104 research outputs found

    GLASS-CLAD SEMICONDUCTOR CORE OPTICAL FIBERS

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    Glass-clad optical fibers comprising a crystalline semiconductor core have garnered considerable recent attention for their potential utility as novel waveguides for applications in nonlinear optics, sensing, power delivery, and biomedicine. As research into these fibers has progressed, it has become evident that excessive losses are limiting performance and so greater understanding of the underlying materials science, coupled with advances in fiber processing, is needed. More specifically, the semiconductor core fibers possess three performance-limiting characteristics that need to be addressed: (a) thermal expansion mismatches between crystalline core and glass cladding that lead to cracks, (b) the precipitation of oxide species in the core upon fiber cooling, which results from partial dissolution of the cladding glass by the core melt, and (c) polycrystallinity; all of which lead to scattering and increased transmission losses. This dissertation systematically studies each of these effects and develops both a fundamental scientific understanding of and practical engineering methods for reducing their impact. With respect to the thermal expansion mismatch and, in part, the dissolution of oxides, for the first time to our knowledge, oxide and non-oxide glass compositions are developed for a series of semiconductor cores based on two main design criteria: (1) matching the thermal expansion coefficient between semiconductor core and glass cladding to minimize cracking and (2) matching the viscosity-temperature dependences, such that the cladding glass draws into fiber at a temperature slightly above the melting point of the semiconductor in order to minimize dissolution and improve the fiber draw process. The x[Na2O:Al2O3] + (100 - 2x)SiO2 glass compositional family was selected due to the ability to tailor the glass properties to match the aforementioned targets through slight variations in composition and adjusting the ratios of bridging and non-bridging oxygen; experimental results show a decrease in fiber core oxygen content in the fibers drawn with the tailored glass composition. In a further attempt to reduce the presence of oxide species in the core, a reactive molten core approach to semiconductor optical fibers are developed. Specifically, the addition of silicon carbide (SiC) into a silicon (Si) core provides an in-situ reactive getter of oxygen during the draw process to achieve oxygen-free silicon optical fibers. Elemental analysis and x-ray diffraction of fibers drawn using this reactive chemistry approach show negligible oxygen concentration in the highly crystalline silicon core, a significant departure from the nearly 18 atom percent oxygen in previous fibers. Scattering of light out of the core is shown qualitatively to have been reduced in the process. The role of the cross-sectional geometry on the resultant core crystallography with respect to the fiber axis is explored in a continued effort to better understand the nature of the crystal formation and structural properties in these semiconductor core optical fibers. A square cross-sectional geometry was explored to determine if core non-circularity can enhance or promote single crystallinity, as the semiconductors studied have a preference to form cubic crystals. Resultant crystallography of the non-circular core showed a significant improvement in maintaining a preferred crystallographic orientation, with the square core fibers exhibiting a 90% preference for the \u3c 1 1 0 \u3e family of directions occurring closest to the longitudinal direction of the fiber. The ability to orient the crystallography with respect to the fiber axis could be of great value to future nonlinear optical fiber-based devices. In summary, this dissertation begins to elucidate some of the microstructural features, not present in conventional glass optical fibers, which could be important for future low-loss single crystalline semiconductor optical fibers. Additionally, this dissertation offers novel insight into the various aspects of materials science of non-conventional glass optical fibers, such as crystallization and solidification under highly non-equilibrium and confined conditions, phase equilibria and in-situ reactions, and the interplay between thermodynamics and kinetics

    Structure and Assembly of Membrane-Containing dsDNA Bacteriophages

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    Electron cryo-microscopy studies of bacteriophage phi8 and archaeal virus SH1

