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- Genre: Doctoral Dissertation
Interactions driving the collapse of islet amyloid polypeptide: implications for amyloid aggregation
Description
Human islet amyloid polypeptide (hIAPP), also known as amylin, is a 37-residue intrinsically disordered hormone involved in glucose regulation and gastric emptying. The aggregation of hIAPP into amyloid fibrils is believed to play a causal role in type 2 diabetes. To date, not much is known about the monomeric state of hIAPP or how it undergoes an irreversible transformation from disordered peptide to insoluble aggregate. IAPP contains a highly conserved disulfide bond that restricts hIAPP(1-8) into a short ring-like structure: N_loop. Removal or chemical reduction of N_loop not only prevents cell response upon binding to the CGRP receptor, but also alters the mass per length distribution of hIAPP fibers and the kinetics of fibril formation. The mechanism by which N_loop affects hIAPP aggregation is not yet understood, but is important for rationalizing kinetics and developing potential inhibitors. By measuring end-to-end contact formation rates, Vaiana et al. showed that N_loop induces collapsed states in IAPP monomers, implying attractive interactions between N_loop and other regions of the disordered polypeptide chain . We show that in addition to being involved in intra-protein interactions, the N_loop is involved in inter-protein interactions, which lead to the formation of extremely long and stable β-turn fibers. These non-amyloid fibers are present in the 10 μM concentration range, under the same solution conditions in which hIAPP forms amyloid fibers. We discuss the effect of peptide cyclization on both intra- and inter-protein interactions, and its possible implications for aggregation. Our findings indicate a potential role of N_loop-N_loop interactions in hIAPP aggregation, which has not previously been explored. Though our findings suggest that N_loop plays an important role in the pathway of amyloid formation, other naturally occurring IAPP variants that contain this structural feature are incapable of forming amyloids. For example, hIAPP readily forms amyloid fibrils in vitro, whereas the rat variant (rIAPP), differing by six amino acids, does not. In addition to being highly soluble, rIAPP is an effective inhibitor of hIAPP fibril formation . Both of these properties have been attributed to rIAPP's three proline residues: A25P, S28P and S29P. Single proline mutants of hIAPP have also been shown to kinetically inhibit hIAPP fibril formation. Because of their intrinsic dihedral angle preferences, prolines are expected to affect conformational ensembles of intrinsically disordered proteins. The specific effect of proline substitutions on IAPP structure and dynamics has not yet been explored, as the detection of such properties is experimentally challenging due to the low molecular weight, fast reconfiguration times, and very low solubility of IAPP peptides. High-resolution techniques able to measure tertiary contact formations are needed to address this issue. We employ a nanosecond laser spectroscopy technique to measure end-to-end contact formation rates in IAPP mutants. We explore the proline substitutions in IAPP and quantify their effects in terms of intrinsic chain stiffness. We find that the three proline mutations found in rIAPP increase chain stiffness. Interestingly, we also find that residue R18 plays an important role in rIAPP's unique chain stiffness and, together with the proline residues, is a determinant for its non-amyloidogenic properties. We discuss the implications of our findings on the role of prolines in IDPs.
