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At least 1,117 records · Page 62
All sourcesNASA NTRSDOE OSTI
DOE OSTI2018

Neural network approach for characterizing structural transformations by X-ray absorption fine structure

The knowledge of coordination environment around various atomic species in many functional materials provides a key for explaining their properties and working mechanisms. Many structural motifs and their transformations are difficult to detect and quantify in the process of work (operando conditions), due to their local nature, small changes, low dimensionality of the material, and/or extreme conditions. Here we use artificial neural network approach to extract the information on the local structure and its in-situ changes directly from the X-ray absorption fine structure spectra. We illustrate this capability by extracting the radial distribution function (RDF) of atoms in ferritic and austenitic phases of bulk iron across the temperature-induced transition. Integration of RDFs allows us to quantify the changes in the iron coordination and material density, and to observe the transition from body-centered to face-centered cubic arrangement of iron atoms. Furthermore, this method is attractive for a broad range of materials and experimental conditions

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

Site-Specific Structure at Multiple Length Scales in Kagome Quantum Spin Liquid Candidates

Realizing a quantum spin liquid (QSL) ground state in a real material is a leading issue in condensed matter physics research. In this pursuit, it is crucial to fully characterize the structure and influence of defects, as these can significantly affect the fragile QSL physics. In this work, we perform a variety of cutting-edge synchrotron x-ray scattering and spectroscopy techniques, and we advance new methodologies for site-specific diffraction and L-edge Zn absorption spectroscopy. The experimental results along with our first-principles calculations address outstanding questions about the local and long-range structures of the two leading kagome QSL candidates, Zn-substituted barlowite Cu 3 Zn x Cu 1-x (OH) 6 FBr and herbertsmithite Cu 3 Zn(OH) 6 Cl 2 . On all length scales probed, there is no evidence that Zn substitutes onto the kagome layers, thereby preserving the QSL physics of the kagome lattice. Our calculations show that antisite disorder is not energetically favorable and is even less favorable in Zn-barlowite compared to herbertsmithite. Site-specific x-ray diffraction measurements of Zn-barlowite reveal that Cu 2+ and Zn 2+ selectively occupy distinct interlayer sites, in contrast to herbertsmithite. Using the first measured Zn L-edge inelastic x-ray absorption spectra combined with calculations, we discover a systematic correlation between the loss of inversion symmetry from pseudo-octahedral (herbertsmithite) to trigonal prismatic coordination (Zn-barlowite) with the emergence of a new peak. Overall, our measurements suggest that Zn-barlowite has structural advantages over herbertsmithite that make its magnetic properties closer to an ideal QSL candidate: its kagome layers are highly resistant to nonmagnetic defects while the interlayers can accommodate a higher amount of Zn substitution.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Structural evidence for the partially oxidized dipyrromethene and dipyrromethanone forms of the cofactor of porphobilinogen deaminase: structures of the Bacillus megaterium enzyme at near-atomic resolution

The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses a key early step in the biosynthesis of tetrapyrroles in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. Two near-atomic resolution structures of PBGD from B. megaterium are reported that demonstrate the time-dependent accumulation of partially oxidized forms of the cofactor, including one that possesses a tetrahedral C atom in the terminal pyrrole ring. The enzyme porphobilinogen deaminase (PBGD; hydroxymethylbilane synthase; EC 2.5.1.61) catalyses an early step of the tetrapyrrole-biosynthesis pathway in which four molecules of the monopyrrole porphobilinogen are condensed to form a linear tetrapyrrole. The enzyme possesses a dipyrromethane cofactor, which is covalently linked by a thioether bridge to an invariant cysteine residue (Cys241 in the Bacillus megaterium enzyme). The cofactor is extended during the reaction by the sequential addition of the four substrate molecules, which are released as a linear tetrapyrrole product. Expression in Escherichia coli of a His-tagged form of B. megaterium PBGD has permitted the X-ray analysis of the enzyme from this species at high resolution, showing that the cofactor becomes progressively oxidized to the dipyrromethene and dipyrromethanone forms. In previously solved PBGD structures, the oxidized cofactor is in the dipyromethenone form, in which both pyrrole rings are approximately coplanar. In contrast, the oxidized cofactor in the B. megaterium enzyme appears to be in the dipyrromethanone form, in which the C atom at the bridging α-position of the outer pyrrole ring is very clearly in a tetrahedral configuration. It is suggested that the pink colour of the freshly purified protein is owing to the presence of the dipyrromethene form of the cofactor which, in the structure reported here, adopts the same conformation as the fully reduced dipyrromethane form.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