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    Symmetry is a key principle in viral structures, especially the protein capsid shells. However, symmetry mismatches are very common, and often correlate with dynamic functionality of biological significance. The three-dimensional structures of two isometric viruses, bacteriophage phi8 and the archaeal virus SH1 were reconstructed using electron cryo-microscopy. Two image reconstruction methods were used: the classical icosahedral method yielded high resolution models for the symmetrical parts of the structures, and a novel asymmetric in-situ reconstruction method allowed us to resolve the symmetry mismatches at the vertices of the viruses. Evidence was found that the hexameric packaging enzyme at the vertices of phi8 does not rotate relative to the capsid. The large two-fold symmetric spikes of SH1 were found not to be responsible for infectivity. Both virus structures provided insight into the evolution of viruses. Comparison of the phi8 polymerase complex capsid with those of phi6 and other dsRNA viruses suggests that the quaternary structure in dsRNA bacteriophages differs from other dsRNA viruses. SH1 is unusual because there are two major types of capsomers building up the capsid, both of which seem to be composed mainly of single beta-barrels perpendicular to the capsid surface. This indicates that the beta-barrel may be ancestral to the double beta-barrel fold.Virukset koostuvat yksinkertaisimmillaan perimäaineksesta (DNA tai RNA) ja sitä suojaavasta proteiinikuoresta. Proteiinikuoren rakenne on usein symmetrinen: monta kopiota samaa proteiinia nivoutuu yhteen säännölliseen muodostelmaan. Symmetria on yleensä joko helikaalinen (kierreportaat), jolloin virus on sauvamainen, tai ikosahedraalinen (5- ja 6-kulmioista ommeltu jalkapallo), jolloin syntyy pallomaisia viruksia. On kuitenkin tavallista, että jotkin viruksen toiminnan kannalta tärkeät rakenteet eivät noudata symmetriaa. Jalkapallossa esimerkiksi on vain yksi venttiilin paikka, eli yksi nahkapalasista poikkeaa muista. Viruksen tapauksessa taas vastaavalla tavalla muista poikkeavassa paikassa saattaa olla perimäaineksen pakkaamiseen tarvittava koneisto. Tässä työssä on tutkittu kahden pallomaisen viruksen, phi8:n ja SH1 kolmiulotteisia (3D) rakenteita. phi8 sairastuttaa erästä bakteeria, joka puolestaan sairastuttaa tiettyjä palkokasveja. SH1 sairastuttaa arkkieliöitä (bakteerien tapaisia yksisoluisia eliöitä), joita löytyy vaaleanpunaisista suolajärvistä Australiasta. Rakenteet määritettiin elektronimikroskooppikuvista laskennallisin keinoin. Perusajatus on, että kun kaksiulotteisissa mikroskooppikuvissa virus näkyy monesta eri suunnasta, nämä kuvat yhdistämällä saadaan selville viruksen 3D rakenne. Virukset erottuvat heikosti mikroskooppikuvissa, joten myös laskettu 3D rakenne on epäselvä. Sitä voidaan kuitenkin selkeyttää käyttäen hyväksi symmetriaa. Tällöin oletetaan, että virus on täysin symmetrinen, mistä seuraa, että laskettu 3D rakenne näyttää virheellisesti ne osat, jotka eivät seuraa symmetriaa. Esimerkiksi jalkapallon venttiilin paikka saattaisi ilmaantua 12 eri paikkaan tai kadota kokonaan näkyvistä. Tässä työssä jatkokehitettiin menetelmää, jonka avulla voidaan saada oikea kuva ventiilinpaikoista. Menetelmää sovellettiin molempiin tutkittuihin viruksiin. Virusten rakenteet kertovat niiden sukulaisuussuhteista, joten rakennetutkimus on myös sukututkimusta. Vain yhden phi8:n lähisukulaisen rakenne tunnettiin aiemmin, joten määritetty rakenne mahdollisti perheen sisäisen vertailun. SH1:n perheestä puolestaan ei ollut mitään tietoa, eikä sen rakennekaan nyt paljastanut varmuudella sen olevan sukua tunnetuille viruksille. On tosin mahdollista, että eräs yleinen viruskuoriproteiinityyppi on kehittynyt SH1:n tapaisen viruksen kuoresta

    Caracterización estructural y funcional de películas delgadas nanoporosas mediante microscopías electrónicas de transmisiónbarrido y espectroscopías ópticas

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    Nano-structuration of materials at the mesoscale to give rise to porosity-controlled coatings represents an important breakthrough in the area of Materials Science and Engineering, offering new and enhanced functionalities of interest in fields such as optics, optronics and optoelectronics. In order to optimize their performances, in-depth analyses are required: local information about the morphology, composition and atomic structure, the compactness distribution, but also layer homogeneity, interface and interpenetration between stacked layers or oxidation are extremely important factors that can ruin their way of operation. In this particular context, the objective of the present PhD Thesis is to make significant contributions to the study and development of multifunctional porous nanostructured systems, from their design and elaboration, to the maximum knowledge of their structure and properties, through advanced (S)TEM methods, including 3D reconstructions, elemental analyses at the nanoscale and atomic-scale imaging, combined with optical spectroscopy techniques. In the first instance, given the great potential of the slanted nanostructures generated by means of oblique angle depositions, in which the refractive index gradient can be tuned by the columns tilt and density imposed via the growth angles and parameters, OAD broadband antireflective coatings based on Si, Ge or SiO2 OAD films have been designed, manufactured, and extensively characterized with the aim of maximizing the performance of the optical elements in the vis-IR wavelength range. This same approach has also been implemented to enhance the antireflective capabilities of transparent conductive ITO thin films in the near-IR window without compromising too much their electrical response. On the other hand, the advanced structural and functional characterization of porosity-controlled GaN NW arrays grown by plasma-assisted MBE through (S)TEM methods and vis-IR SE elliposmetry, has helped not only to improve growth processes but also to optimize their resulting optical and electrical properties. Finally, the knowledge and methodologies acquired during the study and optimization of the previous porous systems have been transferred to the development of a two-step procedure, based on the deposition and the subsequent fast oxidation of vanadium-based OAD films in open air atmosphere, for the synthesis of thermochromic VO2 coatings of tunable metal-to-insulator response and controlled grain sizes and crystallinities

