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At least 937 records · Page 52
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase

The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.

Science & Technology - Other Topics↗
DOE OSTI2013

Electron momentum density, band structure, and structural properties of SrS

The electron momentum density, the electronic band structure, and the structural properties of SrS are presented in this paper. The isotropic Compton profile, anisotropies in the directional Compton profiles, the electronic band structure and density of states are calculated using the ab initio periodic linear combination of atomic orbitals method with the CRYSTAL06 code. Structural parameters of SrS-lattice constants and bulk moduli in the B1 and B2 phases-are computed together with the transition pressure. The computed parameters are well in agreement with earlier investigations. To compare the calculated isotropic Compton profile, measurement on polycrystalline SrS is performed using 5Ci-{sup 241}Am Compton spectrometer. Additionally, charge transfer is studied by means of the Compton profiles computed from the ionic model. The nature of bonding in the isovalent SrS and SrO compounds is compared on the basis of equal-valenceelectron-density profiles and the bonding in SrS is found to be more covalent than in SrO.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2018

Effect of Cr Spacer on Structural and Magnetic Properties of Fe/Gd Multilayers

Here, we analyze the role of a thin Cr spacer between Fe and Gd layers on the structure and magnetic properties of a [Fe(35 Å)/Cr(t Cr )/Gd(50 Å)/Cr(t Cr )] 12 superlattice. Samples without the Cr spacer (t Cr = 0) and with a thin spacer (t Cr = 4 Å) are investigated using X-ray diffraction, polarized neutron and resonance X-ray magnetic reflectometry, static magnetometry, magneto-optical Kerr effect, and ferromagnetic resonance techniques. Magnetic properties are studied experimentally in a wide temperature range 4–300 K and analyzed theoretically using numerical simulation on the basis of the mean-field model. We show that a reasonable agreement with the experimental data can be obtained considering temperature dependence of the effective field parameter in gadolinium layers. In conclusion, the analysis of the experimental data shows that besides a strong reduction of the antiferromagnetic coupling between Fe and Gd, the introduction of Cr spacers into Fe/Gd superlattice leads to modification of both structural and magnetic characteristics of the ferromagnetic layers.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Synthesis, structure, electronic characterization, and halogenation of gold(III) phlorin complexes

The metalation chemistry of the phlorin, which is a non-aromatic tetrapyrrole macrocycle containing a single sp 3 -hybridized meso-carbon has remained underdeveloped, as compared to that of more traditional tetrapyrroles such as porphyrins, corroles and phthalocyanines. There have been few prior efforts to prepare metallophlorins, and those that have been reported have relied on either reduction or nucleophilic attack of parent metalloporphyrins, rather than direct metalation of freebase phlorin constructs. In this work, an alternate synthetic approach for preparation of gold(III) phlorin complexes that involves the first direct metalation of two different freebase phlorin derivatives (3H(Phl tBu ) and 3H(Phl F )) with AuBr 3 to produce the stable and fully isolable gold(III) phlorin complexes Au(Phl tBu ) and Au(Phl F ) is reported. The first structural characterization of a metallophlorin bearing geminal dimethyl substituents at the sp 3 -hybridized meso-carbon via X-ray crystallography is also reported. In addition to the preparation of Au(Phl tBu ) and Au(Phl F ), the UV-vis absorption and redox properties of these two gold(III) phlorins in comparison to those of their freebase homologues is also detailed. Notably, the metallophlorins are characterized by panchromatic absorbance profiles and intense and broad bands that span the long-visible and into the near-IR regions, as well as two fully reversible oxidation and reduction waves as probed by cyclic voltammetry. Lastly, the chlorination of Au(Phl tBu ) using PhI(Cl 2 ) was probed and it was found that this regioslective reaction generates monochlorinated (Au(Phl tBu Cl)) and dichlorinated (Au(Phl tBu Cl 2 )) products, which were both structurally characterized by X-ray crystallography.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Vertical Structure of Radiative Heating Rates of the MJO during DYNAMO

