Quinoa (Chenopodium quinoa Willd.) is a pseudocereal native to the Andean region of South America and a staple crop for subsistence farmers in the altiplano of Bolivia and Peru. Downy mildew is the most significant disease of quinoa caused by the pathogen Peronospora farinosa f.sp. chenopodii Byford. This disease greatly impacts quinoa crops with yield losses up to 99%. As fungicides are expensive for farmers, the development of resistant cultivars appears to be the most efficient means for controlling downy mildew. The quinoa germplasm bank contains high amounts of genetic diversity, some of which exhibit mildew resistance. Methods for evaluating mildew severity are important for finding resistant genotypes that are useful in breeding programs. The main objectives of this study were to evaluate and investigate downy mildew resistance in quinoa through several different methods. A simple inoculation method was developed for downy mildew disease assessment by placing a damp piece of cheesecloth on a leaf, pipetting a known spore solution onto the cloth, and subjecting the plants to specific humidity cycles in a growth chamber. After inoculation of five quinoa-breeding lines in a growth chamber, accession 0654 was found to be the most resistant, while genotypes NL6 and Sayana showed moderate resistance. Each of these genotypes displayed some potential for resistance breeding programs. Investigation of the growth and development of P. farinosa through resistant and susceptible quinoa genotypes revealed fewer sporangiophores, hyphal strands, and haustoria among leaf tissues of accession 0654 than in the susceptible Chucapaca cultivar. Peronospora farinosa growth was detected in leaf, petiole, and stem tissues with polymerase chain reaction (PCR) using ITSP primers designed from the internal transcribed spacer (ITS) region of the pathogen. Scanning electron microscopy (SEM) also revealed that P. farinosa penetrated stomata via appressoria, secreted extracellular matrices during sporangia germination, grew intercellularly in leaf and petiole tissues, and exited leaf tissue through stomata. Future research requiring knowledge of resistant quinoa genotypes, P. farinosa growth and development, or inoculation methods for large numbers of small quinoa plants would benefit from this report.

The aim of this study is the three-dimensional structural characterization of the genome packaging inside viral capsids via cryo-electron microscopy and three-dimensional reconstruction. The genome of some single-stranded viruses can be densely packaged within their capsid shells. Several stretches of the genome are known to adopt stable secondary structures, however, to date, little is known about the three-dimensional organization of the genome inside their capsid shells. Two techniques have been developed to facilitate the structural elucidation of genome packaging: the asymmetric random-model method, and the symmetry-mismatch, random model method. Both techniques were successfully tested with model and experimental data. The new algorithms were applied to study the genome structure of poliovirus and satellite tobacco mosaic virus. We have not yet found a consistent structure for the two genomes. Nevertheless, we have found that the genome of satellite tobacco mosaic genome is very stable, supporting a model where the RNA acts as a scaffold, with potential implications in capsid stability and assembly.

Vanadium dioxide (VO_2) is a material of particular interest due to its exhibited metal to insulator phase transition at 68°C that is accompanied by an abrupt and significant change in its electronic and optical properties. Since this material can exhibit a reversible drop in resistivity of up to five orders of magnitude and a reversible drop in infrared optical transmission of up to 80%, this material holds promise in several technological applications. Solid phase crystallization of VO_2 thin films was obtained by a post-deposition annealing process of a VO_{x,x approx 2} amorphous film sputtered on an amorphous silicon dioxide (SiO_2) layer. Scanning electron microscopy (SEM) and electron-backscattered diffraction (EBSD) were utilized to study the morphology of the solid phase crystallization that resulted from this post-deposition annealing process. The annealing parameters ranged in temperature from 300°C up to 1000°C and in time from 5 minutes up to 12 hours. Depending on the annealing parameters, EBSD showed that this process yielded polycrystalline vanadium dioxide thin films, semi-continuous thin films, and films of isolated single-crystal particles. In addition to these films on SiO_2, other VO_2 thin films were deposited onto a-, c-, and r-cuts of sapphire and on TiO_2(001) heated single-crystal substrates by pulsed-laser deposition (PLD). The temperature of the substrates was kept at ~500°C during deposition. EBSD maps and orientation imaging microscopy were used to study the epitaxy and orientation of the VO_2 grains deposited on the single crystal substrates, as well as on the amorphous SiO_2 layer. The EBSD/OIM results showed that: 1) For all the sapphire substrates analyzed, there is a predominant family of crystallographic relationships wherein the rutile VO_2{001} planes tend to lie parallel to the sapphire's {10-10} and the rutile VO_2{100} planes lie parallel to the sapphire's {1-210} and {0001}. Furthermore, while this family of relationships accounts for the majority of the VO_2 grains observed, due to the sapphire substrate's geometry there were variations within these rules that changed the orientation of VO_2 grains with respect to the substrate's normal direction. 2) For the TiO_2, a substrate with a lower lattice mismatch, we observe the expected relationship where the rutile VO_2 [100], [110], and [001] crystal directions lie parallel to the TiO_2 substrate's [100], [110], and [001] crystal directions respectively. 3) For the amorphous SiO_2 layer, all VO_2 crystals that were measurable (those that grew to the thickness of the deposited film) had a preferred orientation with the the rutile VO_2[001] crystal direction tending to lie parallel to the plane of the specimen. The use of transmission electron microscopy (TEM) is presented as a tool for further characterization studies of this material and its applications. In this work TEM diffraction patterns taken from cross-sections of particles of the a- and r-cut sapphire substrates not only solidified the predominant family mentioned, but also helped lift the ambiguity present in the rutile VO_2{100} axes. Finally, a focused-ion beam technique for preparation of cross-sectional TEM samples of metallic thin films deposited on polymer substrates is demonstrated.

