SEARCH · Search NASA
Results for “structural variation”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Crystal Chemistry and Structural Variations for Zircon Samples from Various Localities
This study investigates the variations of structural parameters and chemistry of a partially metamict and seven detrital zircon samples from different localities using single-crystal X-ray diffraction, synchrotron high-resolution powder X-ray diffraction, and electron-probe micro-analysis techniques. The unit-cell parameters for the eight zircon samples vary linearly with increasing unit-cell volume, V. A zircon sample from the Canadian Arctic Islands has the smallest unit-cell parameters, bond distances, ideal stoichiometric composition, unaffected by α-radiation damage, and is chemically pure. A zircon sample from Jemaa, Nigeria has the largest unit-cell parameters because of the effect of α-radiation doses received over a long time (2384 Ma). All the samples show good correlations between Zr and Si apfu (atom per formula unit) versus unit-cell volume, V. The α-radiation doses in the samples are lower than ~3.5 × 1015 α-decay events/mg. Substitutions of other cations at the Zr and Si sites control the variations of the structural parameters. Relatively large unit-cell parameters and bond distances occur because the Zr site accommodates other cations that have larger ionic radii than the Zr atom. Geological age increases the radiation doses in zircon and it is related to V.
Exposing structural variations in SARS-CoV-2 evolution
The mutation of SARS-CoV-2 influences viral function as residue replacements affect both physiochemical properties and folding conformations. Although a large amount of data on SARS-CoV-2 is available, the investigation of how viral functions change in response to mutations is hampered by a lack of effective structural analysis. Here, we exploit the advances of protein structure fingerprint technology to study the folding conformational changes induced by mutations. With integration of both protein sequences and folding conformations, the structures are aligned for SARS-CoV to SARS-CoV-2, including Alpha variant (lineage B.1.1.7) and Delta variant (lineage B.1.617.2). The results showed that the virus evolution with change in mutational positions and physicochemical properties increased the affinity between spike protein and ACE2, which plays a critical role in coronavirus entry into human cells. Additionally, these structural variations impact vaccine effectiveness and drug function over the course of SARS-CoV-2 evolution. The analysis of structural variations revealed how the coronavirus has gradually evolved in both structure and function and how the SARS-CoV-2 variants have contributed to more severe acute disease worldwide.
Direct Observation of the Pressure-Induced Structural Variation in Gold Nanoclusters and the Correlated Optical Response
The ability to gradually modify the atomic structures of nanomaterials and directly identify such structural variation is important in nanoscience research. Here, we present the first example of a high-pressure single-crystal X-ray diffraction analysis of atomically precise metal nanoclusters. The pressure-dependent, subangstrom structural evolution of an ultrasmall gold nanoparticle, Au 25 S 18 , has been directly identified. We found that a 0.1 Å decrease of the Au–Au bond length could induce a blue-shift of 30 nm in the photoluminescence spectra of gold nanoclusters. From theoretical calculations, the origins of the blue-shift and enhanced photoluminescence under pressure are investigated, which are ascribed to molecular orbital symmetry and conformational locking, respectively. Here, the combination of the high-pressure in situ X-ray results with both theoretical and experimental optical spectra provides a direct and generalizable avenue to unveil the underlying structure–property relations for nanoclusters and nanoparticles which cannot be obtained through traditional physical chemistry measurements.
Genomic patterns of structural variation among diverse genotypes of Sorghum bicolor and a potential role for deletions in local adaptation
Genomic structural mutations, especially deletions, are an important source of variation in many species and can play key roles in phenotypic diversification and evolution. Previous work in many plant species has identified multiple instances of structural variations (SVs) occurring in or near genes related to stress response and disease resistance, suggesting a possible role for SVs in local adaptation. Sorghum [Sorghum bicolor (L.) Moench] is one of the most widely grown cereal crops in the world. It has been adapted to an array of different climates as well as bred for multiple purposes, resulting in a striking phenotypic diversity. In this study, we identified genome-wide SVs in the Biomass Association Panel, a collection of 347 diverse sorghum genotypes collected from multiple countries and continents. Using Illumina-based, short-read whole-genome resequencing data from every genotype, we found a total of 24,648 SVs, including 22,359 deletions. The global site frequency spectrum of deletions and other types of SVs fit a model of neutral evolution, suggesting that the majority of these mutations were not under any types of selection. Clustering results based on single nucleotide polymorphisms separated the genotypes into eight clusters which largely corresponded with geographic origins, with many of the large deletions we uncovered being unique to a single cluster. Even though most deletions appeared to be neutral, a handful of cluster-specific deletions were found in genes related to biotic and abiotic stress responses, supporting the possibility that at least some of these deletions contribute to local adaptation in sorghum.
