ASU Scholarship Showcase

We present results from experiments at the Linac Coherent Light Source (LCLS) demonstrating that serial femtosecond crystallography (SFX) can be performed to high resolution (~2.5 Å) using protein microcrystals deposited on an ultra-thin silicon nitride membrane and embedded in a preservation medium at room temperature. Data can be acquired at a high acquisition rate using x-ray free electron laser sources to overcome radiation damage, while sample consumption is dramatically reduced compared to flowing jet methods. We achieved a peak data acquisition rate of 10 Hz with a hit rate of ~38%, indicating that a complete data set could be acquired in about one 12-hour LCLS shift using the setup described here, or in even less time using hardware optimized for fixed target SFX. This demonstration opens the door to ultra low sample consumption SFX using the technique of diffraction-before-destruction on proteins that exist in only small quantities and/or do not produce the copious quantities of microcrystals required for flowing jet methods.

Novel hydride chemistries are employed to deposit light-emitting Ge_1-y Sn_yalloys with y ≤ 0.1 by Ultra-High Vacuum Chemical Vapor Deposition (UHV-CVD) on Ge-buffered Si wafers. The properties of the resultant materials are systematically compared with similar alloys grown directly on Si wafers. The fundamental difference between the two systems is a fivefold (and higher) decrease in lattice mismatch between film and virtual substrate, allowing direct integration of bulk-like crystals with planar surfaces and relatively low dislocation densities. For y ≤ 0.06, the CVD precursors used were digermane Ge₂H₆ and deuterated stannane SnD₄. For y ≥ 0.06, the Ge precursor was changed to trigermane Ge₃H₈, whose higher reactivity enabled the fabrication of supersaturated samples with the target film parameters. In all cases, the Ge wafers were produced using tetragermane Ge₄H₁₀ as the Ge source. The photoluminescence intensity from Ge_1-y Sn_y /Ge films is expected to increase relative to Ge_1-y Sn_y /Si due to the less defected interface with the virtual substrate. However, while Ge_1-y Sn_y /Si films are largely relaxed, a significant amount of compressive strain may be present in the Ge_1-y Sn_y /Ge case. This compressive strain can reduce the emission intensity by increasing the separation between the direct and indirect edges. In this context, it is shown here that the proposed CVD approach to Ge_1-y Sn_y /Ge makes it possible to approach film thicknesses of about 1  μm, for which the strain is mostly relaxed and the photoluminescence intensity increases by one order of magnitude relative to Ge_1-y Sn_y /Si films. The observed strain relaxation is shown to be consistent with predictions from strain-relaxation models first developed for the Si_1-x Ge_x /Si system. The defect structure and atomic distributions in the films are studied in detail using advanced electron-microscopy techniques, including aberration corrected STEM imaging and EELS mapping of the average diamond–cubic lattice.

Photosynthesis, a process catalysed by plants, algae and cyanobacteria converts sunlight to energy thus sustaining all higher life on Earth. Two large membrane protein complexes, photosystem I and II (PSI and PSII), act in series to catalyse the light-driven reactions in photosynthesis. PSII catalyses the light-driven water splitting process, which maintains the Earth’s oxygenic atmosphere. In this process, the oxygen-evolving complex (OEC) of PSII cycles through five states, S₀ to S₄, in which four electrons are sequentially extracted from the OEC in four light-driven charge-separation events. Here we describe time resolved experiments on PSII nano/microcrystals from Thermosynechococcus elongatus performed with the recently developed technique of serial femtosecond crystallography. Structures have been determined from PSII in the dark S₁ state and after double laser excitation (putative S₃ state) at 5 and 5.5 Å resolution, respectively. The results provide evidence that PSII undergoes significant conformational changes at the electron acceptor side and at the Mn₄CaO₅ core of the OEC. These include an elongation of the metal cluster, accompanied by changes in the protein environment, which could allow for binding of the second substrate water molecule between the more distant protruding Mn (referred to as the ‘dangler’ Mn) and the Mn₃CaO_x cubane in the S₂ to S₃ transition, as predicted by spectroscopic and computational studies. This work shows the great potential for time-resolved serial femtosecond crystallography for investigation of catalytic processes in biomolecules.