In the infection process, native poliovirus (160S) first converts to a cell-entry intermediate (135S) particle, which causes the externalization of capsid proteins VP4 and the N-terminus of VP1 (residues 1-53). The externalization of these entities is followed by release of the RNA genome, leaving an empty (80S) particle. Three antibodies were utilized to track the location of VP1 residues in different states of poliovirus by cryogenic electron microscopy (cryo-EM). "P1" antibody binds to N-terminal residues 24-40 of VP1. Three-dimensional reconstruction of 135S-P1 showed that P1 binds to a prominent capsid peak known as the "propeller tip". In contrast, our initial 80S-P1 reconstruction showed P1 Fabs also binding to a second site, ~60 Å distant, at the icosahedral twofold axes. Analysis of 80S-P1 reconstructions showed that the overall population of 80S-P1 particles consisted of three kinds of capsids: those with P1 Fabs bound only at the propeller tips; only at the twofold axes; or simultaneously at both positions. Our results indicate that, in 80S particles, a significant fraction of VP1 can deviate from icosahedral symmetry. Similar deviations from icosahedral symmetry may be biologically significant during other viral transitions. "C3" antibody binds to 93-103 residues (BC loop) of VP1. The C3 epitope shifts outwards in radius by 4.5% and twists through 15° in the 160S-to-135S transition, but appears unchanged in the 135S-to-80S transition. In addition, binding of C3 to either 160S or 135S particles causes residues of the BC loop to move an estimated 5 (±2) Å, indicating flexibility. The flexibility of BC loop may play a role in cell-entry interactions. At 37°C, the structure of poliovirus is dynamic, and internal polypeptides VP4 and the N-terminus of VP1 externalize reversibly. An antibody, binding to the residues 39-55 of VP1, was utilized to track the location of the N-terminus of VP1 in 160S particle in the "breathing" state. The resulting reconstruction showed the capsid expands similarly to the irreversibly altered 135S particle, but the N-terminus of VP1 is located near the twofold axes, instead of the propeller tip as in 135S particles.

InGaAs quantum dot chains were grown with a low-temperature variation of the Stranski-Krastanov method, the conventional epitaxial method. This new method seeks to reduce indium segregation and intermixing in addition to giving greater control in the growth process. We used photoluminescence spectroscopy techniques to characterize the quality and electronic structure of these samples. We have recently used a transmission electron microscope to show how the quantum dots vary with annealing temperature. Some questions relating to the morphology of the samples cannot be answered by photoluminescence spectroscopy alone. Using transmission electron microscopy, we verified flattening of the quantum dots with annealing temperature and resolved the chemical composition with cross-section cuts and plan view cuts.

