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At least 1,477 records · Page 82
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structure of ice VII with Hirshfeld atom refinement

In the refinement of the crystal structures of ice, the best results obtained so far have been with neutron diffraction because the most troublemaking aspects are the hydrogen atoms. In nine out of twenty ice structures, the hydrogen atoms are disordered, which makes proper refinement more difficult. In our previous paper describing the structure of ice VI we proved that, using Hirshfeld atom refinement (HAR) based on synchrotron X-ray data, it is possible to obtain results comparable with those from neutron experiments. In this work, we investigate another structure of high-pressure disordered ice, cubo-ice (ice VII). Single crystals of cubo-ice were grown under pressure in diamond anvil cells. X-ray diffraction measurements were conducted at a synchrotron source facility (APS, University of Chicago, USA) as well as on our regular in-house laboratory diffractometer with Ag radiation. The data collected were further refined with HAR. Comparison of the structural parameters obtained with those derived from neutron diffraction showed very good agreement in terms of bond lengths and fairly good agreement in terms of hydrogen atom ADPs. We were also able to perform unconstrained refinements with various split-atom models.

Chemistry↗
DOE OSTI2020

High-resolution crystal structures of Escherichia coli FtsZ bound to GDP and GTP

Bacterial cytokinesis is mediated by the Z-ring, which is formed by the prokaryotic tubulin homolog FtsZ. Recent data indicate that the Z-ring is composed of small patches of FtsZ protofilaments that travel around the bacterial cell by treadmilling. Treadmilling involves a switch from a relaxed (R) state, favored for monomers, to a tense (T) conformation, which is favored upon association into filaments. The R conformation has been observed in numerous monomeric FtsZ crystal structures and the T conformation in Staphylococcus aureus FtsZ crystallized as assembled filaments. However, while Escherichia coli has served as a main model system for the study of the Z-ring and the associated divisome, a structure has not yet been reported for E. coli FtsZ. To address this gap, structures were determined of the E. coli FtsZ mutant FtsZ(L178E) with GDP and GTP bound to 1.35 and 1.40 Å resolution, respectively. The E. coli FtsZ(L178E) structures both crystallized as straight filaments with subunits in the R conformation. These high-resolution structures can be employed to facilitate experimental cell-division studies and their interpretation in E. coli .

protofilaments↗
DOE OSTI2020

The crystal structures of Fe-bearing MgCO 3 sp 2 - and sp 3 -carbonates at 98 GPa from single-crystal X-ray diffraction using synchrotron radiation

The crystal structure of MgCO 3 -II has long been discussed in the literature where DFT-based model calculations predict a pressure-induced transition of the carbon atom from the sp 2 to the sp 3 type of bonding. We have now determined the crystal structure of iron-bearing MgCO 3 -II based on single-crystal X-ray diffraction measurements using synchrotron radiation. We laser-heated a synthetic (Mg 0.85 Fe 0.15 )CO 3 single crystal at 2500 K and 98 GPa and observed the formation of a monoclinic phase with composition (Mg 2.53 Fe 0.47 )C 3 O 9 in the space group C 2/ m that contains tetrahedrally coordinated carbon, where CO 4 4- tetrahedra are linked by corner-sharing oxygen atoms to form three-membered C 3 O 9 6- ring anions. The crystal structure of (Mg 0.85 Fe 0.15 )CO 3 (magnesium iron carbonate) at 98 GPa and 300 K is reported here as well. In comparison with previous structure-prediction calculations and powder X-ray diffraction data, our structural data provide reliable information from experiments regarding atomic positions, bond lengths, and bond angles.

Chariton, Stella (ORCID:0000000155220498)↗
DOE OSTI2021

Challenges in solving structures from radiation-damaged tomograms of protein nanocrystals assessed by simulation

Structure-determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular-weight threshold required for single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure-determination methods. Here, a data-processing scheme is presented that combines routines from X-ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image-processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade-off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Metalloprotein catalysis: structural and mechanistic insights into oxidoreductases from neutron protein crystallography

Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

An integrated integral projection model ( IPM 2 ) to disentangle size‐structured harvest and natural mortality