    From Dopant to Source: The Use of Zinc as an Enabler in the Synthesis of Nanostructures by Metalorganic Vapour Phase Epitaxy

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    As conventional methods of semiconductor fabrication approach fundamental physical limits, new paradigms are required for progress. One concept with the potential to deliver such a paradigm shift is the bottom-up synthesis of semiconductor nanostructures. Beyond further scaling, bottom-up methods promise novel geometries and heterostructures unavailable by conventional top-down methods. This is particularly true in the case of nanostructure growth by the vapour-liquid-solid (VLS) method. Commonly realised using existing vapour phase epitaxy techniques, a range of high-performance VLS devices have now been demonstrated including photovoltaic cells, lasers and high-frequency-transistors. In this dissertation, selected applications of diethylzinc (DEZn) are used to step through a range of opportunities and challenges arising from the VLS synthesis of semiconductor nanostructures by metal-organic vapour phase epitaxy (MOVPE). These applications are broadly grouped into four chapters focusing on the use of zinc firstly as a dopant and then morphological agent, internal quantum efficiency (IQE) enhancer and finally, source. In the context of doping, relatively high DEZn flows are shown to alter the morphology of GaAs nanowires by introducing planar defects, kinking and seed-splitting. Growth studies are used to establish the threshold for these effects and thus the range of DEZn flows suitable for doping. Successful incorporation of up to 5 x1020 Zn/cm3 is demonstrated through atom probe tomography (APT) and electrical characterisation. Building on these results, DEZn is then used to generate periodic twinning in GaAs nanowires. The morphology and overgrowth of these twinning superlattice (TSL) nanowires is studied. Unlike for other III-V materials, twin spacing is found to be a linear function of nanowire diameter. By analysing the probability of twin formation, this result is related to the relatively high twin plane and solid-liquid interface energies of GaAs. Values for the wetting angle and supersaturation of the seed particle during growth are also extracted. In addition to acting as a dopant, zinc is also shown to produce an orders of magnitude increase in the IQE of GaAs nanowires. Performance gains are quantified by measuringthe absolute efficiency of individual nanowires. This increase in IQE with doping enables room-temperature lasing from unpassivated GaAs nanowires. The performance of doped nanolasers, including the transition to lasing, is fully characterised. In addition to increasing radiative efficiency, Zn doping also increases differential gain while reducing the transparency carrier density. The threshold pump power of a Zn doped nanowire is thus shown to be less than that of an equivalent AlGaAs passivated structure. In the final chapter, DEZn is used as a source for the growth of ZnAs, ZnP and ZnSb nanostructures by MOVPE. A range of growth conditions, substrates and seed materials are investigated. Individual nanostructures of both ZnAs and ZnP are shown to exhibit excellent optoelectronic performance with emission from individual nanostructures at 1.0 and 1.5 eV respectively. Overall, this thesis underlines the vast range of possibilities offered by VLS growth and opens to the door to both a variety of new techniques and new family of semiconductor nanomaterials

