Electronic structure and dynamics analysis of the Cu-Ag binary alloy by a tight-binding parametrization
Not provided.
Materials Science↗
SEARCH · Search NASA
Results for “structures analysis”
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.
Advancements in cerium/titanium metal-organic frameworks: Unparalleled stability in CO oxidation
Due to the excellent catalytic properties of Ce-based materials, the development of thermally stable metal-organic frameworks (MOFs) based on Ce-oxo clusters has attracted significant attention but remains challenging. In this work, we report the synthesis of an unreported Ce 4 Ti 2 -TMA (Ce IV 4 Ti IV 2 O 4 (OH) 4 (C(CH 3 ) 3 COO) 12 ·3H 2 O·3MeCN) cluster, which serves as an ideal source for the assembly of robust Ce/Ti-MOFs. Using this cluster, we constructed two isostructural MOFs, denoted as NU-3000 and NU-3001. Single-crystal X-ray diffraction analysis confirms these MOFs as mesoporous structures with 12-coordinated Ce 3 Ti 3 nodes. Furthermore, structural analysis reveals a plane triangular node structure that likely contributes to the excellent thermal stability of these MOFs. Finally, both MOFs show catalytic activity toward high-temperature (250°C) CO oxidation and maintain significant porosity, emphasizing the thermal stability of these materials under practical catalytic conditions. Furthermore, the straightforward synthesis of thermally robust Ce/Ti-MOFs from the Ce 4 Ti 2 -TMA cluster will pave the way for future Ce/Ti-MOF-based catalyst development.
36 MATERIALS SCIENCE↗
Insights into the Complexation of Actinides by Diethylenetriaminepentaacetic Acid from Characterization of the Americium(III) Complex
Diethylenetriaminepentaacetic acid (DTPA) is a frequently used chelator in the nuclear and medical industries, especially for the complexation of trivalent actinides. However, structural data on these complexes in the solid-state have long remained elusive. Herein, a detailed structural analysis of the presented crystal structures of [C(NH 2 ) 3 ] 4 [Nd(DTPA)] 2 · n H 2 O and [C(NH 2 ) 3 ] 4 [Am(DTPA)] 2 · n H 2 O, where [C(NH 2 ) 3 ] + is guanidinium, details the subtle differences in the Lewis acidity between a lanthanide/actinide pair of similar ionic sizes. Contractions in nitrogen–metal bond lengths between neodymium(III) and americium(III) were observed, while the metal–oxygen bonds remained relatively consistent, highlighting the marginal favorability for actinide complexation over the lanthanides with moderately soft N-donors. Spectroscopic analysis shows significant splitting of many transitions and relatively strong electronic interactions with traditionally low-intensity transitions in the americium complex, as is demonstrated in the 7 F 0 → 7 F 5 transitions. Pressure-induced spectroscopic analysis showed surprisingly little effect on the americium complex, with 5 f →5 f transitions either not shifting or marginally shifting from 2 to 3 nm at 11.93 ± 0.06 GPa─atypical of a soft, N-donor americium complex under pressure. Finally, large voids occupied by water molecules in between the complexes within the crystal structure may be responsible for the lack of pressure response in the 5 f →5 f transitions.
absorption spectroscopy↗
A fragment-based approach to discovery of Receptor for Advanced Glycation End products inhibitors
Explore the source record for details and available documents.
Kozlyuk, Natalia↗
Turbulence Modeling with Nek5000/RS, SOD2D and Alya
We present Validation and Verification (V & V) study of two high-order spectral element method (SEM) based Computational Fluid Dyanimcs (CFD) codes that we will utilize for work on turbulence modeling: Nek5000 and SOD2D. While the former solves the incompressible form of Navier-Stokes equation, the latter works with compressible set of equations and uses an entropy-viscosity formulation to account for the discontinuities for high Mach number flows. We demonstrate the accuracy of these codes for two benchmark sub-sonic turbulent flows: periodic channel and pipe flow, by carrying out first and second order statistical analysis, grid convergence and turbulent structure analysis using wall-resolved large eddy simulations (WRLES). Later, we report on the implementation and testing of various wall-modeling strategies for large eddy simulation of turbulent flows in Nek5000. These include both classical log-law based and decision-tree based machine-learning models. Accuracy of these closure strategies are analyzed and necessary future work is outlined.