Abstract Body size is one of the most important traits governing individual‐level demographic rates and modulating population‐level processes. Multiple size‐dependent demographic rates can simultaneously change population structure, so distinguishing their individual contributions to overall population dynamics remains a challenge. Disentangling size‐dependent harvest rates from other demographic rates is critical for assessing the impact of removal on populations of invasive species. Inference about invasive populations can be difficult, however, as observations are often collected opportunistically as part of removal programs, rather than experimentally designed. Yet accurate inference is essential for understanding the feasibility of population suppression and optimising management decisions. We develop an integrated integral projection model (IPM 2 ) that leverages the strengths of the integrated population model and integral projection model to enable inference about complex, size‐structured demographic rates from imperfect observations. We apply the IPM 2 in the context of invasive European green crab ( Carcinus maenas ), a species for which individual body size strongly regulates both the observation‐generating process and latent, population dynamics. The IPM 2 facilitates the distinct estimation of green crab size‐structured harvest and natural mortality rates, parameters for which no explicit data is collected and that are unidentifiable in component datasets of the integrated population model. The model represents how the green crab population changes over time, providing the first estimates of size‐structured abundance of this high‐priority species. By forecasting the stable size distribution and equilibrium population size under varying removal efforts, we demonstrate that extremely high levels of removal effort can reduce the equilibrium green crab population size. Yet these high mortality rates also shift the stable size distribution and increase the equilibrium abundance of smaller crabs, since size‐selective removal alters intraspecific interactions. The ecological outcome of this shift in size structure will be variable, as green crab size modulates only some of its interactions with other species. These results highlight the value of the IPM 2 framework for inferring complex population dynamics with information needs that outpace information in individual observational datasets, providing a path forward for accurate assessment of conservation programs.

Keller, Abigail G. [Department of Environment Scie↗
DOE OSTI2022

Improving Structural Integrity of Direct Laser-Deposited Ni – Co – Cr – Al – Y Superalloys by Alloy Modification

Abstract Ni- and Co-based M–Cr–Al–Y (M = Ni and/or Co), dual phase β and γ/γ′, β—Ni–Al, γ—Ni(Co, Cr), and γ′—Ni3–Al superalloys exhibit several beneficial high-temperature (>1000 °C) (2012 °F) strength and corrosion resistance properties. Our study investigates the feasibility of fabricating a commercially available Ni–Co–Cr–AlY alloy (tradename “Amdry 386”) using laser directed energy deposition (laser-DED). A significant challenge for laser fabrication of bulk Amdry 386 (A386) structures stems from the presence of relatively higher amounts of the β phase than γ/γ′ phases. While prior studies report laser fabrication of these materials in coating and cladding configurations, bulk structures have not been realized. To investigate these challenges, this study was developed to systematically evaluate the effects of modifying the A386 alloy by adding 10, 20, and 30% by weight of a Ni–20%Cr (Ni–Cr) alloy (mainly γ/γ′). Laser-DED-fabricated A386 coupons exhibited a metastable, rapidly solidified β-rich microstructure typical to laser processes. The A386 + Ni–Cr mixtures were processed using laser-DED, and small coupons from each composition were evaluated using SEM, XRD, and microhardness to characterize the as-processed microstructure. Thermodynamic modeling was performed to determine the phase evolution as a function of the alloy composition. The dominating phase switches from β to γ/γ’ between the A386 and A386 + 10% Ni–Cr mixtures, but the increase in structural integrity is not observed until the Ni–Cr additions reach a minimum of 20%. Our results show that the alloy chemistry can be successfully modified to improve the structural integrity of laser-processed structures.

Engineering↗
DOE OSTI2023

Experimental and Numerical Investigation of Flow Boiling in Additive Manufactured Foam Structures With Vapor Pathways

Abstract The unique properties of metal foams make them potential candidates for a range of applications, including microsystem thermal management. Using additive manufacturing to create foam-type structures can improve upon prior thermal solutions by eliminating thermal interface materials and allowing for customization/local control of parameters. In the present investigation, flow boiling in additive-manufactured metal foams is investigated both experimentally and numerically. Two test samples, one with uniform structure and the other with pathways for vapor removal, are compared both experimentally and numerically. A conjugate computational fluid dynamics and heat transfer (CFD-HT) model utilizing a three-dimensional volume of fluid (VOF) model with accompanying evaporation/condensation model provided in-depth visualization of the boiling flow phenomena. The experiments generated the thermohydraulic performance over a range of heat fluxes, demonstrating that the sample incorporating dedicated vapor pathways performed better in both pressure and heat transfer performance metrics compared to the uniform foam. Additionally, negative system-level effects (i.e., hydraulic oscillations) were shown to be abated using the vapor removal structures. The numerical model yielded further insight into the factors contributing to the improved performance. Results indicated the pathways functioned as vapor removal channels, allowing the generated vapor to vent from the foam structure into the lanes. Further computational investigations demonstrated changes in flow regimes, where the addition of vapor channels caused the flow to change from churn to annular. Bubble behavior unique to the vapor pathway structure was studied, showing stagnant regions that eject vapor into the channel.

