Matching Items (49)
Description
The work contained in this dissertation is focused on the optical properties of direct band gap semiconductors which crystallize in a wurtzite structure: more specifically, the III-nitrides and ZnO. By using cathodoluminescence spectroscopy, many of their properties have been investigated, including band gaps, defect energy levels, carrier lifetimes, strain states, exciton binding energies, and effects of electron irradiation on luminescence. Part of this work is focused on p-type Mg-doped GaN and InGaN. These materials are extremely important for the fabrication of visible light emitting diodes and diode lasers and their complex nature is currently not entirely understood. The luminescence of Mg-doped GaN films has been correlated with electrical and structural measurements in order to understand the behavior of hydrogen in the material. Deeply-bound excitons emitting near 3.37 and 3.42 eV are observed in films with a significant hydrogen concentration during cathodoluminescence at liquid helium temperatures. These radiative transitions are unstable during electron irradiation. Our observations suggest a hydrogen-related nature, as opposed to a previous assignment of stacking fault luminescence. The intensity of the 3.37 eV transition can be correlated with the electrical activation of the Mg acceptors. Next, the acceptor energy level of Mg in InGaN is shown to decrease significantly with an increase in the indium composition. This also corresponds to a decrease in the resistivity of these films. In addition, the hole concentration in multiple quantum well light emitting diode structures is much more uniform in the active region when Mg-doped InGaN (instead of Mg-doped GaN) is used. These results will help improve the efficiency of light emitting diodes, especially in the green/yellow color range. Also, the improved hole transport may prove to be important for the development of photovoltaic devices. Cathodoluminescence studies have also been performed on nanoindented ZnO crystals. Bulk, single crystal ZnO was indented using a sub-micron spherical diamond tip on various surface orientations. The resistance to deformation (the "hardness") of each surface orientation was measured, with the c-plane being the most resistive. This is due to the orientation of the easy glide planes, the c-planes, being positioned perpendicularly to the applied load. The a-plane oriented crystal is the least resistive to deformation. Cathodoluminescence imaging allows for the correlation of the luminescence with the regions located near the indentation. Sub-nanometer shifts in the band edge emission have been assigned to residual strain the crystals. The a- and m-plane oriented crystals show two-fold symmetry with regions of compressive and tensile strain located parallel and perpendicular to the ±c-directions, respectively. The c-plane oriented crystal shows six-fold symmetry with regions of tensile strain extending along the six equivalent a-directions.
ContributorsJuday, Reid (Author) / Ponce, Fernando A. (Thesis advisor) / Drucker, Jeff (Committee member) / Mccartney, Martha R (Committee member) / Menéndez, Jose (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2013
Description
Solution conformations and dynamics of proteins and protein-DNA complexes are often difficult to predict from their crystal structures. The crystal structure only shows a snapshot of the different conformations these biological molecules can have in solution. Multiple different conformations can exist in solution and potentially have more importance in the biological activity. DNA sliding clamps are a family of proteins with known crystal structures. These clamps encircle the DNA and enable other proteins to interact more efficiently with the DNA. Eukaryotic PCNA and prokaryotic β clamp are two of these clamps, some of the most stable homo-oligomers known. However, their solution stability and conformational equilibrium have not been investigated in depth before. Presented here are the studies involving two sliding clamps: yeast PCNA and bacterial β clamp. These studies show that the β clamp has a very different solution stability than PCNA. These conclusions were reached through various different fluorescence-based experiments, including fluorescence correlation spectroscopy (FCS), Förster resonance energy transfer (FRET), single molecule fluorescence, and various time resolved fluorescence techniques. Interpretations of these, and all other, fluorescence-based experiments are often affected by the properties of the fluorophores employed. Often the fluorescence properties of these fluorophores are influenced by their microenvironments. Fluorophores are known to sometimes interact with biological molecules, and this can have pronounced effects on the rotational mobility and photophysical properties of the dye. Misunderstanding the effect of these photophysical and rotational properties can lead to a misinterpretation of the obtained data. In this thesis, photophysical behaviors of various organic dyes were studied in the presence of deoxymononucleotides to examine more closely how interactions between fluorophores and DNA bases can affect fluorescent properties. Furthermore, the properties of cyanine dyes when bound to DNA and the effect of restricted rotation on FRET are presented in this thesis. This thesis involves studying fluorophore photophysics in various microenvironments and then expanding into the solution stability and dynamics of the DNA sliding clamps.
