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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Emergence of Intermediate Range Order in Jammed Packings

We perform a structural analysis of large scale jammed packings of monodisperse, frictionless and frictional spheres to elucidate structural signatures of the static structure factor in the low-to-intermediate wave number region. We employ discrete element method simulations containing up to 8×10^{7} particles, in which the particle friction coefficient(s), including sliding, rolling, and twisting interactions, are varied. At intermediate wave number values, corresponding to length scales that lie between that of the nearest neighbor primary peak and the system size, we find the emergence of a prepeak-a signature of intermediate range order-that grows with increasing friction. We correlate the emergence of this peak to real space fluctuations in the local particle coordination number, which exhibits a grainy fluctuating field throughout the packing process that is retained in the final, mechanically stable state. While the formation of the prepeak shows varying degrees of robustness to packing protocol changes, our results suggest that preparation history may be used to construct packings with variable large length scale structural properties.

Monti, Joseph M↗
DOE OSTI2016

One-dimensional mercury(II) halide coordination polymers of 3,6-bis(2-pyridyl)-1,2,4,5-tetrazine ligand: Synthesis, crystal structure, spectroscopic and DFT studies

Three new coordination polymers, [Hg(μ-bptz)X{sub 2}]{sub n} (X=Cl (1), Br (2)) and [Hg{sub 2}(μ-bptz)(μ-I){sub 2}I{sub 2}]{sub n} (3) (bptz=3,6-bis(2-pyridyl)-1,2,4,5-tetrazine) were synthesized. X-ray structural analysis indicated that compounds 1 and 2 are composed of one-dimensional (1D) linear chains while the compound 3 has 1D stair-stepped structure. The electronic band structure along with density of states (DOS) calculated by the DFT method indicates that compound 1 and 2 are direct band gap semiconductors; however, compound 3 is an indirect semiconductor. The linear optical properties of the compounds are also calculated by DFT method. According to the DFT calculations, the observed emission band of the compounds in solid state is due to electron transfer from an excited bptz-π* state (CBs) to the top of VBs. {sup 1}H NMR spectra of the compounds indicate that, in solution phase, the compounds don’t decompose completely. Thermal stability of the compounds is studied using TG, DTA methods. - Graphical abstract: Synthesis, crystal structure and emission spectra of [Hg(μ-bptz)X{sub 2}]{sub n} (X=Cl and Br) and [Hg{sub 2}(μ-bptz)(μ-I){sub 2}I{sub 2}]{sub n} are presented. The electronic band structure and linear optical properties of the compounds are calculated by the DFT method. - Highlights: • Three 1D Hg(II) halide coordination polymers with bptz ligand have been prepared. • The structures of the compounds are determined by single crystal XRD. • DFT calculations show that [Hg(μ-bptz)X{sub 2}]{sub n} (X=Cl and Br) have a direct band gap. • DFT calculations show that [Hg{sub 2}(μ-bptz)(μ-I){sub 2}I{sub 2}]{sub n} has an indirect band gap. • The compounds show an intraligand electron transfer emission band in solid state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Structural dynamics of a methionine γ-lyase for calicheamicin biosynthesis: Rotation of the conserved tyrosine stacking with pyridoxal phosphate

CalE6 from Micromonospora echinospora is a (pyridoxal 50 phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. Here, we report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Angular correlations of photons from solution diffraction at a free-electron laser encode molecular structure

During X-ray exposure of a molecular solution, photons scattered from the same molecule are correlated. If molecular motion is insignificant during exposure, then differences in momentum transfer between correlated photons are direct measurements of the molecular structure. In conventional small- and wide-angle solution scattering, photon correlations are ignored. This report presents advances in a new biomolecular structural analysis technique, correlated X-ray scattering (CXS), which uses angular intensity correlations to recover hidden structural details from molecules in solution. Due to its intense rapid pulses, an X-ray free electron laser (XFEL) is an excellent tool for CXS experiments. A protocol is outlined for analysis of a CXS data set comprising a total of half a million X-ray exposures of solutions of small gold nanoparticles recorded at the Spring-8 Ångström Compact XFEL facility (SACLA). From the scattered intensities and their correlations, two populations of nanoparticle domains within the solution are distinguished: small twinned, and large probably non-twinned domains. Finally, it is shown analytically how, in a solution measurement, twinning information is only accessible via intensity correlations, demonstrating how CXS reveals atomic-level information from a disordered solution of like molecules.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2013