The genus Fusarium has a wide host range and causes many different forms of plant disease. These include seed rot and seedling blight diseases of cultivated plants. The Fusarium-caused diseases of wild plants are less well-known. In this study we examined Fusarium sp. n-caused disease development on non-dormant seeds of the important rangeland weed Bromus tectorum as part of broader studies of the phenomenon of stand failure or ‘die-off’ in this annual grass. We previously isolated an undescribed species in the Fusarium tricinctum species complex from die-off soils and showed that it is pathogenic on seeds. It can cause high mortality of non-dormant B. tectorum seeds, especially under conditions of water stress, but rarely attacks dormant seeds. In this study, we used scanning electron microscopy (SEM) to investigate the mode of attack used by this pathogen. Non-dormant B. tectorum seeds (i.e., florets containing caryopses) were inoculated with isolate Skull C1 macroconidia. Seeds were then exposed to water stress conditions (-1.5MPa) for 7 d, then transferred to free water. Time lapse SEM photographs of healthy vs. infected seeds revealed that hyphae under water stress conditions grew toward and culminated their attack at the abscission layer of the floret attachment scar. A prominent infection cushion, apparent macroscopically as a white tuft of mycelium at the radicle end of the seed, developed within 48 hours after inoculation. Seeds which lacked an infection cushion completed germination upon transfer to free water, whereas seeds with an infection cushion were almost always killed. In addition, hyphae on seeds that did not initiate germination lacked directional growth and did not develop the infection cushion. This strongly suggests that the fungal attack is triggered by seed exudates released through the floret attachment scar at the initiation of germination. Images of cross-sections of infected seeds showed that the fungal hyphae first penetrated the caryposis wall, then entered the embryo, and later ramified throughout the endosperm, completely destroying the seed.

There has been an urge for increasing the efficiency in advanced gas turbine engines. To fulfill these needs the inlet gas temperatures should be increased in the gas turbine engines, thermal barrier coatings (TBCs) have gained significant applications in increasing the gas inlet temperatures. Insulating characteristics of ceramic TBCs allow the operation at up to 150~250 ˚C higher gas temperatures. Because of the severe turbine engine operating conditions that include high temperature, steep temperature gradient, thermal cycling, oxidation and hot-corrosion, TBCs can fail by spallation at the interface between the metal and ceramic. The lack of understanding in failure mechanisms and their prediction warrant a development of non-destructive evaluation technique that can monitor the quality and degradation of TBCs. In addition, the development of NDE technique must be based on a robust correlation to the characteristics of TBC failure. The objective of this study is to develop electrochemical impedance spectroscopy (EIS) as a Non-destructive evaluation (NDE) technology for application to TBCs. To have a better understanding of the multilayer TBCs using EIS they were divided into individual layers and EIS were performed on them. The individual layers included polycrystalline ZrO2-7~8 wt.%Y2O3 (YSZ) (topcoat) of two different densities were subjected to sintering by varying the sintering temperature and holding time for three different thickness and hot extruded NiAl alloy buttons which were subjected to isothermal oxidation with varying temperature and time. NiAl is as similar to the available commercial bondcoats used in TBCs. Then degradation monitoring with electrolyte penetration was carried out on electron beam physical vapor deposited (EB PVD) TBCs as a function of isothermal exposure. Quality control for air plasma sprayed TBCs were carried out as a function of density, thickness and microstructure. Dense vertically cracked TBCs were tested as a function of vertical crack density and thickness. Electrochemical impedance response was acquired from all specimens at room temperature and analyzed with an AC equivalent circuit based on the impedance response as well as multi-layered structure and micro-constituents of specimens. Physical and microstructural features of these specimens were also examined by optical and electron microscopy. The EIS measurement was carried out in a three-electrode system using a standard Flat Cell (K0235) from Princeton Applied Research™ and IM6e BAS ZAHNER™ frequency response analyzer. The electrolyte employed in this investigation was 0.01M (molar) potassium Ferri/Ferro Cyanide {(K3Fe(CN)6/K4Fe(CN)6·3H2O)}. The thickness and density were directly related to the resistance and capacitance of the polycrystalline YSZ with varying thickness and open pores. As the effective thickness of the YSZ increased with sintering time and temperature, the resistance of the YSZ (RYSZ) increased proportionally. The variation in capacitance of YSZ (CYSZ) with respect to the change in porosity/density and thickness was clearly detected by EIS. The samples with high porosity (less dense) exhibited large capacitance, CYSZ, compared to those with less porosity (high density), given similar thickness. Cracking in the YSZ monoliths resulted in decrease of resistance and increase in capacitance and this was related to the electrolyte penetration. Growth and spallation of TGO scale on NiAl alloys during isothermal oxidation at various temperatures and holding time was also correlated with resistance and capacitance of the TGO scale. With an increase in the TGO thickness, the resistance of the TGO (RTGO) increased and capacitance of the TGO (CTGO) decreased. This trend in the resistance and capacitance of the TGO changed after prolonged heat treatment. This is because of the spallation of the TGO scale from the metal surface. The parabolic growth of TGO during high temperature oxidation was inversely proportional to the capacitance of TGO, excluding the abrupt changes associated with the failure. As a function of isothermal exposure for EB-PVD TBCs, initial increase in the resistance of YSZ with thermal exposure was observed perhaps due to the high temperature sintering of YSZ. The parabolic growth of TGO during high temperature oxidation was inversely proportional to the capacitance of TGO. An explanation based on electrolyte penetration into sub-critical damage is proposed for the gradual decrease in the resistances of YSZ and TGO with prolonged thermal exposure. Observation of exposed metallic bond coat surface on the fracture surface, which readily provides conduction, was related to the abrupt and large increase in the capacitance of YSZ and TGO. A direct relation between the resistance of the YSZ (RYSZ) and density of the YSZ was observed for APS TBCs with varying topcoat density. APS TBCs with varying topcoat chemistry and thickness were tested and directly related to resistance of topcoat. With the increase in the topcoat thickness, the capacitance decreased and the resistance increased. The higher values of CCAT and RCAT compared to that of CYSZ and RYSZ were related to the higher dielectric constant and resistivity of CaTiO3. Dense vertically cracked TBCs were tested with varying crack density were tested and the variation in the resistance was related indirectly to the cracks and directly to the difference in the thickness of the topcoat. EB-PVD TBCs with varying density (dense and columnar) were tested and the variation in resistance was attributed to the dense structure and columnar structure of the topcoat with columnar structure having lower resistance because of more electrolyte penetration through the columnar structure. From this study, EIS showed a potential as a NDE technique for quality assurance and lifetime remain assessment of TBCs. Future work should continue on developing a mathematical model to study the impedance curves and come up with a model for individual layers of TBC and then sum them up to get the multilayered TBC response. The flexible instrument probe of EIS needs to be designed and tested for field evaluation of TBCs.