ContributorsCope, Stephanie M (Author) / Vaiana, Sara M (Thesis advisor) / Ghirlanda, Giovanna (Committee member) / Ros, Robert (Committee member) / Lindsay, Stuart M (Committee member) / Ozkan, Sefika B (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
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
The thesis studies new methods to fabricate optoelectronic Ge1-ySny/Si(100) alloys and investigate their photoluminescence (PL) properties for possible applications in Si-based photonics including IR lasers. The work initially investigated the origin of the difference between the PL spectrum of bulk Ge, dominated by indirect gap emission, and the PL spectrum of Ge-on-Si films, dominated by direct gap emission. It was found that the difference is due to the supression of self-absorption effects in Ge films, combined with a deviation from quasi-equilibrium conditions in the conduction band of undoped films. The latter is confirmed by a model suggesting that the deviation is caused by the shorter recombination lifetime in the films relative to bulk Ge. The knowledge acquired from this work was then utilized to study the PL properties of n-type Ge1-ySny/Si (y=0.004-0.04) samples grown via chemical vapor deposition of Ge2H6/SnD4/P(GeH3)3. It was found that the emission intensity (I) of these samples is at least 10x stronger than observed in un-doped counterparts and that the Idir/Iind ratio of direct over indirect gap emission increases for high-Sn contents due to the reduced gamma-L valley separation, as expected. Next the PL investigation was expanded to samples with y=0.05-0.09 grown via a new method using the more reactive Ge3H8 in place of Ge2H6. Optical quality, 1-um thick Ge1-ySny/Si(100) layers were produced using Ge3H10/SnD4 and found to exhibit strong, tunable PL near the threshold of the direct-indirect bandgap crossover. A byproduct of this study was the development of an enhanced process to produce Ge3H8, Ge4H10, and Ge5H12 analogs for application in ultra-low temperature deposition of Group-IV semiconductors. The thesis also studies synthesis routes of an entirely new class of semiconductor compounds and alloys described by Si5-2y(III-V)y (III=Al, V= As, P) comprising of specifically designed diamond-like structures based on a Si parent lattice incorporating isolated III-V units. The common theme of the two thesis topics is the development of new mono-crystalline materials on ubiquitous silicon platforms with the objective of enhancing the optoelectronic performance of Si and Ge semiconductors, potentially leading to the design of next generation optical devices including lasers, detectors and solar cells.
ContributorsGrzybowski, Gordon (Author) / Kouvetakis, John (Thesis advisor) / Chizmeshya, Andrew (Committee member) / Menéndez, Jose (Committee member) / Arizona State University (Publisher)
Created2013
Description
In this dissertation, remote plasma interactions with the surfaces of low-k interlayer dielectric (ILD), Cu and Cu adhesion layers are investigated. The first part of the study focuses on the simultaneous plasma treatment of ILD and chemical mechanical polishing (CMP) Cu surfaces using N2/H2 plasma processes. H atoms and radicals in the plasma react with the carbon groups leading to carbon removal for the ILD films. Results indicate that an N2 plasma forms an amide-like layer on the surface which apparently leads to reduced carbon abstraction from an H2 plasma process. In addition, FTIR spectra indicate the formation of hydroxyl (Si-OH) groups following the plasma exposure. Increased temperature (380 °C) processing leads to a reduction of the hydroxyl group formation compared to ambient temperature processes, resulting in reduced changes of the dielectric constant. For CMP Cu surfaces, the carbonate contamination was removed by an H2 plasma process at elevated temperature while the C-C and C-H contamination was removed by an N2 plasma process at elevated temperature. The second part of this study examined oxide stability and cleaning of Ru surfaces as well as consequent Cu film thermal stability with the Ru layers. The ~2 monolayer native Ru oxide was reduced after H-plasma processing. The thermal stability or islanding of the Cu film on the Ru substrate was characterized by in-situ XPS. After plasma cleaning of the Ru adhesion layer, the deposited Cu exhibited full coverage. In contrast, for Cu deposition on the Ru native oxide substrate, Cu islanding was detected and was described in terms of grain boundary grooving and surface and interface energies. The thermal stability of 7 nm Ti, Pt and Ru ii interfacial adhesion layers between a Cu film (10 nm) and a Ta barrier layer (4 nm) have been investigated in the third part. The barrier properties and interfacial stability have been evaluated by Rutherford backscattering spectrometry (RBS). Atomic force microscopy (AFM) was used to measure the surfaces before and after annealing, and all the surfaces are relatively smooth excluding islanding or de-wetting phenomena as a cause of the instability. The RBS showed no discernible diffusion across the adhesion layer/Ta and Ta/Si interfaces which provides a stable underlying layer. For a Ti interfacial layer RBS indicates that during 400 °C annealing Ti interdiffuses through the Cu film and accumulates at the surface. For the Pt/Cu system Pt interdiffuion is detected which is less evident than Ti. Among the three adhesion layer candidates, Ru shows negligible diffusion into the Cu film indicating thermal stability at 400 °C.