Purification and SAXS Analysis of the Integrin Linked Kinase, PINCH, Parvin (IPP) Heterotrimeric Complex

The heterotrimeric protein complex containing the integrin linked kinase (ILK), parvin, and PINCH proteins, termed the IPP complex, is an essential component of focal adhesions, where it interacts with many proteins to mediate signaling from integrin adhesion receptors. Here we conduct a biochemical and structural analysis of the minimal IPP complex, comprising full-length human ILK, the LIM1 domain of PINCH1, and the CH2 domain of α-parvin. We provide a detailed purification protocol for IPP and show that the purified IPP complex is stable and monodisperse in solution. Using small-angle X-ray scattering (SAXS), we also conduct the first structural characterization of IPP, which reveals an elongated shape with dimensions 120×60×40 Å. Flexibility analysis using the ensemble optimization method (EOM) is consistent with an IPP complex structure with limited flexibility, raising the possibility that inter-domain interactions exist. However, our studies suggest that the inter-domain linker in ILK is accessible and we detect no inter-domain contacts by gel filtration analysis. This study provides a structural foundation to understand the conformational restraints that govern the IPP complex.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Characterization of Potential Micrometeorites by Synchrotron Analysis

Micrometeorites (MMs) are small particles that account for most of the extraterrestrial material deposited on Earth. Synchrotron X-ray fluorescence and diffraction allowed for chemical and mineral characterization to distinguish MM from atmospheric particulate. The relative components of iron, nickel, and other elements were considered in the identification of ferrous MM while high amounts of titanium were considered an indication that the particles were of atmospheric origin. Out of 100 samples collected by high school students and teachers, eight were taken to a synchrotron for analysis. Of those eight, three exhibited extraterrestrial compositions. X-ray absorption near-edge structure analysis revealed that the same three samples contained sulfide, the main sulfur form constituent in MM. X-ray microdiffraction analysis showed the presence of the minerals pentlandite and forsterite. Collectively, these results support the extraterrestrial nature of the three particles.

58 GEOSCIENCES↗
DOE OSTI2012

Development of the local and average structure of a V-Mo-Nb oxide catalyst with Mo 5 O 14 -like structure during synthesis from nanostructured precursors

A combination of X-ray and neutron PDF measurements with powder diffraction and EXAFS data was used to determine the structures of a V-Mo-Nb-oxide catalyst and its poorly crystallized precursors that exhibit the strongest catalytic activities. The crystalline material belongs to space group P-4 2 1 m, a = 22.8, c = 4.002, and is build up of pentagonal MeO 7 bipyramids surrounded by edge sharing Me-octahedrons (Me = Mo, V, Nb). In the average structure all MeO 7 units are at the same z-level, while the local structure analysis shows systematic shifts along [001]. Samples synthesized at 300 °C and 400 °C exhibit a nanostructure, whose local structure predates the final crystalline structure. Initial nanoparticles are spherical and grow predominantly along the c-axis. The successful analysis required a reverse analysis that took the crystalline material as starting model for the samples synthesized at lower temperatures.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Exploring poly-crystallization in semiconductors through assumption-less growth simulations: CdTe/CdS case study

Crystal growth is a complex process with far-reaching implications for high-performance materials across various fields. Recent advancements in structural analysis methods such as polyhedral template matching, which allows semiconductor-specific analysis, coupled with simulation technology, have enabled the comprehensive study of crystallization dynamics in semiconductors. However, the exploration of polycrystalline semiconductors created with minimal external intervention of the crystallization processes is relatively uncharted in comparison with metals. In this study, we employ molecular dynamics to simulate the growth of polycrystalline CdTe/CdS with the assumptions of classical mechanics, a Stillinger–Weber potential, an amorphous substrate, and common vapor growth conditions to allow the polycrystalline structures to evolve naturally. Post-simulation, we identify and analyze impactful structures and events, comparing them to theory and experiment to gain insight into various modes of crystallization dynamics. Two research questions guided the study: (1) How realistic are assumption-less simulated polycrystalline semiconductor structures? (2) To what extent can the approach provide insight into crystallization? The simulations, performed with minimal external control, yield polycrystalline structures mirroring experimental findings. The analysis reveals key crystallization insights, such as the role of amorphous atoms in the transition from nucleation to grain growth and the transformative impact of single events, such as dislocations, on crystallization dynamics. The method paves the way for reproducing and analyzing realistic polycrystalline semiconductor structures with minimal simulation assumptions across various growth modes.