The structure of allophycocyanin B from Synechocystis PCC 6803 reveals the structural basis for the extreme redshift of the terminal emitter in phycobilisomes

Allophycocyanin B (AP-B) is one of the two terminal emitters in phycobilisomes, the unique light-harvesting complexes of cyanobacteria and red algae. Its low excitation-energy level and the correspondingly redshifted absorption and fluorescence emission play an important role in funnelling excitation energy from the hundreds of chromophores of the extramembraneous phycobilisome to the reaction centres within the photosynthetic membrane. In the absence of crystal structures of these low-abundance terminal emitters, the molecular basis for the extreme redshift and directional energy transfer is largely unknown. Here, the crystal structure of trimeric AP-B [(ApcD/ApcB) 3 ] from Synechocystis sp. PCC 6803 at 1.75 Å resolution is reported. In the crystal lattice, eight trimers of AP-B form a porous, spherical, 48-subunit assembly of 193 Å in diameter with an internal cavity of 1.1 × 10 6 Å 3 . While the overall structure of trimeric AP-B is similar to those reported for many other phycobiliprotein trimers, the chromophore pocket of the α-subunit, ApcD, has more bulky residues that tightly pack the phycocyanobilin (PCB). Ring D of the chromophores is further stabilized by close interactions with ApcB from the adjacent monomer. The combined contributions from both subunits render the conjugated rings B, C and D of the PCB in ApcD almost perfectly coplanar. Together with mutagenesis data, it is proposed that the enhanced planarity effectively extends the conjugation system of PCB and leads to the redshifted absorption (λ max = 669 nm) and fluorescence emission (679 nm) of the ApcD chromophore in AP-B, thereby enabling highly efficient energy transfer from the phycobilisome core to the reaction centres.

Peng, Pan-Pan↗
DOE OSTI2018

Structural basis for light control of cell development revealed by crystal structures of a myxobacterial phytochrome

Phytochromes are red-light photoreceptors that were first characterized in plants, with homologs in photosynthetic and non-photosynthetic bacteria known as bacteriophytochromes (BphPs). Upon absorption of light, BphPs interconvert between two states denoted Pr and Pfr with distinct absorption spectra in the red and far-red. They have recently been engineered as enzymatic photoswitches for fluorescent-marker applications in non-invasive tissue imaging of mammals. This article presents cryo- and room-temperature crystal structures of the unusual phytochrome from the non-photosynthetic myxobacterium Stigmatella aurantiaca (SaBphP1) and reveals its role in the fruiting-body formation of this photomorphogenic bacterium. SaBphP1 lacks a conserved histidine (His) in the chromophore-binding domain that stabilizes the Pr state in the classical BphPs. Instead it contains a threonine (Thr), a feature that is restricted to several myxobacterial phytochromes and is not evolutionarily understood. SaBphP1 structures of the chromophore binding domain (CBD) and the complete photosensory core module (PCM) in wild-type and Thr-to-His mutant forms reveal details of the molecular mechanism of the Pr/Pfr transition associated with the physiological response of this myxobacterium to red light. Specifically, key structural differences in the CBD and PCM between the wild-type and the Thr-to-His mutant involve essential chromophore contacts with proximal amino acids, and point to how the photosignal is transduced through the rest of the protein, impacting the essential enzymatic activity in the photomorphogenic response of this myxobacterium.