The vertical structure of radiative heating rates over the region of the tropi-cal Indian Ocean associated with the MJO during the DYNAMO/ARM MJO Investigation Experiment is presented. The mean and variability of heating rates during active, suppressed, and disturbed phases are determined from the Paci?c Northwest National Laboratory combined remote sensing retrieval (CombRet) from Gan Island, Maldives (0.69? S, 73.15? E). TOA and surface ?uxes from the CombRet product are compared with collocated three-hourly CERES SYN1deg Ed4A satellite retrievals. The ?uxes are correlated in time with correlation coef?cients around 0.9, yet CombRet time-mean OLR is 15 W m-2 larger. Previous work has suggested that CombRet under-samples high clouds, due to attenuation by low-level clouds and reduced instrument sensitivity with altitude. However, mean OLR differs between CombRet and CERES for all values of OLR, not just the lowest values corresponding to widespread high clouds. The discrepancy peaks for mid-range OLR, sugges-tive of precipitating, towering cumulus convective clouds, rather than strati-form cirrus clouds. Biases in the cloud-top height of thick clouds substantially contribute to the overestimate of OLR by CombRet. CombRet data is used to generate composite shortwave and longwave atmospheric heating rate pro-?les as a function of the local OLR. Though there is considerable variability in CombRet not directly related to OLR, the time-height structure of mean heating rate composites generated using OLR as the interpolant is broadly representative of tropical convective variability on intraseasonal time scales.

Shell, Karen M.↗
DOE OSTI2021

Coupling of regional geophysics and local soil-structure models in the EQSIM fault-to-structure earthquake simulation framework

Accurate understanding and quantification of the risk to critical infrastructure posed by future large earthquakes continues to be a very challenging problem. Earthquake phenomena are quite complex and traditional approaches to predicting ground motions for future earthquake events have historically been empirically based whereby measured ground motion data from historical earthquakes are homogenized into a common data set and the ground motions for future postulated earthquakes are probabilistically derived based on the historical observations. This procedure has recognized significant limitations, principally due to the fact that earthquake ground motions tend to be dictated by the particular earthquake fault rupture and geologic conditions at a given site and are thus very site-specific. Historical earthquakes recorded at different locations are often only marginally representative. There has been strong and increasing interest in utilizing large-scale, physics-based regional simulations to advance the ability to accurately predict ground motions and associated infrastructure response. However, the computational requirements for simulations at frequencies of engineering interest have proven a major barrier to employing regional scale simulations. In a U.S. Department of Energy Exascale Computing Initiative project, the EQSIM application development is underway to create a framework for fault-to-structure simulations. This framework is being prepared to exploit emerging exascale platforms in order to overcome computational limitations. This article presents the essential methodology and computational workflow employed in EQSIM to couple regional-scale geophysics models with local soil-structure models to achieve a fully integrated, complete fault-to-structure simulation framework. Here, the computational workflow, accuracy and performance of the coupling methodology are illustrated through example fault-to-structure simulations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Nop9 recognizes structured and single-stranded RNA elements of preribosomal RNA

Nop9 is an essential factor in the processing of preribosomal RNA. Its absence in yeast is lethal, and defects in the human ortholog are associated with breast cancer, autoimmunity, and learning/language impairment. PUF family RNA-binding proteins are best known for sequence-specific RNA recognition, and most contain eight α-helical repeats that bind to the RNA bases of single-stranded RNA. Nop9 is an unusual member of this family in that it contains eleven repeats and recognizes both RNA structure and sequence. Here we report a crystal structure of Saccharomyces cerevisiae Nop9 in complex with its target RNA within the 20S preribosomal RNA. This structure reveals that Nop9 brings together a carboxy-terminal module recognizing the 5' single-stranded region of the RNA and a bifunctional amino-terminal module recognizing the central double-stranded stem region. We further show that the 3' single-stranded region of the 20S target RNA adds sequence-independent binding energy to the RNA–Nop9 interaction. Both the amino- and carboxy-terminal modules retain the characteristic sequence-specific recognition of PUF proteins, but the amino-terminal module has also evolved a distinct interface, which allows Nop9 to recognize either single-stranded RNA sequences or RNAs with a combination of single-stranded and structured elements.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural color from a coupled nanowire pair beyond the bonding and antibonding model

Optical resonances in nanostructures can be harnessed to produce a wide range of structural colors. Conversely, the analysis of structural colors has been used to clarify the nature of optical resonances. Here, we show that silicon nanowire (NW) pairs can display a wide range of structural colors by controlling their radiative coupling. This is accomplished by exciting a series of Fabry–Pérot-like modes where light is repeatedly scattered between two NWs. These modes are beyond the expectation from the conventional chemical bonding model under a quasi-electrostatic approximation, in which only bonding and antibonding modes can be formed in a pair system through modal hybridization. The additional eigenmodes found in a two-resonator system originate from the nonlinear, frequency-dependent coupling strength derived from the radiative nature of low- Q resonators. The Fabry–Pérot modes can be tuned across the entire visible frequency range by varying the distance between two NWs, leading to what we believe is a new type of universal building blocks that can provide structural color within a subwavelength footprint. The presented results pave the way toward the design and usage of highly tunable resonances that exploit the radiative coupling of high-index nanostructures.