Abdullah, Sharmin↗
DOE OSTI2011

Dielectric, Electrical and Magnetic Properties of PbZr{sub 0.53}Ti{sub 0.47} O{sub 3}-Ni{sub 0.65}Zn{sub 0.35}Fe{sub 2}O{sub 4} Multiferroic Composite

Novel ferroelectric/ferrimagnetic multiferroic composite of PbZr{sub 0.53}Ti{sub 0.47}O{sub 3}(PZT)-Ni{sub 0.65}Zn{sub 0.35}Fe{sub 2}O{sub 4}(NZFO)(80:20 wt%) were fabricated by a conventional solid-state reaction technique. Structural analysis carried out by X ray diffraction technique, reveals the presence of both PZT and NZFO binary phase in this composite. Detailed analysis of dielectric and ferroelectric properties in a wide temperature range (30-400 deg. C) showed a ferro to paraelectric phase transition at 293 deg. C. The electrical properties of the composite samples were investigated in a frequency range of 100 Hz-1 MHz using complex impedance spectroscopic technique. Complex impedance analysis showed the presence of grains and grain boundaries contribution for electrical conduction in this composite. Temperature dependent magnetic hysteresis (M-H) loops in the temperature range of 80-300 K show excellent non-saturating ferrimagnetic behavior with coercive field (Hc) in the range of 60-45 Oe in this multiferroic PZT/NZFO composite.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Complex Structural Disorder in a Polar Orthorhombic Perovskite Observed through the Maximum Entropy Method/Rietveld Technique

Ambient pressure stable perovskite oxides with all Bi3+ on the A-site are rare, with only four examples known. Due to the lone pair on Bi 3+ , these materials are seen as the best alternative to Pb-based piezoelectrics, which are used widely in society. The industry standard piezoelectric, Pb (Zr 1 – x Ti x )O 3 , relies on the [001] polarization of PbTiO 3 , but there are currently no ambient pressure stable Bi-based perovskites with this polarization vector, preventing the creation of an analogous system. We present the full structural analysis of the orthorhombic phase of (1 – x)Bi (Ti 3/8 Fe 2/8 Mg 3/8 )O 3 – x CaTiO 3 , which crystallizes in Pna2 1 symmetry with [001] polarization. This symmetry is rare and has only been reported twice for perovskites at ambient conditions. Analysis of maximum entropy method (MEM) models using synchrotron radiation powder X-ray diffraction reveals a disordered A-site configuration, and the MEM/Rietveld technique generates a structural model of this extreme disorder. Combined Rietveld analysis of X-ray and neutron diffraction data yields an accurate description of the local A-site configuration, which we use to understand our dielectric, ferroelectric, and piezoelectric measurements. These results give insight into how to stabilize this unique symmetry and inspire new design principles for Bi-based piezoelectrics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Influence of BaTiO{sub 3} on Magnetic and Transport Properties of La{sub 0.7}Sr{sub 0.3}MnO{sub 3}-BaTiO{sub 3} Nanocomposite

La{sub 0.7}Sr{sub 0.3}MnO{sub 3} (LSMO)-BaTiO{sub 3} (BTO) nanocomposites have been synthesized by adding different amounts of BTO using the sol-gel method. The structural analysis confirms that both phases coexist in the composite samples with the rhombohedral and tetragonal structure for LSMO and BTO, respectively. The magnetization measurement shows a decrease in magnetization with the increase in BTO concentration and a signature of the spin glass-like characteristics of the nanocomposite. The dielectric behavior indicates the existence of the magneto-electric coupling between LSMO and BTO phase. The measurement of transport properties shows that resistivity increases with BTO concentration and metal-insulator (M-I) transition temperature shifts towards lower temperature. The low-temperature (T < 50 K) resistivity behavior of the samples is analyzed by using the Kondo-like transport model. The results show the spin-disordered scattering increases with the increase in the amount of BTO in LSMO phase. The low-field magnetoresistance (LFMR) of the nanocomposite is improved as compared to the pure LSMO. The highest value of LFMR achieved for LSMO-BTO composite at 10 K is 35.5% with a 1 T magnetic field.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Structural interactions of TLP18.3 and Psb27-H1 to the luminal CP43 and Rubredoxin-ENH1 to the stromal side of Photosystem II in higher plants