In NiTi, a reversible thermoelastic martensitic transformation can be induced by temperature or stress between a cubic (B2) austenite phase and a monoclinic (B19') martensite phase. Ni-rich binary compositions are cubic at room temperature (requiring stress or cooling to transform to the monoclinic phase), while Ti-rich binary compositions are monoclinic at room temperature (requiring heating to transform to the cubic phase). The stress induced transformation results in the superelastic effect, while the thermally induced transformation is associated with strain recovery that results in the shape memory effect. Ternary elemental additions such as Fe can additionally introduce an intermediate rhombohedral (R) phase between the cubic and monoclinic phase transformation. This work was initiated with the broad objective of connecting the macroscopic behavior in shape memory alloys with microstructural observations from transmission electron microscopy (TEM). Specifically, the goals were to examine (i) the effect of mechanical cycling and plastic deformation in superelastic NiTi; (ii) the effect of thermal cycling during loading in shape memory NiTi; (iii) the distribution of twins in martensitic NiTi-TiC composites; and (iv) the R-phase in NiTiFe. Both in situ and ex situ lift out focused ion beam (FIB) and electropolishing techniques were employed to fabricate shape memory alloy samples for TEM characterization. The Ni rich NiTi samples were fully austenitic in the undeformed state. The introduction of plastic deformation (8% and 14% in the samples investigated) resulted in the stabilization of martensite in the unloaded state. An interlaying morphology of the austenite and martensite was observed and the martensite needles tended to orient themselves in preferred orientations. The aforementioned observations were more noticeable in mechanically cycled samples. The observed dislocations in mechanically cycled samples appear to be shielded from the external applied stress via mismatch accommodation since they are not associated with unrecoverable strain after a load-unload cycle. On application of stress, the austenite transforms to martensite and is expected to accommodate the stress and strain mismatch through preferential transformation, variant selection, reorientation and coalescence. The stabilized martensite (i.e., martensite that exists in the unloaded state) is expected to accommodate the mismatch through variant reorientation and coalescence. On thermally cycling a martensitic NiTi sample under load through the phase transformation, significant variant coalescence, variant reorientation and preferred variant selection was observed. This was attributed to the internal stresses generated as a result of the thermal cycling. A martensitic NiTi-TiC composite was also characterized and the interface between the matrix and the inclusion was free of twins while significant twins were observed at a distance away from the matrix-inclusion interface. Incorporating a cold stage, diffraction patterns from NiTiFe samples were obtained at temperatures as low as -160ºC. Overall, this work provided insight in to deformation phenomena in shape memory materials that have implications for engineering applications (e.g., cyclic performance of actuators, engineering life of superelastic components, stiffer shape memory composites and low-hysteresis R-phase based actuators). This work was supported in part by an NSF CAREER award (DMR 0239512).