A comparative look at structural variation among RC–LH1 ‘Core’ complexes present in anoxygenic phototrophic bacteria
All purple photosynthetic bacteria contain RC–LH1 ‘Core’ complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC–LH1 ‘Core’ complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chloroflexi species, Roseiflexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC–LH1 ‘Core’ complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these different structures and looks at the functional significance of these variations from two main standpoints: energy transfer and quinone exchange.
Chemical Environment and Structural Variations in High Entropy Oxide Thin Film Probed with Electron Microscopy
For this work, we employ analytical transmission electron microscopy (TEM) to correlate the structural and chemical environment variations within a stacked epitaxial thin film of the high entropy oxide (HEO) Mg 0.2 Co 0.2 Ni 0.2 Cu 0.2 Zn 0.2 O (J14), with two layers grown at different substrate temperatures (500 and 200 °C) using pulsed laser deposition (PLD). Electron diffraction and atomically resolved STEM imaging reveal the difference in out-of-plane lattice parameters in the stacked thin film, which is further quantified on a larger scale using four-dimensional STEM (4D-STEM). In the layer deposited at a lower temperature, electron energy loss spectroscopy (EELS) mapping indicates drastic changes in the oxidation states and bonding environment for Co ions, and energy-dispersive X-ray spectroscopy (EDX) mapping detects more significant cation deficiency. Ab initio density functional theory (DFT) calculations validate that vacancies on the cation sublattice of J14 result in significant electronic and structural changes. The experimental and computational analyses indicate that low temperatures during film growth result in cation deficiency, an altered chemical environment, and reduced lattice parameters while maintaining a single phase. Our results demonstrate that the complex correlation of configurational entropy, kinetics, and thermodynamics can be utilized for accessing a range of metastable configurations in HEO materials without altering cation proportions, enabling further engineering of functional properties of HEO materials.
Understanding Differences in Water Adsorption Isotherms: Structural Variations, Force Fields, and Monte Carlo Simulation Approaches
Accurate prediction of water adsorption in micro- and mesoporous materials with hydrophobic pores is essential for the design and characterization of advanced adsorbent materials for separation and energy applications. Here, we assess the reproducibility and consistency of water adsorption isotherms in two microporous all-silica MFI zeolite structures (MFI-K and MFI-O) using two different zeolite force fields and three simulation approaches: grand canonical Monte Carlo (GCMC), Gibbs ensemble Monte Carlo (GEMC), and transition matrix Monte Carlo (TMMC). We demonstrate that consistent treatment of the bulk fluid phase in GCMC and TMMC simulations is critical for reconciling isotherms across methods, and we construct simulation-based equations of state for the TIP4P water model to enable rigorous fugacity-to-pressure conversions. Large shifts in the isotherms are observed for two zeolite force fields developed using different parametrization strategies, with the GCS force field representing implicitly a defect-containing all-silica zeolite, whereas the TraPPE-zeo force field accurately represents an essentially defect-free all-silica zeolite. While water in the van Koningsveld structure of MFI exhibits a first-order phase transition and condensation-like step for adsorption near room temperature, water in the Olson structure of MFI displays continuous adsorption, attributed to differences in the adsorption free energy landscapes. Structural analysis reveals that small geometric variations, particularly Si–O–Si bond angles near the strongest adsorption sites, lead to these substantial differences in adsorption behavior. Furthermore, our results highlight the sensitivity of simulated water adsorption isotherms in hydrophobic frameworks to seemingly small differences in the framework structures, force field parametrization, and simulation approaches.