TLP18.3 and Psb27 are known proteins on the luminal side of photosystem II. The structural locations of these two proteins are still absent in the currently available higher plant photosystem II cryo-EM structures. We interrogated the structural locations of these proteins using chemical cross-linking followed by liquid chromatography/tandem MS analysis. Structural mass spectrometry results then provided chemical restrains to direct structural modelling to determine the collective binding/stabilization of these two proteins to the luminal PSII CP43 protein. Using this pipeline, we also found the structural location of a Rubredoxin protein on the stromal side of PSII. Discovery of this redox active iron-sulfur protein in the vicinity of PSII subunit D1/D2 proteins, greatly showcases the importance of the redox processes that are potentially involved in PSII assembly or less known steady state functionality or photoprotection. This structural mass spectrometry platform high-lights its powerful applicability in protein complex discovery.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Dielectric and ferroelectric properties of Pb{sub 0.88}La{sub 0.12}(Ti{sub 1−x}Mn{sub x}){sub 0.97}O{sub 3} nanoceramics

Graphical abstract: - Highlights: • The nanoceramics of La/Mn modified PbTiO{sub 3} are synthesized by mechano-thermal route. • Materials have been characterized using various experimental methods. • Drastic change in dielectric and electrical properties of PbTiO{sub 3} has been observed. • The high dielectric constant makes the material very promising candidate for DRAM. • The Mn substitution also makes the material useful for piezoelectric devices. - Abstract: The polycrystalline samples of Pb{sub 0.88}La{sub 0.12}(Ti{sub 1−x}Mn{sub x}){sub 0.97}O{sub 3} (x = 0.0, 0.04, 0.07, 0.10) (PLMT) were prepared using a mechano-thermal method. Preliminary structural analysis of the above samples, carried out using X-ray diffraction data, shows tetragonal structure. This study also shows that the basic compound PLT (Pb{sub 0.88}La{sub 0.12}TiO{sub 3}) retains its tetragonal structure even up to 10% of Mn substitution at the Ti-site. The transmission electron micrographs (TEM) of PLMT samples exhibit that materials prepared by the above method are found to be of nano-size. The temperature–frequency dependence of dielectric studies exhibits increase in relative permittivity with rise in Mn-concentration in PLMT, and hence it can make the materials useful for device applications. The temperature dependence of ac conductivity shows presence of different types of charge species. It is also observed that oxygen vacancies play a significant role in the high-temperature conduction-mechanism and dynamics of polarization of the system. Piezoelectric charge coefficient (d{sub 33}) increases with increase in the Mn content in PLMT.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Molecular basis for lipid recognition by the prostaglandin D 2 receptor CRTH2

Significance Many amphipathic lipids, including cannabinoids, lysophospholipids, prostanoids, and leukotrienes, bind to G protein–coupled receptors (GPCRs) through the lipid bilayer. How these lipid ligands get anchored to their receptors and enter ligand-binding pockets is largely elusive. Our results revealed a distinctive lipid recognition mechanism for the prostaglandin D 2 (PGD 2 ) receptor CRTH2 that is not shared by other prostanoid receptors. Based on the structural analysis, we propose two representative binding modes of lipids in GPCRs. We also identified critical structural motifs and conformational changes of CRTH2 for capturing lipids from the lipidic environment and lipid transition to the binding pocket, thereby offering unprecedented molecular insight into the dynamic lipid-binding processes for GPCRs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Production of an impermeable composite of irradiated graphite and glass by hot isostatic pressing as a long term leach resistant waste form