97 MATHEMATICS AND COMPUTING↗
Target highlights in CASP14: Analysis of models by structure providers
Explore the source record for details and available documents.
Alexander, Leila T.↗
Structure of the polysaccharide sheath from the B race of the green microalga Botryococcus braunii
The green microalga Botryococcus braunii forms a colony of cells held together by an intricate extracellular matrix. This extracellular matrix also acts as a storage location for liquid hydrocarbons initially produced inside the cells. These hydrocarbons can be used as feedstocks to produce transportation fuels. In the B race of B. braunii, the extracellular matrix is composed of several elements: a cross-linked hydrocarbon network filled with the liquid hydrocarbons, a retaining wall to hold the hydrocarbons in the extracellular matrix, an arabinogalactan polysaccharide fibrillar sheath that extends outward from the retaining wall, and a single protein known as polysaccharide associated protein is found at the base of the polysaccharide fibers where they connect to the retaining wall. During growth, colonies of the B race of B. braunii shed fragments of the retaining wall with polysaccharide fibrils attached into the media. Here we describe the isolation and structural analysis of these polysaccharides using a series of chemical degradations in combination with glycosyl residue composition and linkage analysis, as well as 2-dimensional nuclear magnetic resonance spectroscopy. The results demonstrate that the polysaccharide is highly branched, consisting of a galactan backbone with short branches comprised of Dgalactopyranose, L-arabinofuranose, 4-O-methyl-D-glucopyranuronic acid, and 6-deoxy-D-altropyranose. To our knowledge, this is the first description of 6-deoxyaltrose in algae or plants.
59 BASIC BIOLOGICAL SCIENCES↗
Crystal structure of the Arabidopsis SPIRAL2 C-terminal domain reveals a p80-Katanin-like domain
Epidermal cells of dark-grown plant seedlings reorient their cortical microtubule arrays in response to blue light from a net lateral orientation to a net longitudinal orientation with respect to the long axis of cells. The molecular mechanism underlying this microtubule array reorientation involves katanin, a microtubule severing enzyme, and a plant-specific microtubule associated protein called SPIRAL2. Katanin preferentially severs longitudinal microtubules, generating seeds that amplify the longitudinal array. Upon severing, SPIRAL2 binds nascent microtubule minus ends and limits their dynamics, thereby stabilizing the longitudinal array while the lateral array undergoes net depolymerization. To date, no experimental structural information is available for SPIRAL2 to help inform its mechanism. To gain insight into SPIRAL2 structure and function, we determined a 1.8 Å resolution crystal structure of the Arabidopsis thaliana SPIRAL2 C-terminal domain. The domain is composed of seven core α-helices, arranged in an α-solenoid. Amino-acid sequence conservation maps primarily to one face of the domain involving helices α1, α3, α5, and an extended loop, the α6-α7 loop. The domain fold is similar to, yet structurally distinct from the C-terminal domain of Ge-1 (an mRNA decapping complex factor involved in P-body localization) and, surprisingly, the C-terminal domain of the katanin p80 regulatory subunit. The katanin p80 C-terminal domain heterodimerizes with the MIT domain of the katanin p60 catalytic subunit, and in metazoans, binds the microtubule minus-end factors CAMSAP3 and ASPM. Structural analysis predicts that SPIRAL2 does not engage katanin p60 in a mode homologous to katanin p80. The SPIRAL2 structure highlights an interesting evolutionary convergence of domain architecture and microtubule minus-end localization between SPIRAL2 and katanin complexes, and establishes a foundation upon which structure-function analysis can be conducted to elucidate the role of this domain in the regulation of plant microtubule arrays.