Major impacts of widespread structural variation on sorghum
Genetic diversity is critical to crop breeding and improvement, and dissection of the genomic variation underlying agronomic traits can both assist breeding and give insight into basic biological mechanisms. Although recent genome analyses in plants reveal many structural variants (SVs), most current studies of crop genetic variation are dominated by single-nucleotide polymorphisms (SNPs). The extent of the impact of SVs on global trait variation, as well as their utility in genome-wide selection, is not yet understood. In this study, we built an SV data set based on whole-genome resequencing of diverse sorghum lines (n = 363), validated the correlation of photoperiod sensitivity and variety type, and identified SV hotspots underlying the divergent evolution of cellulosic and sweet sorghum. In addition, we showed the complementary contribution of SVs for heritability of traits related to sorghum adaptation. Importantly, inclusion of SV polymorphisms in association studies revealed genotype–phenotype associations not observed with SNPs alone. Three-way genome-wide association studies (GWAS) based on whole-genome SNP, SV, and integrated SNP + SV data sets showed substantial associations between SVs and sorghum traits. The addition of SVs to GWAS substantially increased heritability estimates for some traits, indicating their important contribution to functional allelic variation at the genome level. Our discovery of the widespread impacts of SVs on heritable gene expression variation could render a plausible mechanism for their disproportionate impact on phenotypic variation. This study expands our knowledge of SVs and emphasizes the extensive impacts of SVs on sorghum.
Grass xylan structural variation suggests functional specialization and distinctive interaction with cellulose and lignin
SUMMARY Xylan is the most abundant non‐cellulosic polysaccharide in grass cell walls, and it has important structural roles. The name glucuronoarabinoxylan (GAX) is used to describe this variable hemicellulose. It has a linear backbone of β‐1,4‐xylose (Xyl) residues that may be substituted with α‐1,2‐linked (4‐ O ‐methyl)‐glucuronic acid (GlcA), α‐1,3‐linked arabinofuranose (Ara f ), and sometimes acetylation at the O ‐2 and/or O ‐3 positions. The role of these substitutions remains unclear, although there is increasing evidence that they affect the way xylan interacts with other cell wall components, particularly cellulose and lignin. Here, we used substitution‐dependent endo‐xylanase enzymes to investigate the variability of xylan substitution in grass culm cell walls. We show that there are at least three different types of xylan: (i) an arabinoxylan with evenly distributed Ara f substitutions without GlcA (AXe); (ii) a glucuronoarabinoxylan with clustered GlcA modifications (GAXc); and (iii) a highly substituted glucuronoarabinoxylan (hsGAX). Immunolocalization of AXe and GAXc in Brachypodium distachyon culms revealed that these xylan types are not restricted to a few cell types but are instead widely detected in Brachypodium cell walls. We hypothesize that there are functionally specialized xylan types within the grass cell wall. The even substitutions of AXe may permit folding and binding on the surface of cellulose fibrils, whereas the more complex substitutions of the other xylans may support a role in the matrix and interaction with other cell wall components.
Influence of Surface and Structural Variations in Donor–Acceptor–Donor Sensitizers on Photoelectrocatalytic Water Splitting
Conjugated organic chromophores composed of linked donor (D) and acceptor (A) moieties have attracted considerable attention for photoelectrochemical applications. In this work, we compare the optoelectronic properties and photoelectrochemical performance of two D–A–D structural isomers with thiophene-X-carboxylic acid (X denotes 3 and 2 positions) derivatives and 2,1,3-benzothiadiazole as the D and A moieties, respectively. 5,5′-(Benzo[c][1,2,5]thiadiazole-4,7-diyl)bis(thiophene-3-carboxylic acid), BTD1, and 5,5′-(benzo[c][1,2,5]thiadiazole-4,7-diyl)bis(thiophene-2-carboxylic acid), BTD2, were employed in the study to understand how structural isomers affect surface attachments within chromophore–catalyst assemblies and their influence on charge-transfer dynamics. Crystal structures revealed that varying the position of the −COOH anchoring group causes the molecules to either contort out of a plane (BTD1) or adopt a near-perfect planar conformation (BTD2). BTD1 and BTD2 were co-loaded with either a water oxidation catalyst, [Ru(2,6-bis(1-methylbenzimidazol-2-yl)pyridine)-(4,4′-((HO) 2 OPCH 2 )2-2,2′-bipyridine)(OH 2 )] 2 , RuCt 2+ , or proton