Thin-film solar cells are potentially low-cost devices to convert sunlight into electricity. Improvements in the conversion efficiencies of these cells reduce material utilization cost and make it commercially viable. Solar cells from the Thin-Film Physics Group, ETH Zurich, Switzerland and the Florida Solar Energy Center (FSEC), UCF were characterized for defects and other microstructural features within the thin-film structure and at the interfaces using transmission electron microscopy (TEM). The present thesis aims to provide a feedback to these groups on their deposition processes to understand the correlations between processing, resulting microstructures, and the conversion efficiencies of these devices. Also, an optical equipment measuring photocurrents from a solar cell was developed for the identification of defect-prone regions of a thin-film solar cell. The focused ion beam (FIB) technique was used to prepare TEM samples. Bright-field TEM along with scanning transmission electron microscopy (STEM) and energy dispersive X-ray spectroscopy (EDS) including elemental distribution line scans and maps were extensively used for characterizing the absorber layer and interfaces both above and below the absorber layer. Energy-filtered transmission electron microscopy (EFTEM) was applied in cases where EDS results were inconclusive due to the overlap of X-ray energies of certain elements, especially molybdenum and sulfur. Samples from ETH Zurich were characterized for changes in the CIGS (Cu(In,Ga)Se2) microstructure due to sodium incorporation from soda-lime glass or from a post-deposition treatment with NaF as a function of CIGS deposition temperature. The CIGS-CdS interface becomes smoother and the small columnar CIGS grains close to the Mo back contact disappear with increasing CIGS deposition temperature. At 773 K the two sodium incorporation routes result in large differences in the microstructures with a significantly larger grain size for the samples after post-deposition Na incorporation. Porosity was observed in the absorber layer close to the back contact in the samples from FSEC. The reason for porosity could be materials evaporation in the gallium beam of the FIB or a processing effect. The porosity certainly indicates heterogeneities of the composition of the absorber layer near the back contact. A Mo-Se rich layer (possibly MoSe2) was formed at the interface between CIGS/CIGSS and Mo improving the quality of the junction. Other chemical heterogeneities include un-sulfurized Cu-Ga deposits, residual Se from the selenization/ sulfurization chamber in CIGS2 and the formation of Cu-rich regions which are attributed to decomposition effects in the Ga beam of the FIB. Wavy absorber surfaces were observed for some of the cells with occasional discontinuities in the metal grids. The 50 nm thick CdS layer, however, remained continuous in all the samples under investigation. For a sample with a transparent back contact, a 10 nm Mo layer was deposited on ITO (indium tin oxide) before deposition of the CIGS2 (Cu(In,Ga)S2) layer. EFTEM maps indicate that a MoS2 layer does not form for such a Mo/MoS2-ITO back contact. Instead, absorber layer material diffuses through the thin Mo layer onto the ITO forming two layers of CIGS2 on either side of Mo with different compositions. Furthermore, an optical beam induced current (OBIC) system with micron level resolution was successfully developed and preliminary photocurrent maps were acquired to microscopically identify regions within a thin-film solar cell with undesirable microstructural features. Such a system, when fully operational, will provide the means for the identification of special regions from where samples for TEM analysis can be obtained using the FIB technique to study specifically the defects responsible for local variations in solar cell properties.

Scanning transmission electron microscopy (STEM) has been widely used for characterization of materials; to identify micro- and nano-structures within a sample and to analyze crystal and defect structures. High-angle annular dark field (HAADF) STEM imaging using atomic number (Z) contrast has proven capable of resolving atomic structures with better than 2 A lateral resolution. In this work, the HAADF STEM imaging mode is used in combination with multislice simulations. This combination is applied to the investigation of the temperature dependence of the intensity collected by the HAADF detector in silicon, and to convergent beam electron diffraction (CBED) to measure the degree of chemical order in intermetallic nanoparticles. The experimental and simulation results on the high–angle scattering of 300 keV electrons in crystalline silicon provide a new contribution to the understanding of the temperature dependence of the HAADF intensity. In the case of 300 keV, the average high-angle scattered intensity slightly decreases as the temperature increases from 100 K to 300 K, and this is different from the temperature dependence at 100 keV and 200 keV where HAADF intensity increases with temperature, as had been previously reported by other workers. The L10 class of hard magnetic materials has attracted continuous attention as a candidate for high-density magnetic recording media, as this phase is known to have large magnetocrystalline anisotropy, with magnetocrystalline anisotropy constant, Ku, strongly dependent on the long-range chemical order parameter, S. A new method is developed to assess the degree of chemical order in small FePt L10 nanoparticles by implementing a CBED diffraction technique. Unexpectedly, the degree of order of individual particles is highly variable and not a simple function of particle size or sample composition. The particle-to-particle variability observed is an important new aspect to the understanding of phase transformations in nanoparticle systems.