis thermal melting, fluorescence titration, circular dichroism titration, and surface plasmon resonance analysis. For fluorescence and selectivity properties, cyanine dyes, therefore, have the potential to become the detections and/or therapeutic drugs to target cancers and many other fatal diseases.

With the manufacture of nano-scale features in the last ten years, it is possible to do optical experiments on features as small as a tenth/hundredth wavelength. It turns out that the experimental data cannot be explained by classical diffraction theories. Thus, it is necessary to develop new methods or use existing approaches which are effective in other fields, to solve problems in photonics. We use finite difference time domain (FDTD), to study transmission properties of sub-wavelength slits in a metallic film. By doing simulations on periodic and single slits, we confirm that the TE mode has a cutoff while a TM mode always has a propagating mode in the small apertures. Then we find that the transmittance is minimum when the array period is equal to the wavelength of surface plasmon polariton (SPP) at normal incidence. In fact, the SPP-like waves exist in both periodic and isolated slits, and they help the transmittance of small apertures. In order to establish the role of SPP in the transmission mechanism, it is necessary to single out each mode from the total fields. We developed Bloch mode method (BMM) to calculate the amplitudes of the lowest N orders, and the amplitudes tell us which one is dominant (not including the guided mode) at high and low transmission. BMM converges very fast and it is more accurate than FDTD since it does not suffer from numerical dispersion. Both methods can resolve the Wood anomaly and SPP anomaly; however, FDTD converges very slowly at the SPP resonance and oscillates around the value obtained through BMM at the Wood anomaly. BMM is not sensitive to material types, incident angles, and anomalies; it will be a useful tool to investigate similar problems.

Calpains are a family of intracellular cysteine proteases activated by calcium. They participate in many processes including cell motility, cell cycle progression and cell death, in response to calcium signaling. Because calpain over-activation as a result of calcium dysregulation is a contributing factor to many disease states, these enzymes are important therapeutic targets. Within the cell, calpains 1 and 2 are regulated by the protein inhibitor calpastatin. This unstructured protein is specific for calpain, binds tightly, and recognizes only the activated form of the enzyme. Detailed kinetic data obtained using surface plasmon resonance allowed the association and dissociation rates of each of the four calpastatin inhibitory domains to be measured. Based on this, inhibitory domain 4 was selected to be co-crystallized bound to calpain 2. The X-ray crystal structure of this complex provided both the first view of the active enzyme, as well as the first view of how it is inhibited. Calpastatin wraps around the enzyme making contact with each domain. It lies in the active site as a contiguous polypeptide chain and escapes cleavage by forming a loop away from the catalytic cysteine. In addition to inhibiting substrate cleavage, calpastatin protects calpain in two ways; it prevents autoproteolysis, and it prevents calcium-dependent aggregation. The crystal structure of the calpastatin:calpain complex revealed no obvious reason for this stabilization. To elucidate how this protection occurs, peptides were synthesized corresponding to conserved subdomains of calpastatin. Surprisingly, each peptide alone was capable of preventing aggregation in vitro, by blocking hydrophobic patches exposed upon activation. The increased hydrophobic surface of the activated enzyme may alter calpain’s affinity for other proteins such as substrates. By binding across many domains of calpain, calpastatin could act to block protein-protein interactions. These studies have characterized calpastatin’s interaction with calpain, which will further our understanding of the enzyme’s regulation and aid in the development of better calpain inhibitors. / Thesis (Ph.D, Biochemistry) -- Queen's University, 2010-04-29 15:27:16.208

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