ContributorsRanjit, Suman (Author) / Levitus, Marcia (Thesis advisor) / Lindsay, Stuart (Committee member) / Yan, Hao (Committee member) / Arizona State University (Publisher)
Created2013
Description
This dissertation is focused on material property exploration and analysis using computational quantum mechanics methods. Theoretical calculations were performed on the recently discovered hexahydride materials A2SiH6 (A=Rb, K) to calculate the lattice dynamics of the systems in order to check for structural stability, verify the experimental Raman and infrared spectrospcopy results, and obtain the theoretical free energies of formation. The electronic structure of the systems was calculated and the bonding and ionic properties of the systems were analyzed. The novel hexahydrides were compared to the important hydrogen storage material KSiH3. This showed that the hypervalent nature of the SiH62- ions reduced the Si-H bonding strength considerably. These hydrogen rich compounds could have promising energy applications as they link to alternative hydrogen fuel technology. The carbide systems Li-C (A=Li,Ca,Mg) were studied using \emph{ab initio} and evolutionary algorithms at high pressures. At ambient pressure Li2C2 and CaC2 are known to contain C22- dumbbell anions and CaC2 is polymorphic. At elevated pressure both CaC2 and Li2C2 display polymorphism. At ambient pressure the Mg-C system contains several experimentally known phases, however, all known phases are shown to be metastable with respect to the pure elements Mg and C. First principle investigation of the configurational space of these compounds via evolutionary algorithms results in a variety of metastable and unique structures. The binary compounds ZnSb and ZnAs are II-V electron-poor semiconductors with interesting thermoelectric properties. They contain rhomboid rings composed of Zn2Sb2 (Zn2As2) with multi-centered covalent bonds which are in turn covalently bonded to other rings via two-centered, two-electron bonds. Ionicity was explored via Bader charge analysis and it appears that the low ionicity that these materials display is a necessary condition of their multicentered bonding. Both compounds were found to have narrow, indirect band gaps with multi-valley valence and conduction bands; which are important characteristics for high thermopower in thermoelectric materials. Future work is needed to analyze the lattice properties of the II-V CdSb-type systems, especially in order to find the origin of the extremely low thermal conductivity that these systems display.
ContributorsBenson, Daryn Eugene (Author) / Häussermann, Ulrich (Thesis advisor) / Shumway, John (Thesis advisor) / Chamberlin, Ralph (Committee member) / Sankey, Otto (Committee member) / Treacy, Mike (Committee member) / Arizona State University (Publisher)
Created2013
Description
Single molecule DNA Sequencing technology has been a hot research topic in the recent decades because it holds the promise to sequence a human genome in a fast and affordable way, which will eventually make personalized medicine possible. Single molecule differentiation and DNA translocation control are the two main challenges in all single molecule DNA sequencing methods. In this thesis, I will first introduce DNA sequencing technology development and its application, and then explain the performance and limitation of prior art in detail. Following that, I will show a single molecule DNA base differentiation result obtained in recognition tunneling experiments. Furthermore, I will explain the assembly of a nanofluidic platform for single strand DNA translocation, which holds the promised to be integrated into a single molecule DNA sequencing instrument for DNA translocation control. Taken together, my dissertation research demonstrated the potential of using recognition tunneling techniques to serve as a general readout system for single molecule DNA sequencing application.
ContributorsLiu, Hao (Author) / Lindsay, Stuart M (Committee member) / Yan, Hao (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2013
Description
Monte Carlo methods often used in nuclear physics, such as auxiliary field diffusion Monte Carlo and Green's function Monte Carlo, have typically relied on phenomenological local real-space potentials containing as few derivatives as possible, such as the Argonne-Urbana family of interactions, to make sampling simple and efficient. Basis set methods such as no-core shell model or coupled-cluster techniques typically use softer non-local potentials because of their more rapid convergence with basis set size. These non-local potentials are typically defined in momentum space and are often based on effective field theory. Comparisons of the results of the two types of methods are complicated by the use of different potentials. This thesis discusses progress made in using such non-local potentials in quantum Monte Carlo calculations of light nuclei. In particular, it shows methods for evaluating the real-space, imaginary-time propagators needed to perform quantum Monte Carlo calculations using non-local potentials and universality properties of these propagators, how to formulate a good trial wave function for non-local potentials, and how to perform a "one-step" Green's function Monte Carlo calculation for non-local potentials.