It has been suggested that the extended intensity profiles surrounding Bragg reflections that arise when a series of finite crystals of varying size and shape are illuminated by the intense, coherent illumination of an x-ray free-electron laser may enable the crystal’s unit-cell electron density to be obtained ab initio via well-established iterative phasing algorithms. Such a technique could have a significant impact on the field of biological structure determination since it avoids the need for a priori information from similar known structures, multiple measurements near resonant atomic absorption energies, isomorphic derivative crystals, or atomic-resolution data. Here, we demonstrate this phasing technique on diffraction patterns recorded from artificial two-dimensional microcrystals using the seeded soft x-ray free-electron laser FERMI. We show that the technique is effective when the illuminating wavefront has nonuniform phase and amplitude, and when the diffraction intensities cannot be measured uniformly throughout reciprocal space because of a limited signal-to-noise ratio.

In this paper, we report on the highly conductive layer formed at the crystalline γ-alumina/SrTiO₃ interface, which is attributed to oxygen vacancies. We describe the structure of thin γ-alumina layers deposited by molecular beam epitaxy on SrTiO3 (001) at growth temperatures in the range of 400–800 °C, as determined by reflection-high-energy electron diffraction, x-ray diffraction, and high-resolution electron microscopy. In situ x-ray photoelectron spectroscopy was used to confirm the presence of the oxygen-deficient layer. Electrical characterization indicates sheet carrier densities of ∼1013 cm−2 at room temperature for the sample deposited at 700 °C, with a maximum electron Hall mobility of 3100 cm²V^-1s^-1 at 3.2 K and room temperature mobility of 22 cm²V^-1s^-1. Annealing in oxygen is found to reduce the carrier density and turn a conductive sample into an insulator.

The development of non-volatile logic through direct coupling of spontaneous ferroelectric polarization with semiconductor charge carriers is nontrivial, with many issues, including epitaxial ferroelectric growth, demonstration of ferroelectric switching and measurable semiconductor modulation. Here we report a true ferroelectric field effect—carrier density modulation in an underlying Ge(001) substrate by switching of the ferroelectric polarization in epitaxial c-axis-oriented BaTiO₃ grown by molecular beam epitaxy. Using the density functional theory, we demonstrate that switching of BaTiO₃ polarization results in a large electric potential change in Ge. Aberration-corrected electron microscopy confirms BaTiO₃ tetragonality and the absence of any low-permittivity interlayer at the interface with Ge. The non-volatile, switchable nature of the single-domain out-of-plane ferroelectric polarization of BaTiO₃ is confirmed using piezoelectric force microscopy. The effect of the polarization switching on the conductivity of the underlying Ge is measured using microwave impedance microscopy, clearly demonstrating a ferroelectric field effect.

We report a study of the magnetic domain structure of nanocrystalline thin films of nickel-zinc ferrite. The ferrite films were synthesized using aqueous spin-spray coating at low temperature (∼90 °C) and showed high complex permeability in the GHz range. Electron microscopy and microanalysis revealed that the films consisted of columnar grains with uniform chemical composition. Off-axis electron holography combined with magnetic force microscopy indicated a multi-grain domain structure with in-plane magnetization. The correlation between the magnetic domain morphology and crystal structure is briefly discussed.