59 BASIC BIOLOGICAL SCIENCES↗
Z-Contrast Enhancement in Au–Pt Nanocatalysts by Correlative X-ray Absorption Spectroscopy and Electron Microscopy: Implications for Composition Determination
The properties of bimetallic nanoparticles (BNPs) vary widely as a function of their composition and size distributions. X-ray absorption fine structure analysis is commonly used to characterize their structure, but its application to elements that are close to each other in the periodic table is hampered by poor Z-contrast. For this study, we trained an artificial neural network to recognize the partial coordination numbers in AuPt NPs synthesized via peptide templating using their X-ray absorption near-edge structure spectra. This approach, combined with scanning transmission electron microscopy analysis, revealed unique details of this prototype catalytic system that has different forms of heterogeneities at both the intra- and inter-particle levels. Our method based on the enhancement of Z-contrast of metal species will have implications for compositional studies of BNPs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Evaluating the pressure dependence of PZT structures using a virtual reality environment
Pb–Zr–Ti–O (PZT) perovskites span a large solid-solution range and have found widespread use due to their piezoelectric and ferroelectric properties that also span a large range. Crystal structure analysis via Rietveld refinement facilitates materials analysis via the extraction of the structural parameters. These parameters, often obtained as a function of an additional dimension (e.g., pressure), can help to diagnose materials response within a use environment. Often referred to as “ in-situ ” studies, these experiments provide an abundance of data. Viewing structural changes due to applied pressure conditions can give much-needed insight into materials performance. However, challenges exist for viewing/presenting results when the details are inherently three-dimensional (3D) in nature. For PZT perovskites, the use of polyhedra (e.g., Zr/Ti–O 6 octahedra) to view bonding/connectivity is beneficial; however, the visualization of the octahedra behavior with pressure dependence is less easily demonstrated due to the complexity of the added pressure dimension. We present a more intuitive visualization by projecting structural data into virtual reality (VR). We employ previously published structural data for Pb 0.99 (Zr 0.95 Ti 0.05 ) 0.98 Nb 0.02 O 3 as an exemplar for VR visualization of the PZT R3c crystal structure between ambient and 0.62 GPa pressure. This is accomplished via our in-house CAD2VR™ software platform and the new CrystalVR plugin. The use of the VR environment enables a more intuitive viewing experience, while enabling on-the-fly evaluation of crystal data, to form a detailed and comprehensive understanding of in-situ datasets. Discussion of methodology and tools for viewing are given, along with how recording results in video form can enable the viewing experience.
Rodriguez, Mark A. (ORCID:0000000269405044)↗
Conformational heterogeneity of the BTK PHTH domain drives multiple regulatory states
Full-length Bruton’s tyrosine kinase (BTK) has been refractory to structural analysis. The nearest full-length structure of BTK to date consists of the autoinhibited SH3–SH2–kinase core. Precisely how the BTK N-terminal domains (the Pleckstrin homology/Tec homology [PHTH] domain and proline-rich regions [PRR] contain linker) contribute to BTK regulation remains unclear. We have produced crystals of full-length BTK for the first time but despite efforts to stabilize the autoinhibited state, the diffraction data still reveal only the SH3–SH2–kinase core with no electron density visible for the PHTH–PRR segment. Cryo-electron microscopy (cryoEM) data of full-length BTK, on the other hand, provide the first view of the PHTH domain within full-length BTK. CryoEM reconstructions support conformational heterogeneity in the PHTH–PRR region wherein the globular PHTH domain adopts a range of states arrayed around the autoinhibited SH3–SH2–kinase core. On the way to activation, disassembly of the SH3–SH2–kinase core opens a new autoinhibitory site on the kinase domain for PHTH domain binding that is ultimately released upon interaction of PHTH with phosphatidylinositol (3,4,5)-trisphosphate. Membrane-induced dimerization activates BTK and we present here a crystal structure of an activation loop swapped BTK kinase domain dimer that likely represents the conformational state leading to trans-autophosphorylation. Together, these data provide the first structural elucidation of full-length BTK and allow a deeper understanding of allosteric control over the BTK kinase domain during distinct stages of activation.
59 BASIC BIOLOGICAL SCIENCES↗
Ion-Electron Coupling-Driven Redox Behavior in Metal–Organic Frameworks
Redox-active metal–organic frameworks (MOFs) have long been proposed as electronic transport platforms, yet the microscopic origin of their conductivity remains debated. A theoretical demonstration reveals charge transport in a Zn(pyrazole–naphthalene diimide (NDI)) MOF arising not from delocalized band-like states but from redox hopping between discrete linker sites. Using ab initio molecular dynamics simulations combined with electronic structure analysis, we established a direct link among electron injection, structural reorganization, and transport. Electron accumulation proceeds sequentially and site-selectively from imide and carbonyl groups of the NDI core progressively involving pyrazole N atoms at higher reduction states, through a hierarchy of redox-active sites. In contrast, Zn nodes remain essentially redox-inactive, which confirms their structural role. Density-of-states analysis corroborates a transport regime dominated by linker-centered states with evolving p-character upon reduction, resulting in dynamically reconfigured conduction networks. Real-time trajectories reveal anisotropic linker-to-linker electron transfer modulated by counterion coordination. This cooperative ion–electron regime emerges from potential energy surface collapse into a single low-barrier transition (ΔG ‡ ≈ 45 meV), where ionic and electronic motions evolve adiabatically on the same free-energy landscape. Elucidating redox conductivity in Zn(pyrazole–NDI) MOFs provides a theoretical framework for use in neuromorphic computing and related technologies.