Engineering↗
DOE OSTI2023

An over-approximation of entropy for elemental multiconfigurational ground state electronic structures

The ability to predict the chemical and physical properties of a material is directly related to the structure and interactions of its electrons. For materials comprised of f-block elements (the lanthanides and actinides found in the last two rows of the periodic table), the complexity of electronic structure has presented great difficulty in understanding, modeling, and predicting material properties. The complexity of multiconfigurational ground state electronic structures is illustrated herein by the combinatorics of electron permutations within individual and cumulative occupancy configurations. A non-integer orbital occupancy representation of multiconfigurational ground states is described for superposition mixing between multiple near-energy degenerate occupancy configurations and generalized in such a way that established ground states are returned by approximation for elements with less-complex electronic structures. By considering the occupancy configurations as statistical mechanics macrostates, and the permutations of electrons as statistical mechanics microstates within those macrostates, an over-approximation of entropy for multiconfigurational elemental ground state electronic structures has been calculated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Picoscale structural insight into superconductivity of monolayer FeSe/SrTiO 3

Remarkable enhancement of the superconducting transition temperature ( c ) has been observed for monolayer (ML) FeSe films grown on SrTiO 3 substrates. The atomic-scale structure of the FeSe/SrTiO 3 interface is an important determinant of both the magnetic and interfacial electron-phonon interactions and is a key ingredient to understanding its high- T c superconductivity. We resolve the atomic-scale structure of the FeSe/SrTiO 3 interface through a complementary analysis of scanning transmission electron microscopy and in situ surface x-ray diffraction. We find that the interface is more strongly bonded for a particular registration, which leads to a coherently strained ML. We also determine structural parameters, such as the distance between ML FeSe and the oxide, Se-Fe-Se bond angles, layer-resolved distances between Fe-Se, and registry of the FeSe lattice relative to the oxide. This picoscale structure determination provides an explicit structural framework and constraint for theoretical approaches addressing the high- T c mechanism in FeSe/SrTiO 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

The narrative arc: Revealing core narrative structures through text analysis

Scholars across disciplines have long debated the existence of a common structure that underlies narratives. Using computer-based language analysis methods, several structural and psychological categories of language were measured across ~40,000 traditional narratives (e.g., novels and movie scripts) and ~20,000 nontraditional narratives (science reporting in newspaper articles, TED talks, and Supreme Court opinions). Across traditional narratives, a consistent underlying story structure emerged that revealed three primary processes: staging, plot progression, and cognitive tension. No evidence emerged to indicate that adherence to normative story structures was related to the popularity of the story. Last, analysis of fact-driven texts revealed structures that differed from story-based narratives.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Structural response of α-quartz under plate-impact shock compression

Because of its far-reaching applications in geophysics and materials science, quartz has been one of the most extensively examined materials under dynamic compression. Despite 50 years of active research, questions remain concerning the structure and transformation of SiO 2 under shock compression. Continuum gas-gun studies have established that under shock loading quartz transforms through an assumed mixed-phase region to a dense high-pressure phase. While it has often been assumed that this high-pressure phase corresponds to the stishovite structure observed in static experiments, there have been no crystal structure data confirming this. In this study, we use gas-gun shock compression coupled with in situ synchrotron x-ray diffraction to interrogate the crystal structure of shock-compressed α-quartz up to 65 GPa. Our results reveal that α-quartz undergoes a phase transformation to a disordered metastable phase as opposed to crystalline stishovite or an amorphous structure, challenging long-standing assumptions about the dynamic response of this fundamental material.

58 GEOSCIENCES↗
DOE OSTI2021

Amorphization mechanism of SrIrO 3 electrocatalyst: How oxygen redox initiates ionic diffusion and structural reorganization

The use of renewable electricity to prepare materials and fuels from abundant molecules offers a tantalizing opportunity to address concerns over energy and materials sustainability. The oxygen evolution reaction (OER) is integral to nearly all material and fuel electrosyntheses. However, very little is known about the structural evolution of the OER electrocatalyst, especially the amorphous layer that forms from the crystalline structure. Here, we investigate the interfacial transformation of the SrIrO 3 OER electrocatalyst. The SrIrO 3 amorphization is initiated by the lattice oxygen redox, a step that allows Sr 2+ to diffuse and O 2− to reorganize the SrIrO 3 structure. This activation turns SrIrO 3 into a highly disordered Ir octahedral network with Ir square-planar motif. The final Sr y IrO x exhibits a greater degree of disorder than IrO x made from other processing methods. Our results demonstrate that the structural reorganization facilitated by coupled ionic diffusions is essential to the disordered structure of the SrIrO 3 electrocatalyst.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Structures of artificially designed discrete RNA nanoarchitectures at near-atomic resolution