Woitowich, Nicole C.↗
DOE OSTI2018

High-resolution crystal structures of the D1 and D2 domains of protein tyrosine phosphatase epsilon for structure-based drug design

Here, new crystal structures are presented of the isolated membrane-proximal D1 and distal D2 domains of protein tyrosine phosphatase epsilon (PTPε), a protein tyrosine phosphatase that has been shown to play a positive role in the survival of human breast cancer cells. A triple mutant of the PTPε D2 domain (A455N/V457Y/E597D) was also constructed to reconstitute the residues of the PTPε D1 catalytic domain that are important for phosphatase activity, resulting in only a slight increase in the phosphatase activity compared with the native D2 protein. The structures reported here are of sufficient resolution for structure-based drug design, and a microarray-based assay for high-throughput screening to identify small-molecule inhibitors of the PTPε D1 domain is also described.

Lountos, George T.↗
DOE OSTI2013

Studies of Nucleon Resonance Structure in Exclusive Meson Electroproduction

The studies of N* structure represent a key direction in the N* Program with CLAS detector. After 12 GeV Upgrade, the dedicated experiment on the studies of N* structure at largest photon virtualities ever achieved Q^2<12 GeV^2 is scheduled for the first year of running with the CLAS12 detector. The current status and plans for theory support of the N* structure studies in exclusive meson electroproduction are presented. They include the recent advances in the reaction theory for extraction of N* electrocouplings from the data and the approaches for high level theoretical interpretation of these fundamental quantities, allowing us to access dynamics of non-perturbative strong interaction which is responsible for the resonance formation and explore how it emerges from QCD.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

Multifunctional structural lithium-ion battery for electric vehicles

An innovative concept for a multifunctional structural battery using lithium-ion battery materials as load bearing elements in a sandwich panel construction has been demonstrated. The structural battery prototype has exhibited an initial capacity of 17.85 Ah, an energy density of 248 Wh L −1 , a specific energy of 102 Wh kg −1 , and a capacity retention of 85.8% after 190 charge–discharge cycles at ~ C/3 rate and eight mechanical loading cycles (upto 1060 N). The mechanical stiffness in three-point bend tests follows expectations based on sandwich beam theory, proving that the battery materials are sharing in the load-carrying function of the sandwich panel. While areas for improvement of the fabrication and performance of the prototype still exist, the results of the current investigation demonstrate the promising potential of the proposed structural battery concept for the efficient use of space and mass in an electric vehicle.

Zhang, Yancheng↗
DOE OSTI2020

Nanometer-scale structure differences in the myofilament lattice spacing of two cockroach leg muscles correspond to their different functions

ABSTRACT Muscle is highly organized across multiple length scales. Consequently, small changes in the arrangement of myofilaments can influence macroscopic mechanical function. Two leg muscles of a cockroach have identical innervation, mass, twitch responses, length–tension curves and force–velocity relationships. However, during running, one muscle is dissipative (a ‘brake’), while the other dissipates and produces significant positive mechanical work (bifunctional). Using time-resolved X-ray diffraction in intact, contracting muscle, we simultaneously measured the myofilament lattice spacing, packing structure and macroscopic force production of these muscles to test whether structural differences in the myofilament lattice might correspond to the muscles' different mechanical functions. While the packing patterns are the same, one muscle has 1 nm smaller lattice spacing at rest. Under isometric stimulation, the difference in lattice spacing disappeared, consistent with the two muscles' identical steady-state behavior. During periodic contractions, one muscle undergoes a 1 nm greater change in lattice spacing, which correlates with force. This is the first identified structural feature in the myofilament lattice of these two muscles that shares their whole-muscle dynamic differences and quasi-static similarities.

Tune, Travis Carver↗
DOE OSTI2021

Structural and genetic convergence of HIV-1 neutralizing antibodies in vaccinated non-human primates

A primary goal of HIV-1 vaccine development is the consistent elicitation of protective, neutralizing antibodies. While highly similar neutralizing antibodies (nAbs) have been isolated from multiple HIV-infected individuals, it is unclear whether vaccination can consistently elicit highly similar nAbs in genetically diverse primates. Here, we show in three outbred rhesus macaques that immunization with Env elicits a genotypically and phenotypically conserved nAb response. From these vaccinated macaques, we isolated four antibody lineages that had commonalities in immunoglobulin variable, diversity, and joining gene segment usage. Atomic-level structures of the antigen binding fragments of the two most similar antibodies showed nearly identical paratopes. The Env binding modes of each of the four vaccine-induced nAbs were distinct from previously known monoclonal HIV-1 neutralizing antibodies, but were nearly identical to each other. The similarities of these antibodies show that the immune system in outbred primates can respond to HIV-1 Env vaccination with a similar structural and genotypic solution for recognizing a particular neutralizing epitope. These results support rational vaccine design for HIV-1 that aims to reproducibly elicit, in genetically diverse primates, nAbs with specific paratope structures capable of binding conserved epitopes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural response of 3D-printed rubber lattice structures under compressive fatigue