ContributorsLiu, Xin (Author) / Nemanich, Robert (Thesis advisor) / Chamberlin, Ralph (Committee member) / Chen, Tingyong (Committee member) / Smith, David (Committee member) / Ponce, Fernando (Committee member) / Arizona State University (Publisher)
Created2012
Description
One dimensional (1D) and quasi-one dimensional quantum wires have been a subject of both theoretical and experimental interest since 1990s and before. Phenomena such as the "0.7 structure" in the conductance leave many open questions. In this dissertation, I study the properties and the internal electron states of semiconductor quantum wires with the path integral Monte Carlo (PIMC) method. PIMC is a tool for simulating many-body quantum systems at finite temperature. Its ability to calculate thermodynamic properties and various correlation functions makes it an ideal tool in bridging experiments with theories. A general study of the features interpreted by the Luttinger liquid theory and observed in experiments is first presented, showing the need for new PIMC calculations in this field. I calculate the DC conductance at finite temperature for both noninteracting and interacting electrons. The quantized conductance is identified in PIMC simulations without making the same approximation in the Luttinger model. The low electron density regime is subject to strong interactions, since the kinetic energy decreases faster than the Coulomb interaction at low density. An electron state called the Wigner crystal has been proposed in this regime for quasi-1D wires. By using PIMC, I observe the zig-zag structure of the Wigner crystal. The quantum fluctuations suppress the long range correla- tions, making the order short-ranged. Spin correlations are calculated and used to evaluate the spin coupling strength in a zig-zag state. I also find that as the density increases, electrons undergo a structural phase transition to a dimer state, in which two electrons of opposite spins are coupled across the two rows of the zig-zag. A phase diagram is sketched for a range of densities and transverse confinements. The quantum point contact (QPC) is a typical realization of quantum wires. I study the QPC by explicitly simulating a system of electrons in and around a Timp potential (Timp, 1992). Localization of a single electron in the middle of the channel is observed at 5 K, as the split gate voltage increases. The DC conductance is calculated, which shows the effect of the Coulomb interaction. At 1 K and low electron density, a state similar to the Wigner crystal is found inside the channel.
ContributorsLiu, Jianheng, 1982- (Author) / Shumway, John B (Thesis advisor) / Schmidt, Kevin E (Committee member) / Chen, Tingyong (Committee member) / Yu, Hongbin (Committee member) / Ros, Robert (Committee member) / Arizona State University (Publisher)
Created2012
Description
The theory of quantum electrodynamics predicts that beta decay of the neutron into a proton, electron, and anti-neutrino should be accompanied by a continuous spectrum of photons. A recent experiment, RDK I, reported the first detection of radiative decay photons from neutron beta decay with a branching ratio of (3.09 ± 0.32) × 10-3 in the energy range of 15 keV to 340 keV. This was achieved by prompt coincident detection of an electron and photon, in delayed coincidence with a proton. The photons were detected by using a single bar of bismuth germanate scintillating crystal coupled to an avalanche photodiode. This thesis deals with the follow-up experiment, RDK II, to measure the branching ratio at the level of approximately 1% and the energy spectrum at the level of a few percent. The most significant improvement of RDK II is the use of a photon detector with about an order of magnitude greater solid angle coverage than RDK I. In addition, the detectable energy range has been extended down to approximately 250 eV and up to the endpoint energy of 782 keV. This dissertation presents an overview of the apparatus, development of a new data analysis technique for radiative decay, and results for the ratio of electron-proton-photon coincident Repg to electron-proton coincident Rep events.
ContributorsO'Neill, Benjamin (Author) / Alarcon, Ricardo (Thesis advisor) / Drucker, Jeffery (Committee member) / Lebed, Richard (Committee member) / Comfort, Joseph (Committee member) / Chamberlin, Ralph (Committee member) / Arizona State University (Publisher)
Created2012
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
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