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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Synergistic role of Sn-doping on the thermal and electrical properties of sinnerite Cu 6 As 4 S 9

Sinnerite Cu 6 As 4 S 9 has been identified as a promising material for optoelectronic applications, with potential for other energy-related applications; however, knowledge of the electrical and thermal properties as well as the mechanisms underlying transport in sinnerite is lacking. Here, we present an investigation of the synthesis, structural, thermal and electrical transport properties of stoichiometric and Sn-doped Cu 6 As 4 S 9 . Sinnerite has a triclinic lattice structure, with highly distorted local atomic coordination environments that, in part, results in its complex structure and bonding. Our results and analyses indicate As 4s 2 lone pair-induced distortions and strong lattice anharmonicity that leads to a relatively short phonon mean free path, resulting in intrinsically very low thermal conductivity. The electrical resistivity for both compositions, Cu 6 As 4-x Sn x S 9 (x = 0, 0.2), are relatively high and varies little with temperature, typical of degenerate semiconductors. An increase in mobility and electrical conductivity was obtained by Sn doping in Cu 6 As 3.8 Sn 0.2 S 9 . This work demonstrates an effective route to synthesize bulk sinnerite as well as advances the knowledge of the properties of sinnerite, as this and other ternary chalcogenides continue to be of interest for potential technologically significant applications.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Chemical interactions that govern the structures of metals

Most metals adopt simple structures such as body-centered cubic (BCC), face-centered cubic (FCC), and hexagonal close-packed (HCP) structures in specific groupings across the periodic table, and many undergo transitions to surprisingly complex structures on compression, not expected from conventional free-electron-based theories of metals. First-principles calculations have been able to reproduce many observed structures and transitions, but a unified, predictive theory that underlies this behavior is not yet in hand. Discovered by analyzing the electronic properties of metals in various lattices over a broad range of sizes and geometries, a remarkably simple theory shows that the stability of metal structures is governed by electrons occupying local interstitial orbitals and their strong chemical interactions. The theory provides a basis for understanding and predicting structures in solid compounds and alloys over a broad range of conditions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Probing conformational states of glutaryl-CoA dehydrogenase by fragment screening

Glutaric acidemia type 1 is an inherited metabolic disorder which can cause macrocephaly, muscular rigidity, spastic paralysis and other progressive movement disorders in humans. The defects in glutaryl-CoA dehydrogenase (GCDH) associated with this disease are thought to increase holoenzyme instability and reduce cofactor binding. Here, the first structural analysis of a GCDH enzyme in the absence of the cofactor flavin adenine dinucleotide (FAD) is reported. The apo structure of GCDH from Burkholderia pseudomallei reveals a loss of secondary structure and increased disorder in the FAD-binding pocket relative to the ternary complex of the highly homologous human GCDH. After conducting a fragment-based screen, four small molecules were identified which bind to GCDH from B. pseudomallei. Complex structures were determined for these fragments, which cause backbone and side-chain perturbations to key active-site residues. Structural insights from this investigation highlight differences from apo GCDH and the utility of small-molecular fragments as chemical probes for capturing alternative conformational states of preformed protein crystals.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

APR1400 In-Core Instrumentation Penetration Failure by Zirconia Melt

Light water reactors have many penetrations at the reactor vessel lower head which are called ICI (in-core instrumentation tubes), ICM-GT (in-core monitoring guide tubes), CRGT (control rod guide tubes) and drain tubes. For Korean PWRs (pressurized water reactors), there are dozens of bottom-up type ICI penetration tubes (45 for OPR1000 and 61 for APR1400). For the typical BWRs (boiling water reactors), hundreds of penetrations are positioned at the reactor vessel lower head due to the structural complexity at the reactor upper head. These penetrations are regarded as the most vulnerable structures during a severe accident as they could be failed by high temperature of melt (or debris) and its decay heat. That is, tube rupture and/or tube ejection could occur because there exist an empty hole inside the penetration tube which can be a melt flow path, and they are attached to the inside of the reactor vessel by a partial weld with a gap between the tubes and reactor vessel. Therefore, the research on the penetration failure is of importance, as it could lead to melt discharge into the containment and subsequent release of radioactive materials to the environment due to the containment failure. This paper focuses on the experimental investigation on the tube ejection failure for the APR1400 ICI penetration. The tube ejection experiments were performed as it was exposed to high temperature of zirconia melt and high pressure. The tube ejection failure experiments were performed for the APR1400 in-core instrumentation penetration nozzle. Zirconia melt was used as a simulant of molten corium and interacted with the penetration specimen. The specimen was pressurized up to 2.6 bar during the interaction with melt to induce the tube ejection. The penetration weld was heated up to its melting temperature, and the penetration tube and weld above the reactor vessel surface were eroded severely by the melt. However, even though it was estimated that the weld failure occurred and the reactor vessel with stainless steel cladding was ablated severely by the melt, the tube ejection did not take place, and consequently the integrity for the APR1400 ICI penetration was confirmed in the present experimental conditions. The goal of this research is to improve the penetrations failure models in MAAP5 codes based on the experimental data. To achieve this goal, it is necessary to increase the heat flux and pressure acting on the penetration tube to find the conditions for the tube ejection failure. Moreover, the penetration failure experiments will be performed by delivering melt into the penetration specimen to simulate the melt relocation process in a real severe accident situation. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗
DOE OSTI2020