Charge transfer↗
Evaluating size exclusion chromatography for nucleic acid removal in Klebsiella pneumoniae cell surface polysaccharide purification
Cell surface-associated polysaccharides in Klebsiella are major virulence determinants and crucial targets for developing vaccines. Traditionally, the purification of these cell surface polysaccharides from Klebsiella pneumoniae involves a multi-step process comprising phenol extraction, nuclease digestion, ultracentrifugation, and repeated ethanol extractions. In this study, we evaluated size exclusion chromatography for effectively eliminating nucleic acid contamination while purifying high molecular weight cell surface-associated polysaccharides. Post-initial extraction, the nucleic acid content remains significantly elevated, and kinetic analysis reveals that DNase I and RNase A digestion is neither economically viable nor effective for removing these contaminants. Employing an appropriate size exclusion resin removes over 99 % of nucleic acid contamination, as confirmed by nucleic acid content analysis and agarose gel electrophoresis. Purity and structural analysis using 1H 1D-NMR and 2D-NMR demonstrate that the cell surface-associated polysaccharide purified with this study is highly homogeneous and identified as antigenic O-polysaccharide. This approach streamlines the purification process by removing the need for nuclease digestion and additional ethanol precipitation steps.
60 APPLIED LIFE SCIENCES↗
Structure and composition of blueberry fiber pectin and xyloglucan that bind anthocyanins during fruit puree processing
Blueberry is a well-known source of antioxidants and prebiotic dietary fiber yet the fate of these health-beneficial ingredients during fruit processing it is not understood. Detailed composition and structure of blueberry pomace (PF) remaining after commercial blueberry fruit puree processing, as well as the water soluble and water insoluble fractions, were determined. The PF was comprised of dietary fiber (60.8%) that was largely insoluble (46.2% vs. 14.6% soluble dietary fiber) pectin, xyloglucan, arabinoxylan and mannan polysaccharides, fructose (11.22%) and glucose (10.37%) free sugars, protein (9%), fat (5%), and anthocyanins (6444.5 μg/g). The most abundant anthocyanins detected in PF were malvidin 3-arabinoside and peonidin 3-glucoside and the pectin was determined to be methyl-esterified and acetylated rhamnogalacturonan I with a 4,5-unsaturated function at the non-reducing end based on oligosaccharide structural analysis. Blueberry PF xyloglucan oligosaccharide side chain structures included xylose, arabinose and galactose consistent with arabino-xyloglucan structure. Additionally, microwave-assisted extraction of blueberry PF (pH 2 for 10 min at 80 °C) was performed to more clearly elucidate pectin structure, and revealed a pectin polymer with high molar mass (1072 kDa) and viscosity that was dependent upon the molar mass. A random coil shape was confirmed for both the blueberry PF and microwave extracted blueberry pectin, which agreed with previous reports that flexible blueberry pectin contributes to strong anthocyanin binding. In summary, the blueberry pomace anthocyanin content was slightly higher than that reported for fresh whole blueberry fruit, which suggests that most blueberry anthocyanins adhered to the pomace fiber, and most likely the insoluble pectin, during and after processing.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Solvent-dependent complex reaction pathways of bromoform revealed by time-resolved X-ray solution scattering and X-ray transient absorption spectroscopy
The photochemical reaction pathways of CHBr3 in solution were unveiled using two complementary X-ray techniques, time-resolved X-ray solution scattering (TRXSS) and X-ray transient absorption spectroscopy, in a wide temporal range from 100 ps to tens of microseconds. By performing comparative measurements in protic (methanol) and aprotic (methylcyclohexane) solvents, we found that the reaction pathways depend significantly on the solvent properties. In methanol, the major photoproducts are CH3OCHBr2 and HBr generated by rapid solvolysis of iso-CHBr2-Br, an isomer of CHBr3. In contrast, in methylcyclohexane, iso-CHBr2-Br returns to CHBr3 without solvolysis. In both solvents, the formation of CHBr2 and Br is a competing reaction channel. From the structural analysis of TRXSS data, we determined the structures of key intermediate species, CH3OCHBr2 and iso-CHBr2-Br in methanol and methylcyclohexane, respectively, which are consistent with the structures from density functional theory calculations.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Thermal Properties of Sodium Borosilicate Glasses as a Function of Sulfur Content