Around 250,000 tons of irradiated graphite (i-graphite) exists worldwide and can be considered as a current waste or future waste stream. The largest national i-graphite inventory is located in UK (∼ 100,000 tons) with significant quantities also in Russia and France [5]. Most of the i-graphite remains in the cores of shutdown nuclear reactors including the MAGNOX type in UK and the UNGG in France. Whilst there are still operational power reactors with graphite cores, such as the Russian RBMKs and the AGRs in UK, all of them will reach their end of life during the next two decades. The most common reference waste management option of i-graphite is a wet or dry retrieval of the graphite blocks from the reactor core and the grouting of these blocks in a container without further conditioning. This produces large waste package volumes because the encapsulation capacity of the grout is limited and large cavities in the graphite blocks could reduce the packing densities. Packing densities from 0.5 to 1 tons per cubic meter have been assumed for grouting solutions. Furthermore the grout is permeable. This could over time allow the penetration of aqueous phases into the waste block and a potential dissolution and release of radionuclides. As a result particularly highly soluble radionuclides may not be retained by the grout. Vitrification could present an alternative, however a similar waste package volume increase may be expected since the encapsulation capacity of glass is potentially similar to or worse than that of grout. FNAG has developed a process for the production of a graphite-glass composite material called Impermeable Graphite Matrix (IGM) [3]. This process is also applicable to irradiated graphite which allows the manufacturing of an impermeable material without volume increase. Crushed i-graphite is mixed with 20 vol.% of glass and then pressed under vacuum at an elevated temperature in an axial hot vacuum press (HVP). The obtained product has zero or negligible porosity and a water impermeable structure. Structural analysis shows that the glass in the composite has replaced the pores in the graphite structure. The typical pore volume of a graphite material is in the range of 20 vol.%. Therefore no volume increase will occur in comparison with the former graphite material. This IGM material will allow the encapsulation of graphite with package densities larger than 1.5 ton per cubic meter. Therefore a huge volume saving can be achieved by such an alternative encapsulation method. Disposal performance is also enhanced since little or no leaching of radionuclides is observed due to the impermeability of the material NNL and FNAG have proved that IGM can be produced by hot isostatic pressing (HIP) which has several advantages for radioactive materials over the HVP process. - The sealed HIP container avoids the release of any radionuclides. - The outside of the waste package is not contaminated. - The HIP process time is shorter than the HVP process time. The isostatic press avoids anisotropic density distributions. - Simple filling of the HIP container has advantages over the filling of an axial die. (authors)

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Investigating the quaternary structure of a homomultimeric catechol 1,2-dioxygenase: An integrative structural biology study

The structural analysis of catechol 1,2 dioxygenase from Stutzerimonas frequens GOM2, SfC12DO, was conducted using various structural techniques. SEC-SAXS experiments revealed that SfC12DO, after lyophilization and reconstitution processes, can form multiple enzymatically active oligomers, including dimers, tetramers, and octamers. These findings differ from previous studies, which reported active dimers in homologous counterparts with available crystallographic structures, or trimers observed exclusively in solution for SfC12DO and its homologous isoA C12DO from Acinetobacter radioresistens under low ionic strength conditions. In some cases, tetramers were also reported, such as for the Rodococcus erythropolis C12DO. The combined results of Small-Angle X-ray Scattering, Dynamic Light Scattering, and Transmission Electron Microscopy experiments provided additional insights into these active oligomers’ shape and molecular organization in an aqueous solution. These results highlight the oligomeric structural plasticity of SfC12DO, proving that it can exist in different oligomeric forms depending on the physicochemical characteristics of the solutions in which the experiments were performed. Remarkably, regardless of its oligomeric state, SfC12DO maintains its enzymatic activity even after prior lyophilization. All these characteristics make SfC12DO a putative candidate for bioremediation applications in polluted soils or waters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Development of a Structural Health Monitoring System for the Life Assessment of Critical Transportation Infrastructure

Recent structural failures such as the I-35W Mississippi River Bridge in Minnesota have underscored the urgent need for improved methods and procedures for evaluating our aging transportation infrastructure. This research seeks to develop a basis for a Structural Health Monitoring (SHM) system to provide quantitative information related to the structural integrity of metallic structures to make appropriate management decisions and ensuring public safety. This research employs advanced structural analysis and nondestructive testing (NDT) methods for an accurate fatigue analysis. Metal railroad bridges in New Mexico will be the focus since many of these structures are over 100 years old and classified as fracture-critical. The term fracture-critical indicates that failure of a single component may result in complete collapse of the structure such as the one experienced by the I-35W Bridge. Failure may originate from sources such as loss of section due to corrosion or cracking caused by fatigue loading. Because standard inspection practice is primarily visual, these types of defects can go undetected due to oversight, lack of access to critical areas, or, in riveted members, hidden defects that are beneath fasteners or connection angles. Another issue is that it is difficult to determine the fatigue damage that a structure has experienced and the rate at which damage is accumulating due to uncertain history and load distribution in supporting members. A SHM system has several advantages that can overcome these limitations. SHM allows critical areas of the structure to be monitored more quantitatively under actual loading. The research needed to apply SHM to metallic structures was performed and a case study was carried out to show the potential of SHM-driven fatigue evaluation to assess the condition of critical transportation infrastructure and to guide inspectors to potential problem areas. This project combines the expertise in transportation infrastructure at New Mexico State University with the expertise at Sandia National Laboratories in the emerging field of SHM.

36 MATERIALS SCIENCE↗