ContributorsLynn, Joel E (Author) / Schmidt, Kevin E (Thesis advisor) / Alarcon, Ricardo (Committee member) / Lebed, Richard (Committee member) / Shovkovy, Igor (Committee member) / Shumway, John (Committee member) / Arizona State University (Publisher)
Created2013
Description
Nitride semiconductors have wide applications in electronics and optoelectronics technologies. Understanding the nature of the optical recombination process and its effects on luminescence efficiency is important for the development of novel devices. This dissertation deals with the optical properties of nitride semiconductors, including GaN epitaxial layers and more complex heterostructures. The emission characteristics are examined by cathodoluminescence spectroscopy and imaging, and are correlated with the structural and electrical properties studied by transmission electron microscopy and electron holography. Four major areas are covered in this dissertation, which are described next. The effect of strain on the emission characteristics in wurtzite GaN has been studied. The values of the residual strain in GaN epilayers with different dislocation densities are determined by x-ray diffraction, and the relationship between exciton emission energy and the in-plane residual strain is demonstrated. It shows that the emission energy increases withthe magnitude of the in-plane compressive strain. The temperature dependence of the emission characteristics in cubic GaN has been studied. It is observed that the exciton emission and donor-acceptor pair recombination behave differently with temperature. The donor-bound exciton binding energy has been measured to be 13 meV from the temperature dependence of the emission spectrum. It is also found that the ionization energies for both acceptors and donors are smaller in cubic compared with hexagonal structures, which should contribute to higher doping efficiencies. A comprehensive study on the structural and optical properties is presented for InGaN/GaN quantum wells emitting in the blue, green, and yellow regions of the electromagnetic spectrum. Transmission electron microscopy images indicate the presence of indium inhomogeneties which should be responsible for carrier localization. The temperature dependence of emission luminescence shows that the carrier localization effects become more significant with increasing emission wavelength. On the other hand, the effect of non-radiative recombination on luminescence efficiency also varies with the emission wavelength. The fast increase of the non-radiative recombination rate with temperature in the green emitting QWs contributes to the lower efficiency compared with the blue emitting QWs. The possible saturation of non-radiative recombination above 100 K may explain the unexpected high emission efficiency for the yellow emitting QWs Finally, the effects of InGaN underlayers on the electronic and optical properties of InGaN/GaN quantum wells emitting in visible spectral regions have been studied. A significant improvement of the emission efficiency is observed, which is associated with a blue shift in the emission energy, a reduced recombination lifetime, an increased spatial homogeneity in the luminescence, and a weaker internal field across the quantum wells. These are explained by a partial strain relaxation introduced by the InGaN underlayer, which is measured by reciprocal space mapping of the x-ray diffraction intensity.
ContributorsLi, Di (Author) / Ponce, Fernando (Thesis advisor) / Culbertson, Robert (Committee member) / Yu, Hongbin (Committee member) / Shumway, John (Committee member) / Menéndez, Jose (Committee member) / Arizona State University (Publisher)
Created2012
Description
High electron mobility transistors (HEMTs) based on Group III-nitride heterostructures have been characterized by advanced electron microscopy methods including off-axis electron holography, nanoscale chemical analysis, and electrical measurements, as well as other techniques. The dissertation was organized primarily into three topical areas: (1) characterization of near-gate defects in electrically stressed AlGaN/GaN HEMTs, (2) microstructural and chemical analysis of the gate/buffer interface of AlN/GaN HEMTs, and (3) studies of the impact of laser-liftoff processing on AlGaN/GaN HEMTs. The electrical performance of stressed AlGaN/GaN HEMTs was measured and the devices binned accordingly. Source- and drain-side degraded, undegraded, and unstressed devices were then prepared via focused-ion-beam milling for examination. Defects in the near-gate region were identified and their correlation to electrical measurements analyzed. Increased gate leakage after electrical stressing is typically attributed to "V"-shaped defects at the gate edge. However, strong evidence was found for gate metal diffusion into the barrier layer as another contributing factor. AlN/GaN HEMTs grown on sapphire substrates were found to have high electrical performance which is attributed to the AlN barrier layer, and robust ohmic and gate contact processes. TEM analysis identified oxidation at the gate metal/AlN buffer layer interface. This thin a-oxide gate insulator was further characterized by energy-dispersive x-ray spectroscopy and energy-filtered TEM. Attributed to this previously unidentified layer, high reverse gate bias up to −30 V was demonstrated and drain-induced gate leakage was suppressed to values of less than 10−6 A/mm. In addition, extrinsic gm and ft * LG were improved to the highest reported values for AlN/GaN HEMTs fabricated on sapphire substrates. Laser-liftoff (LLO) processing was used to separate the active layers from sapphire substrates for several GaN-based HEMT devices, including AlGaN/GaN and InAlN/GaN heterostructures. Warpage of the LLO samples resulted from relaxation of the as-grown strain and strain arising from dielectric and metal depositions, and this strain was quantified by both Newton's rings and Raman spectroscopy methods. TEM analysis demonstrated that the LLO processing produced no detrimental effects on the quality of the epitaxial layers. TEM micrographs showed no evidence of either damage to the ~2 μm GaN epilayer generated threading defects.