    Thermophilic Microbial Electrochemical Cells

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    abstract: Microbial Electrochemical Cell (MXC) technology harnesses the power stored in wastewater by using anode respiring bacteria (ARB) as a biofilm catalyst to convert the energy stored in waste into hydrogen or electricity. ARB, or exoelectrogens, are able to convert the chemical energy stored in wastes into electrical energy by transporting electrons extracellularly and then transferring them to an electrode. If MXC technology is to be feasible for ‘real world’ applications, it is essential that diverse ARB are discovered and their unique physiologies elucidated- ones which are capable of consuming a broad spectrum of wastes from different contaminated water sources. This dissertation examines the use of Gram-positive thermophilic (60 ◦C) ARB in MXCs since very little is known regarding the behavior of these microorganisms in this setting. Here, we begin with the draft sequence of the Thermincola ferriacetica genome and reveal the presence of 35 multiheme c-type cytochromes. In addition, we employ electrochemical techniques including cyclic voltammetry (CV) and chronoamperometry (CA) to gain insight into the presence of multiple pathways for extracellular electron transport (EET) and current production (j) limitations in T. ferriacetica biofilms. Next, Thermoanaerobacter pseudethanolicus, a fermentative ARB, is investigated for its ability to ferment pentose and hexose sugars prior to using its fermentation products, including acetate and lactate, for current production in an MXC. Using CA, current production is tracked over time with the generation and consumption of fermentation products. Using CV, the midpoint potential (EKA) of the T. pseudethanolicus EET pathway is revealed. Lastly, a cellulolytic microbial consortium was employed for the purpose ofassessing the feasibility of using thermophilic MXCs for the conversion of solid waste into current production. Here, a highly enriched consortium of bacteria, predominately from the Firmicutes phylum, is capable of generating current from solid cellulosic materials.Dissertation/ThesisDoctoral Dissertation Biological Design 201

    Self-assembly and Mesocrystal Formation via Non-classical Crystallisation

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    New materials can be fabricated using small scaled building blocks as a repetition unit. Nanoparticles with their unique size-tuneable properties from quantum confinement can especially be utilised to form two- and three-dimensional ordered assemblies to introduce them into what would normally be considered to be incompatible matrices. Furthermore, new collective properties that derive from the ordered arrangement of the building blocks, are accomplished. Additionally, different materials can be combined by mixing different building blocks during self-assembly, so that size ranges and material combinations that are difficult to achieve by other means can be formed. The arrangement of small particles into highly ordered arrangements can be realised via self-assembly. To achieve such assemblies, highly monodisperse nanoparticular building blocks with a size distribution below 5 % have to be synthesised. The production and variation in the size of both lead chalcogenide and noble metal nanoparticles is presented in this work. Moreover, the syntheses of multicomponential nanoparticles (PbSe/PbS and Au/PbS) are investigated. Non-classical crystallisation methodologies with their varyious self-assembly mechanisms are used for the formation of highly symmetrical mesocrystals and supracrystals. Analogous to classical crystallisation methods and their formation processes the interparticle interactions, attractive as well as repulsive, determine the resulting crystalline structure. Variation of the environmental parameters consequently leads to structural variation due to the changing interparticle interactions. In contrast to classical crystallisation the length scale of the interparticle forces stays constant as the size dimension of the self-assembled building unit is changed. Two different non-classical crystallisation pathways are investigated in this work. One pathway focuses on the slow destabilisation of nanoparticles in organic media by the addition of a non-solvent. In this approach optimisation of parameters for the formation of highly symmetrical three-dimensional mesostructures are studied. Furthermore, to shine some light onto the mechanism of self-assembly, the intrinsic arrangement of the building units in a mesocrystal and the steps of non-solvent addition are analysed. The mechanistic investigations explain the differences observed in mesocrystal formation between metal and semiconductor nanoparticles. The lower homogeneity of the building units of the metal nanoparticles leads to smaller and less defined superstructures in comparison to semiconductor building blocks. Another pathway of non-classical crystallisation is the usage of electrostatic interactions as the driving force for self-assembly and supracrystal formation. Therefore, the building blocks are transferred into aqueous media and stabilised with oppositely charged ligands. The well-know procedure for metal nanoparticles was adapted for semiconductor materials. The lower stability of these nanoparticles in aqueous solution induces an agglomeration of the semiconductor nanoparticles without including oppositely charged metal nanoparticles. The destabilisation effect can be increased by the addition of equally charged metal nanoparticles in a salting out type process. In comparison to the slow formation of mesocrystals achieved via destabilisation in an organic media (up to 4 weeks), the salting out procedure takes place within two hours, but the faster agglomeration causes a less well defined assembly of the building units in the mesocrystals. Moreover, the arrangement of semiconductor nanoparticles with organic molecules such as polymers and proteins was investigated in order to use the nanoparticles as a light harvesting component. In combination with the directly bound polymer the charge carrier may be directly transferred to the conductive thiophene-based polymer, so that infrared light can be transformed into an electrical signal for use in further applications such as solar cells. The advantage of the nanoparticle-protein system is the self-assembly across a liquid-liquid interface and additionally a Förster resonance energy transfer can occur at this phase boundary. Hence, it is possible to transfer highly energetic photons directly to biological samples without destroying the biological material