Li, Qitong↗
DOE OSTI2016

Structural and Genetic Studies Demonstrate Neurologic Dysfunction in Triosephosphate Isomerase Deficiency Is Associated with Impaired Synaptic Vesicle Dynamics

Triosephosphate isomerase (TPI) deficiency is a poorly understood disease characterized by hemolytic anemia, cardiomyopathy, neurologic dysfunction, and early death. TPI deficiency is one of a group of diseases known as glycolytic enzymopathies, but is unique for its severe patient neuropathology and early mortality. The disease is caused by missense mutations and dysfunction in the glycolytic enzyme, TPI. Previous studies have detailed structural and catalytic changes elicited by disease-associated TPI substitutions, and samples of patient erythrocytes have yielded insight into patient hemolytic anemia; however, the neuropathophysiology of this disease remains a mystery. This study combines structural, biochemical, and genetic approaches to demonstrate that perturbations of the TPI dimer interface are sufficient to elicit TPI deficiency neuropathogenesis. The present study demonstrates that neurologic dysfunction resulting from TPI deficiency is characterized by synaptic vesicle dysfunction, and can be attenuated with catalytically inactive TPI. Collectively, our findings are the first to identify, to our knowledge, a functional synaptic defect in TPI deficiency derived from molecular changes in the TPI dimer interface.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2021

Crystal Structure of Moganite and Its Anisotropic Atomic Displacement Parameters Determined by Synchrotron X-ray Diffraction and X-ray/Neutron Pair Distribution Function Analyses

The crystal structure of moganite from the Mogán formation on Gran Canaria has been re-investigated using high-resolution synchrotron X-ray diffraction (XRD) and X-ray/neutron pair distribution function (PDF) analyses. Our study for the first time reports the anisotropic atomic displacement parameters (ADPs) of a natural moganite. Rietveld analysis of synchrotron XRD data determined the crystal structure of moganite with the space group I2/a. The refined unit-cell parameters are a = 8.7363(8), b = 4.8688(5), c = 10.7203(9) Å, and β = 90.212(4)°. The ADPs of Si and O in moganite were obtained from X-ray and neutron PDF analyses. The shapes and orientations of the anisotropic ellipsoids determined from X-ray and neutron measurements are similar. The anisotropic ellipsoids for O extend along planes perpendicular to the Si-Si axis of corner-sharing SiO4 tetrahedra, suggesting precession-like movement. Neutron PDF result confirms the occurrence of OH over some of the tetrahedral sites. We postulate that moganite nanomineral is stable with respect to quartz in hypersaline water. The ADPs of moganite show a similar trend as those of quartz determined by single-crystal XRD. In short, the combined methods can provide high-quality structural parameters of moganite nanomineral, including its ADPs and extra OH position at the surface. This approach can be used as an alternative means for solving the structures of crystals that are not large enough for single-crystal XRD measurements, such as fine-grained and nanocrystalline minerals formed in various geological environments.

58 GEOSCIENCES↗
DOE OSTI2019

The Morphology and Structure of Stellar Populations in the Fornax Dwarf Spheroidal Galaxy from Dark Energy Survey Data

Using deep wide-field photometry 3 yr data (Y3) from the Dark Energy Survey (DES), we introduce a panoramic study of the Fornax dwarf spheroidal galaxy. The data discussed here—a small subset of the full survey—uniformly cover a region of 25 deg 2 centered on the galaxy to a depth of g ~ 23.5. We use these data to study the structural properties of Fornax, overall stellar population, and its member stars in different evolutionary phases. We also search for possible signs of tidal disturbance. Fornax is found to be significantly more spatially extended than what early studies suggested. No statistically significant distortions or signs of tidal disturbances were found down to a surface brightness limit of ~32.1 mag arcsec -2 . Yet, there are hints of shell-like features located ~20'–40' from the center of Fornax that may be stellar debris from past merger events. We also find that intermediate-age and young main-sequence populations show different orientation at the galaxy center and have many substructures. The deep DES Y3 data allow us to characterize the age of those young stellar substructures with great accuracy, both those previously known and those newly identified as possible overdensities in this work, on the basis of their color–magnitude diagram morphology. We find that the youngest overdensities are all found on the eastern side of Fornax, where the Fornax field population itself is slightly younger than in the west. In summary, the high-quality DES Y3 data reveal that Fornax has many rich structures and provide insights into its complex formation history.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Structural determinants of nuclear export signal orientation in binding to exportin CRM1