ContributorsJohnson, Michael R. (Author) / Mccartney, Martha R (Thesis advisor) / Smith, David J. (Committee member) / Goodnick, Stephen (Committee member) / Shumway, John (Committee member) / Chen, Tingyong (Committee member) / Arizona State University (Publisher)
Created2012
Description
Spider dragline silk is well known for its outstanding mechanical properties - a combination of strength and extensibility that makes it one of the toughest materials known. Two proteins, major ampullate spidroin 1 (MaSp1) and 2 (MaSp2), comprise dragline silk fibers. There has been considerable focus placed on understanding the source of spider silk's unique mechanical properties by investigating the protein composition, molecular structure and dynamics. Chemical compositional heterogeneity of spider silk fiber is critical to understand as it provides important information for the interactions between MaSp1 and MaSp2. Here, the amino acid composition of dragline silk protein was precisely determined using a solution-state nuclear magnetic resonance (NMR) approach on hydrolyzed silk fibers. In a similar fashion, solution-state NMR was applied to probe the "13"C/"15"N incorporation in silk, which is essential to understand for designing particular solid-state NMR methods for silk structural characterization. Solid-state NMR was used to elucidate silk protein molecular dynamics and the supercontraction mechanism. A "2"H-"13"C heteronuclear correlation (HETCOR) solid-state NMR technique was developed to extract site-specific "2"H quadrupole patterns and spin-lattice relaxation rates for understanding backbone and side-chain dynamics. Using this technique, molecular dynamics were determined for a number of repetitive motifs in silk proteins - Ala residing nanocrystalline &beta-sheet; domains, 3"1"-helical regions, and, Gly-Pro-Gly-XX &beta-turn; motifs. The protein backbone and side-chain dynamics of silk fibers in both dry and wet states reveal the impact of water on motifs with different secondary structures. Spider venom is comprised of a diverse range of molecules including salts, small organics, acylpolyamines, peptides and proteins. Neurotoxins are an important family of peptides in spider venom and have been shown to target and modulate various ion channels. The neurotoxins are Cys-rich and share an inhibitor Cys knot (ICK) fold. Here, the molecular structure of one G. rosea tarantula neurotoxin, GsAF2, was determined by solution-state NMR. In addition, the interaction between neurotoxins and model lipid bilayers was probed with solid-state NMR and negative-staining (NS) transmission electron microscopy (TEM). It is shown that the neurotoxins influence lipid bilayer assembly and morphology with the formation of nanodiscs, worm-like micelles and small vesicles.