reduction catalyst [Ni(P 2 Ph N 2 C 6 H 4 CH 2 PO 3 H 2 ) 2 ] 2+ , NiCt 2+ , on oxide electrodes to facilitate photodriven water splitting reactions. Emission quenching measurements indicate that both BTD1 and BTD2 inject electrons into n-type SnO 2 |TiO 2 electrodes and holes into p-type NiO semiconductors from their respective excited states at high efficiencies >60%. Photocurrent densities of chromophore–catalyst assemblies obtained using linear sweep voltammetry (LSV) show that BTD2-sensitized photoanodes generate significantly more photocurrent than BTD1-sensitized electrodes; however, both exhibit similar performances at the photocathode. Photoelectrocatyltic measurements demonstrate that both BTD1 and BTD2 performed similarly, generating Faradaic efficiencies of 39 and 38% at the anode or 61 and 79% at the cathode. Transient absorption measurements suggest that the differences between the LSV and photoelectrocatalytic measurements result from the differences in quantum yields of the photogenerated redox equivalents, which is also a reflection of the varying metal oxide surface conformation. Our findings suggest that BTD2 should be investigated further in photocathodic studies since it has the structural advantage of being incorporated into diverse types of chromophore–catalyst assemblies.
Understanding Synthesis and Structural Variation of Nanomaterials Through In Situ/Operando XAS and SAXS
Nanostructured materials with high surface area and low coordinated atoms present distinct intrinsic properties from their bulk counterparts. However, nanomaterials' nucleation/growth mechanism during the synthesis process and the changes of the nanomaterials in the working state are still not thoroughly studied. As two indispensable methods, X-ray absorption spectroscopy (XAS) provides nanomaterials' electronic structure and coordination environment, while small-angle X-ray scattering (SAXS) offers structural properties and morphology information. Here, a combination of in situ/operando XAS and SAXS provides high temporal and spatial resolution to monitor the evolution of nanomaterials. This review gives a brief introduction to in situ/operando SAXS/XAS cells. In addition, the application of in situ/operando XAS and SAXS in preparing nanomaterials and studying changes of working nanomaterials are summarized.
Setting the H-mode pedestal structure: variations of particle source location using gas puff and pellet fueling
Experiments in DIII-D show that a particle source location inside the top of the H-mode pedestal (pellets) maintains a higher pedestal pressure than an edge source (gas fueling) through a widening of the electron temperature pedestal with reduction of the temperature gradient. The effect of these two fueling schemes on the H-mode pedestal structure was examined in DIII-D by comparing controlled pellet-fueled and gas-fueled discharges across a fueling scan up to 40 torr 1 s –1 . High resolution electron profiles reveal that gas fueling lowers the pedestal pressure as the density profile shifts radially outwards and the separatrix density increases, while pellet fueling maintains a constant pedestal pressure. The neutral source locations from pellets and gas are determined with the PELLET and UEDGE codes, respectively, and quantify the particle source localization. Pellets provide significant ionization inside the pedestal top while gas puffing localizes ionization in the scrape-off-layer and pedestal foot, broadly consistent with the density profile structure influenced by the source. ELMs are observed to increase in frequency and reduce impurity content as fueling is increased. Stability analysis with ELITE shows that both conditions are near the type-I ELM corner of the peeling–ballooning stability diagram, which is altered significantly by the introduction of pellets. Since transport mechanisms are not observed to change substantially with particle source location, wider pedestals allow the pellet-fueled discharges to retain higher pedestal temperatures at similar pedestal densities. EPED1 is tested to capture the pedestal pressure, under-predicting the height with pellets and over-predicting the height with gas by ~15%. Overall, these results have important implications for future reactors where pellet fueling will be the primary particle source due to an opaque scrape-off-layer by showing that the neutral source location plays a role in setting the structure of the H-mode pedestal.
Structural variations across the nepheline (NaAlSiO4)?kalsilite (KAlSiO4) series
Explore the source record for details and available documents.
XRD and STEM Analysis of Structural Variation in Nanocrystalline Cu-Ag Thin Films
Explore the source record for details and available documents.