    Molecular Typing of Wheat Streak Mosaic Virus for Forensic Applications

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    The field of agricultural biosecurity combines traditional aspects of forensic science with plant pathology. With the threat of agroterrorism growing, steps must be taken in many areas to establish preparedness and to train enforcement personnel and extension agents in tracking and prosecuting the responsible individuals. The purpose of this study was to use Wheat Streak Mosaic Virus as a model system to develop a molecular assay using current, popular forensic laboratory equipment that can effectively compare samples collected from a suspected agroterrorism event against reference samples collected from a potentially responsible clandestine laboratory. Viral RNA extractions were performed with the MagMAX Kit (Ambion, Inc., Foster City, CA). cDNA synthesis and viral genome amplification were performed with the SuperScript One-Step RT-PCR Kit (Invitrogen, Inc., Carlsbad, CA). Single nucleotide polymorphisms were identified from sequencing data of three WSMV isolates. Three primers based upon these SNPs and a fourth primer included as an internal control and diagnostic marker were synthesized and the SNaPshot Kit (ABI, Inc., Foster City, CA) was used to discriminate the three WSMV isolates.Findings and Conclusions: The three SNP-specific primers used during SNaPshot analysis showed distinct qualitative differences between the three WSMV isolates tested. The fourth, internal control primer produced a positive result in every test, confirming the presence of WSMV cDNA within each sample. However, additional, unexpected peaks occurred at various sites in the electropherograms. After repeated SNaPshot reproducibility tests, blank assays, and negative controls, these additional peaks were determined to be evidence of mixed populations of WSMV within two of the three infections. The additional peaks therefore provided a second test for attribution that relied on the quantitative level of infection with genetically distinct isolates of WSMV instead of solely relying on the qualitative polymorphisms associated with an infection. This increased the potential discriminatory power of the assay exponentially. Future study with this assay would allow further testing of the reproducibility of the current isolates, subject previously uninvestigated natural isolates from around the world, and incorporate additional SNP-specific primers.Department of Biochemistry and Molecular Biolog

    High-Temperature Growth of Gallium Nitride Using the Ammonothermal Method with Ammonium Chloride Mineralizer

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    Gallium nitride (GaN) has become an important semiconductor for the optoelectronics and power electronics fields in the pursuit of high efficiency devices. However, the lack of a natural native GaN substrate has forced growth of GaN devices on foreign substrates such as sapphire, silicon carbide, and silicon. To further enhance efficiency and develop devices with longer lifetimes, the number of defects present in devices must be reduced. The development of a native GaN substrate of high crystalline quality would directly enable defect reduction. The ammonothermal method of GaN growth has shown significant promise as a technique for the production of high quality GaN crystals of industrially significant size (crystals on the order of centimeters in the largest dimension). The ammonothermal method is a solvothermal method that uses a mineralizer (here ammonium chloride) with supercritical ammonia to transport GaN from a source material from one temperature zone to grow a seed crystal in another temperature zone. High pressures, high temperatures, and the presence of a highly corrosive chemistry make development of an economical growth reactor challenging. This body of work outlines the development of a growth reactor capable of high temperature ammonothermal growth of GaN using ammonium chloride mineralizer.Initial development of the ammonothermal reactor required identification of suitable reactor materials. A materials stability study was conducted by exposing samples of materials to the ammonothermal environment and measuring mass loss as well as any chemical or mechanical changes that occurred. An Inconel 625 alloy reactor was employed, although the reactor itself was somewhat susceptible to corrosion from the ammonothermal environment. The study yielded a subset of materials that may be suitable for use as gaskets and other single use items which include niobium, molybdenum, titanium, vanadium, tungsten, gold, and platinum. Alloys of molybdenum and cobalt may also be useful. High strength titanium-zirconium-molybdenum (TZM) was also identified as a corrosion resistant material and was selected for reactor design.A TZM reactor was then designed and fabricated. Subsequent high pressure, high temperature tests indicated that TZM was essentially inert and growth of GaN crystals followed. All GaN growth was accomplished at or above 650°C using seed crystals grown by hydride vapor phase epitaxy. Seeds were characterized by micrometer measurements for growth thickness, x-ray diffraction (XRD) for crystalline quality, and secondary ion mass spectrometry (SIMS) for impurity concentrations. The growth quality appeared to match the seed quality as measured by XRD. Growth coloration ranged from slightly gray to green or yellow with growth rates up to 191 µm/day. Most seeds exhibited significant faceting at the edges of the sample, forming semipolar planes. SIMS was performed on a couple of samples which indicated oxygen concentrations of ~1018 cm¬-3
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