The Chromosome Region of Maintenance 1 (CRM1) protein mediates nuclear export of hundreds of proteins through recognition of their nuclear export signals (NESs), which are highly variable in sequence and structure. The plasticity of the CRM1-NES interaction is not well understood, as there are many NES sequences that seem incompatible with structures of the NES-bound CRM1 groove. Crystal structures of CRM1 bound to two different NESs with unusual sequences showed the NES peptides binding the CRM1 groove in the opposite orientation (minus) to that of previously studied NESs (plus). A comparison of minus and plus NESs identified structural and sequence determinants for NES orientation. The binding of NESs to CRM1 in both orientations results in a large expansion in NES consensus patterns and therefore a corresponding expansion of potential NESs in the proteome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Structural determinants of adhesion by Protocadherin-19 and implications for its role in epilepsy

Non-clustered δ-protocadherins are homophilic cell adhesion molecules essential for the development of the vertebrate nervous system, as several are closely linked to neurodevelopmental disorders. Mutations in protocadherin-19 ( PCDH19 ) result in a female-limited, infant-onset form of epilepsy (PCDH19-FE). Over 100 mutations in PCDH19 have been identified in patients with PCDH19-FE, about half of which are missense mutations in the adhesive extracellular domain. Neither the mechanism of homophilic adhesion by PCDH19, nor the biochemical effects of missense mutations are understood. Here we present a crystallographic structure of the minimal adhesive fragment of the zebrafish Pcdh19 extracellular domain. This structure reveals the adhesive interface for Pcdh19, which is broadly relevant to both non-clustered δ and clustered protocadherin subfamilies. In addition, we show that several PCDH19-FE missense mutations localize to the adhesive interface and abolish Pcdh19 adhesion in in vitro assays, thus revealing the biochemical basis of their pathogenic effects during brain development.

Cooper, Sharon R.↗
NASA NTRS1974

Conical isogrid adapter structural test results. Appendix C: Cylindrical isogrid structures

Analysis techniques and data for evaluating the load carrying capabilities of cylindrical isogrid structures subjected to compression and body bending loads are presented. Structural tests were conducted on a 120-inch diameter by 37-inch long cylindrical adapter. Photographs and drawings of the flanged isogrid adapter structure are included. The subjects considered are: (1) summary of the test data resulting from structural analysis, (2) techniques for predicting local and general instability, (3) a method for predicting extended local instability, (4) the effects of basic parameter and constant variations in extended local stability analysis, and (5) evaluation of effective skin width and compression buckling of skin panels on the basis of test data.

Source record↗
NASA NTRS1977

Large space erectable structures - building block structures study

A modular planar truss structure and a long slender boom concept identified as building block approaches to construction of large spacecraft configurations are described. The concepts are compatible in weight and volume goals with the Space Transportation System, use standard structural units, and represent high on-orbit productivity in terms of structural area or beam length. Results of structural trade studies involving static and dynamic analyses of a single module and rigid body deployment analyses to assess kinetics and kinematics of automatic deployment of the building block modules are presented.

Armstrong, W. H.↗
NASA NTRS1982

Experimental measurement of passive material and structural damping for flexible space structures

Among the design objectives for large space structures are the maintenance of tight dimensional tolerance and the reduction of settling time after disturbance input. Two options are under consideration for the design of flexible structures to meet these objectives, including an active control option and a passive control option. In connection with both options, it is necessary to include material and structural damping in the design. A description is presented of the results of an experimental investigation of the damping of metallic and fibrous composite materials, taking into account also the analytical modeling and experimental verification of frictional damping schemes. To demonstrate how material and frictional damping can be combined, a simple structural optimization is performed, indicating the potential for significant savings in mass by the addition of frictional dampers.

Crawley, E. F.↗