SO3 additions, up to 3.0 wt%, were systematically investigated for effects on the physical properties of sodium borosilicate glass melted in air, with a sulfur-free composition of 50SiO2-10Al2O3-12B2O3-21Na2O-7CaO (wt%). Solubility measurements, using electron microscopy chemical analysis, determined the maximum loading to be ~1.5 wt% SO3. It was found that sulfur (here as sulfate) in this glass increased the glass transition temperature, thermal diffusivity, heat capacity, and thermal conductivity, and decreased the mass density. Structural analysis, performed with Raman spectroscopy, indicated that the borosilicate network polymerized with sulfur additions, presumably due to Na2O being required to charge compensate the ionic SO42- additions, thus becoming unavailable to form non-bridging oxygen in the silicate network. It is postulated that this increased crosslinking of the borosilicate backbone lead to a structure with higher dimensionality and average bond energy. This increased the mean free paths and vibration frequency of the phonons, which resulted in the observed increase in thermal properties.
Thermal properties, Borosilicate glass, Sulfur sol↗
Advanced multimaterial shape optimization methods as applied to advanced manufacturing of wind turbine generators
Abstract Currently, many utility‐scale wind turbine generator original equipment manufacturers are dependent on imported rare earth permanent magnets, which are susceptible to market risks from cost instability. To lower the production costs of these generators and stay competitive in the market, several small wind manufacturers are pursuing continuous improvements to both generator design and manufacturing. However, traditional design and manufacturing methods have yielded marginal improvements in wind power performance. This work presents novel methods to redesign a baseline 15‐kW wind turbine generator with reduced rare‐earth permanent magnets by leveraging cutting‐edge three‐dimensional (3D) printed polymer‐bonded permanent magnets and steel. Symmetric, asymmetric, and multimaterial‐magnet parametrization methods are introduced for shape optimization. We extend the symmetric and asymmetric methods to the back iron in the stator to further investigate the impact and opportunities for performance improvements with lesser active materials. We employ a design‐of‐experiments approach with parametric computer‐aided design for shape generation and evaluate different designs by magneto‐thermal modeling and finite‐element analysis. We use adaptive sampling technique to identify better performing designs with lesser magnet mass, higher efficiency, and lower cogging torque when compared with the baseline generator. Asymmetric pole designs resulted in a magnet mass in the range of 4.77–5.37 kg, which was 27%–35% lighter than the baseline generator, suggesting that a new design freedom exists that can be enabled by advanced manufacturing, such as 3D printing. Shaping the back iron in the stator resulted in material savings in electrical steel of up to 14.62 kg, which was 20% lighter than the baseline stator. We conducted a structural analysis to evaluate an optimized asymmetric rotor design from the point of view of mechanical integrity and air‐gap stiffness. The magnetically optimal shape profile was shown as having a positive impact on the radial stiffness, and an optimal solution was discovered to reduce the structural mass by nearly 30 kg, which was 29% lighter than the baseline.
17 WIND ENERGY↗
Measuring the dynamic response of the thylakoid architecture in plant leaves by electron microscopy
The performance of the photosynthesis machinery in plants, including light harvesting, electron transport, and protein repair is controlled by structural changes of the thylakoid membrane system inside the chloroplasts. In particular, the structure of the stacked grana area of thylakoid membranes is highly dynamic, changing in response to different environmental cues such as light intensity. For example, the aqueous thylakoid lumen enclosed by thylakoid membranes in grana has been documented to swell in the presence of light. However, light-induced alteration of the stromal gap in the stacked grana (partition gap) and of the unstacked stroma lamellae have not been well characterized. Light-induced changes of the entire thylakoid membrane system including the lumen in both stacked and unstacked domains as well as the partition gap are presented here, and the functional implications are discussed. This structural analysis was made possible by development of a robust semi-automated image analysis method combined with optimized plant tissue fixation techniques for transmission electron microscopy generating quantitative structural results for the analysis of thylakoid ultrastructure.
59 BASIC BIOLOGICAL SCIENCES↗