Although advances in nanotechnology have enabled the construction of complex and functional synthetic nucleic acid–based nanoarchitectures, high-resolution discrete structures are lacking because of the difficulty in obtaining good diffracting crystals. Here, we report the design and construction of RNA nanostructures based on homooligomerizable one-stranded tiles for x-ray crystallographic determination. We solved three structures to near-atomic resolution: a 2D parallelogram, a 3D nanobracelet unexpectedly formed from an RNA designed for a nanocage, and, eventually, a bona fide 3D nanocage designed with the guidance of the two previous structures. Structural details of their constituent motifs, such as kissing loops, branched kissing loops, and T-junctions, that resemble natural RNA motifs and resisted x-ray determination are revealed, providing insights into those natural motifs. This work unveils the largely unexplored potential of crystallography in gaining high-resolution feedback for nanoarchitectural design and suggests a route to investigate RNA motif structures by configuring them into nanoarchitectures.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mechanism of structural colors in binary mixtures of nanoparticle-based supraballs

Inspired by structural colors in avian species, various synthetic strategies have been developed to produce noniridescent, saturated colors using nanoparticle assemblies. Nanoparticle mixtures varying in particle chemistry and size have additional emergent properties that affect the color produced. For complex multicomponent systems, understanding the assembled structure and a robust optical modeling tool can empower scientists to identify structure-color relationships and fabricate designer materials with tailored color. Here, we demonstrate how we can reconstruct the assembled structure from small-angle scattering measurements using the computational reverse-engineering analysis for scattering experiments method and use the reconstructed structure in finite-difference time-domain calculations to predict color. We successfully, quantitatively predict experimentally observed color in mixtures containing strongly absorbing nanoparticles and demonstrate the influence of a single layer of segregated nanoparticles on color produced. The versatile computational approach that we present is useful for engineering synthetic materials with desired colors without laborious trial-and-error experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation

The assembly of the autophagy initiation machinery nucleates autophagosome biogenesis, including in the PINK1- and Parkin-dependent mitophagy pathway implicated in Parkinson’s disease. The structural interaction between the sole transmembrane autophagy protein, autophagy-related protein 9A (ATG9A), and components of the Unc-51–like autophagy activating kinase (ULK1) complex is one of the major missing links needed to complete a structural map of autophagy initiation. We determined the 2.4-Å x-ray crystallographic structure of the ternary structure of ATG9A carboxyl-terminal tail bound to the ATG13:ATG101 Hop1/Rev7/Mad2 (HORMA) dimer, which is part of the ULK1 complex. We term the interacting portion of the extreme carboxyl-terminal part of the ATG9A tail the “HORMA dimer–interacting region” (HDIR). This structure shows that the HDIR binds to the HORMA domain of ATG101 by β sheet complementation such that the ATG9A tail resides in a deep cleft at the ATG13:ATG101 interface. Disruption of this complex in cells impairs damage-induced PINK1/Parkin mitophagy mediated by the cargo receptor NDP52.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Serial-femtosecond crystallography reveals how a phytochrome variant couples chromophore and protein structural changes

The photoreaction and commensurate structural changes of a chromophore within biological photoreceptors elicit conformational transitions of the protein promoting the switch between deactivated and activated states. We investigated how this coupling is achieved in a bacterial phytochrome variant, Agp2-PAiRFP2. Contrary to classical protein crystallography, which only allows probing (cryo-trapped) stable states, we have used time-resolved serial femtosecond x-ray crystallography (tr-SFX) and pump-probe techniques with various illumination and delay times with respect to photoexcitation of the parent Pfr state. Thus, structural data for seven time frames were sorted into groups of molecular events along the reaction coordinate. They range from chromophore isomerization to the formation of Meta-F, the intermediate that precedes the functional relevant secondary structure transition of the tongue. Structural data for the early events were used to calculate the photoisomerization pathway to complement the experimental data. Late events allow identifying the molecular switch that is linked to the intramolecular proton transfer as a prerequisite for the following structural transitions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural insights into differences in G protein activation by family A and family B GPCRs

Family B heterotrimeric guanine nucleotide–binding protein (G protein)–coupled receptors (GPCRs) play important roles in carbohydrate metabolism. Recent structures of family B GPCR-G s protein complexes reveal a disruption in the α-helix of transmembrane segment 6 (TM6) not observed in family A GPCRs. To investigate the functional impact of this structural difference, we compared the structure and function of the glucagon receptor (GCGR; family B) with the β 2 adrenergic receptor (β 2 AR; family A). We determined the structure of the GCGR-G s complex by means of cryo–electron microscopy at 3.1-angstrom resolution. This structure shows the distinct break in TM6. Guanosine triphosphate (GTP) turnover, guanosine diphosphate release, GTP binding, and G protein dissociation studies revealed much slower rates for G protein activation by the GCGR compared with the β 2 AR. Fluorescence and double electron-electron resonance studies suggest that this difference is due to the inability of agonist alone to induce a detectable outward movement of the cytoplasmic end of TM6.

59 BASIC BIOLOGICAL SCIENCES↗