The current work explores the crystalline perovskite oxide, strontium hafnate, as a potential high-k gate dielectric for Ge-based transistors. SrHfO3 (SHO) is grown directly on Ge by atomic layer deposition and becomes crystalline with epitaxial registry after post-deposition vacuum annealing at ∼700 °C for 5 min. The 2 × 1 reconstructed, clean Ge (001) surface is a necessary template to achieve crystalline films upon annealing. The SHO films exhibit excellent crystallinity, as shown by x-ray diffraction and transmission electron microscopy. The SHO films have favorable electronic properties for consideration as a high-k gate dielectric on Ge, with satisfactory band offsets (>2 eV), low leakage current (<10^-5 A/cm² at an applied field of 1 MV/cm) at an equivalent oxide thickness of 1 nm, and a reasonable dielectric constant (k ∼ 18). The interface trap density (Dit) is estimated to be as low as ∼2 × 10¹² cm^-2 eV^-1 under the current growth and anneal conditions. Some interfacial reaction is observed between SHO and Ge at temperatures above ∼650 °C, which may contribute to increased Dit value. This study confirms the potential for crystalline oxides grown directly on Ge by atomic layer deposition for advanced electronic applications.

The probiotic effects of Lactobacillus reuteri have been speculated to partly depend on its capacity to produce the antimicrobial substance reuterin during the reduction of glycerol in the gut. In this study, the potential of this process to protect human intestinal epithelial cells against infection with Salmonella enterica serovar Typhimurium was investigated. We used a three-dimensional (3-D) organotypic model of human colonic epithelium that was previously validated and applied to study interactions between S. Typhimurium and the intestinal epithelium that lead to enteric salmonellosis. Using this model system, we show that L. reuteri protects the intestinal cells against the early stages of Salmonella infection and that this effect is significantly increased when L. reuteri is stimulated to produce reuterin from glycerol. More specifically, the reuterin-containing ferment of L. reuteri caused a reduction in Salmonella adherence and invasion (1 log unit), and intracellular survival (2 log units). In contrast, the L. reuteri ferment without reuterin stimulated growth of the intracellular Salmonella population with 1 log unit. The short-term exposure to reuterin or the reuterin-containing ferment had no observed negative impact on intestinal epithelial cell health. However, long-term exposure (24 h) induced a complete loss of cell-cell contact within the epithelial aggregates and compromised cell viability. Collectively, these results shed light on a potential role for reuterin in inhibiting Salmonella-induced intestinal infections and may support the combined application of glycerol and L. reuteri. While future in vitro and in vivo studies of reuterin on intestinal health should fine-tune our understanding of the mechanistic effects, in particular in the presence of a complex gut microbiota, this the first report of a reuterin effect on the enteric infection process in any mammalian cell type.

This study presents the first global transcriptional profiling and phenotypic characterization of the major human opportunistic fungal pathogen, Candida albicans, grown in spaceflight conditions. Microarray analysis revealed that C. albicans subjected to short-term spaceflight culture differentially regulated 452 genes compared to synchronous ground controls, which represented 8.3% of the analyzed ORFs. Spaceflight-cultured C. albicans–induced genes involved in cell aggregation (similar to flocculation), which was validated by microscopic and flow cytometry analysis. We also observed enhanced random budding of spaceflight-cultured cells as opposed to bipolar budding patterns for ground samples, in accordance with the gene expression data. Furthermore, genes involved in antifungal agent and stress resistance were differentially regulated in spaceflight, including induction of ABC transporters and members of the major facilitator family, downregulation of ergosterol-encoding genes, and upregulation of genes involved in oxidative stress resistance.

Finally, downregulation of genes involved in actin cytoskeleton was observed. Interestingly, the transcriptional regulator Cap1 and over 30% of the Cap1 regulon was differentially expressed in spaceflight-cultured C. albicans. A potential role for Cap1 in the spaceflight response of C. albicans is suggested, as this regulator is involved in random budding, cell aggregation, and oxidative stress resistance; all related to observed spaceflight-associated changes of C. albicans. While culture of C. albicans in microgravity potentiates a global change in gene expression that could induce a virulence-related phenotype, no increased virulence in a murine intraperitoneal (i.p.) infection model was observed under the conditions of this study. Collectively, our data represent an important basis for the assessment of the risk that commensal flora could play during human spaceflight missions. Furthermore, since the low fluid-shear environment of microgravity is relevant to physical forces encountered by pathogens during the infection process, insights gained from this study could identify novel infectious disease mechanisms, with downstream benefits for the general public.