ContributorsShi, Xiangyan (Author) / Yarger, Jeffery L (Thesis advisor) / Holland, Gregory P (Thesis advisor) / Levitus, Marcia (Committee member) / Marzke, Robert F (Committee member) / Arizona State University (Publisher)
Created2014
Description
Rapid and reliable separation and analysis of proteins require powerful analytical methods. The analysis of proteins becomes especially challenging when only small sample volumes are available, concomitantly with low concentrations of proteins. Time critical situations pose additional challenges. Due to these challenges, conventional macro-scale separation techniques reach their limitations. While microfluidic devices require only pL-nL sample volumes, they offer several advantages such as speed, efficiency, and high throughput. This work elucidates the capability to manipulate proteins in a rapid and reliable manner with a novel migration technique, namely dielectrophoresis (DEP). Since protein analysis can often be achieved through a combination of orthogonal techniques, adding DEP as a gradient technique to the portfolio of protein manipulation methods can extend and improve combinatorial approaches. To this aim, microfluidic devices tailored with integrated insulating obstacles were fabricated to create inhomogeneous electric fields evoking insulator-based DEP (iDEP). A main focus of this work was the development of pre-concentration devices where topological micropost arrays are fabricated using standard photo- and soft lithographic techniques. With these devices, positive DEP-driven streaming of proteins was demonstrated for the first time using immunoglobulin G (IgG) and bovine serum albumin. Experimentally observed iDEP concentrations of both proteins were in excellent agreement with positive DEP concentration profiles obtained by numerical simulations. Moreover, the micropost iDEP devices were improved by introducing nano-constrictions with focused ion beam milling with which numerical simulations suggested enhancement of the DEP effect, leading to a 12-fold increase in concentration of IgG. Additionally, concentration of β-galactosidase was observed, which seems to occur due to an interplay of negative DEP, electroosmosis, electrokinesis, diffusion, and ion concentration polarization. A detailed study was performed to investigate factors influencing protein DEP under DC conditions, including electroosmosis, electrophoresis, and Joule heating. Specifically, temperature rise within the iDEP device due to Joule heating was measured experimentally with spatial and temporal resolution by employing the thermosensitive dye Rhodamine B. Unlike DNA and cells, protein DEP behavior is not well understood to date. Therefore, this detailed study of protein DEP provides novel information to eventually optimize this protein migration method for pre-concentration, separation, and fractionation.
ContributorsNakano, Asuka (Author) / Ros, Alexandra (Thesis advisor) / Hayes, Mark (Committee member) / Levitus, Marcia (Committee member) / Arizona State University (Publisher)
Created2014
Description
Ribulose-1, 5-bisphosphate carboxylase oxygenase, commonly known as RuBisCO, is an enzyme involved in carbon fixation in photosynthetic organisms. The enzyme is subject to a mechanism-based deactivation during its catalytic cycle. RuBisCO activase (Rca), an ancillary enzyme belonging to the AAA+ family of the ATP-ases, rescues RuBisCO by facilitating the removal of the tightly bound sugar phosphates from the active sites of RuBisCO. In this work, we investigated the ATP/ADP dependent oligomerization equilibrium of fluorescently tagged Rca for a wide range of concentrations using fluorescence correlation spectroscopy. Results show that in the presence of ADP-Mg2+, the oligomerization state of Rca gradually changes in steps of two subunits. The most probable association model supports the dissociation constants (K_d) of ∼4, 1, 1 μM for the monomer-dimer, dimer-tetramer, and tetramer-hexamer equlibria, respectively. Rca continues to assemble at higher concentrations which are indicative of the formation of aggregates. In the presence of ATP-Mg2+, a similar stepwise assembly is observed. However, at higher concentrations (30-75 µM), the average oligomeric size remains relatively unchanged around six subunits per oligomer. This is in sharp contrast with observations in ADP-Mg2+, where a marked decrease in the diffusion coefficient of Rca was observed, consistent with the formation of aggregates. The estimated K_d values obtained from the analysis of the FCS decays were similar for the first steps of the assembly process in both ADP-Mg2+ and ATP-Mg2+. However, the formation of the hexamer from the tetramer is much more favored in ATP-Mg2+, as evidenced from 20 fold lower K_d associated with this assembly step. This suggests that the formation of a hexameric ring in the presence of ATP-Mg2+. In addition to that, Rca aggregation is largely suppressed in the presence of ATP-Mg2+, as evidenced from the 1000 fold larger K_d value for the hexamer-24 mer association step. In essence, a fluorescence-based method was developed to monitor in vitro protein oligomerization and was successfully applied with Rca. The results provide a strong hint at the active oligomeric structure of Rca, and this information will hopefully help the ongoing research on the mechanistic enzymology of Rca.
ContributorsChakraborty, Manas (Author) / Levitus, Marcia (Thesis advisor) / Angell, Charles (Committee member) / Lindsay, Stuart (Committee member) / Arizona State University (Publisher)
Created2014