In this work, a new direct UV curing, polyurethane-like, highly stretchable rubber, Elastic ToughRubber 90™ (ETR 90), is demonstrated for 3D printing via photocuring with Texas Instruments DLP® optical systems. An array of test specimens, comprising a sandwich structure with a body-centered cubic lattice core, are 3D printed from ETR 90. The compressive behavior of these specimens is characterized up to 10 k and up to 100 k fatigue-loading cycles. The internal, visually obstructed, structures under loads are visualized using in situ X-ray tomography. All lattice structures remain intact and full recovery is observed, indicating the cyclic durability of the 3D-printed rubber.

36 MATERIALS SCIENCE↗
DOE OSTI2016

A New Light Weight Structural Material for Nuclear Structures

Radiation shielding materials are commonly used in nuclear facilities to attenuate the background ionization radiations to a minimum level for creating a safer workplace, meeting regulatory requirements and maintaining high quality performance. The conventional radiation shielding materials have a number of drawbacks: heavy concrete contains a high amount of elements that are not desirable for an effective shielding such as oxygen, silicon, and calcium; a well known limitation of lead is its low machinability and toxicity, which is causing a major environmental concern. Therefore, an effective and environmentally friendly shielding material with increased attenuation and low mass density is desirable. Close-cell composite metal foams (CMFs) and open-cell Al foam with fillers are light-weight candidate materials that we have studied in this project. Close-cell CMFs possess several suitable properties that are unattainable by conventional radiation shielding materials such as low density and high strength for structural applications, high surface area to volume ratio for excellent thermal isolation with an extraordinary energy absorption capability. Open-cell foam is made up of a network of interconnected solid struts, which allows gas or fluid media to pass through it. This unique structure provided a further motive to investigate its application as radiation shields by infiltrating original empty pores with high hydrogen or boron compounds, which are well known for their excellent neutron shielding capability. The resulting open-cell foam with fillers will not only exhibit light weight and high specific surface area, but also possess excellent radiation shielding capability and good processability. In this study, all the foams were investigated for their radiation shielding efficiency in terms of X-ray, gamma ray and neutron. X-ray transmission measurements were carried out on a high-resolution microcomputed tomography (microCT) system. Gamma-emitting sources: 3.0mCi 60 Co, 1.8mCi 137 Cs, 13.5mCi 241 Am, and 5.0mCi 133 Ba were used for gamma-ray attenuation analysis. The evaluations of neutron transmission measurements were conducted at the Neutron Powder Diffractometer beam facility at North Carolina State University. The experimental results were verified theoretically through XCOM and Monte Carlo Z-particle Transport Code (MCNP). A mechanical investigation was performed by means of quasi-static compressive testing. Thermal characterizations were carried out through effective thermal conductivity and thermal expansion analyses in terms of high temperature guarded-comparative-longitudinal heat flow technique and thermomechanical analyzer (TMA), respectively. The experimental results were compared with analytical results obtained from, respectively, Brailsford and Major’s model and modified Turner’s model for verification. Flame test was performed in accordance with United States Nuclear Regulatory Commission (USNRC) standard. CMF sample and a 304L stainless steel control sample were subjected to a fully engulfing fire with an average flame temperature of 800°C for a period of 30 minutes. Finite Element Analysis was conducted to secure the credibility of the experimental results. This research indicates the potential of utilizing the light-weight close-cell CMFs and open-cell Al foam with fillers as shielding material replacing current heavy structures with additional advantage of high-energy absorption and excellent thermal characteristics.

36 MATERIALS SCIENCE↗