Lone-Electron-Pair Micelles Strengthen Bond Anharmonicity in MnPb16Sb14S38 Complex Sulfosalt Leading to Ultra-Low Thermal Conductivity

Designing crystalline solids in which intrinsic extremely low lattice thermal conductivity mainly arises from its unique bonding nature rather than structure complexity and/or atomic disorder could promote thermal energy manipulation and utilization for applications ranging from thermoelectric energy conversion to thermal barrier coatings. Here, we report an extremely low lattice thermal conductivity of ~0.34 W m-1 K-1 at 300 K in the new complex sulfosalt MnPb16Sb14S38. We attribute the ultra-low lattice thermal conductivity to a synergistic combination of scattering mechanisms involving (1) strong bond anharmonicity in various structural building units, owing to the presence of stereoactive lone-electron-pair (LEP) micelles, and (2) phonon scattering at the interfaces between building units of increasing size and complexity. Remarkably, low-temperature heat capacity measurement revealed a Cp value of 0.206 J g-1 K-1 at T > 300 K, which is 22% lower than the Dulong-Petit value (0.274 J g-1 K-1). Further analysis of the Cp data and sound velocity (ν = 1834 m/s) measurement yielded Debye temperature values of 161 K and 187 K, respectively. Here, the resulting Grüneisen parameter, γ = 1.65, further supports strong bond anharmonicity as the dominant mechanism responsible for the observed extremely low lattice thermal conductivity.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Hierarchical, rotation‐equivariant neural networks to select structural models of protein complexes

Abstract Predicting the structure of multi‐protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage predefined structural features to distinguish accurate structural models from less accurate ones. This raises the question of whether it is possible to learn characteristics of accurate models directly from atomic coordinates of protein complexes, with no prior assumptions. Here we introduce a machine learning method that learns directly from the 3D positions of all atoms to identify accurate models of protein complexes, without using any precomputed physics‐inspired or statistical terms. Our neural network architecture combines multiple ingredients that together enable end‐to‐end learning from molecular structures containing tens of thousands of atoms: a point‐based representation of atoms, equivariance with respect to rotation and translation, local convolutions, and hierarchical subsampling operations. When used in combination with previously developed scoring functions, our network substantially improves the identification of accurate structural models among a large set of possible models. Our network can also be used to predict the accuracy of a given structural model in absolute terms. The architecture we present is readily applicable to other tasks involving learning on 3D structures of large atomic systems.

Eismann, Stephan↗
DOE OSTI2015

Electronic structure and thermoelectric properties of pnictogen-substituted ASn{sub 1.5}Te{sub 1.5} (A = Co, Rh, Ir) skutterudites

Substituting group 14 and 16 elements on the pnictogen site in the skutterudite structure yields a class of valence-precise ternary AX{sub 1.5}Y{sub 1.5} compounds (A = Co, Rh, Ir, X = Sn, Ge, and Y = S, Se, Te), in which X and Y form an ordered sub-structure. Compared with unfilled binary skutterudites, pnictogen-substituted phases exhibit extremely low lattice thermal conductivity due to increased structural complexity. Here, we investigate the role of the transition metal species in determining the electronic structure and transport properties of ASn{sub 1.5}Te{sub 1.5} compounds with A = Co, Rh, Ir. Density functional calculations using fully ordered structures reveal semiconducting behavior in all three compounds, with the band gap varying from 0.2 to 0.45 eV. In CoSn{sub 1.5}Te{sub 1.5}, the electronic density of states near the gap is significantly higher than for A = Ir or Rh, leading to higher effective masses and higher Seebeck coefficients. Experimentally, Ir and Rh samples exhibit relatively large p-type carrier concentrations and degenerate semiconducting behavior. In contrast, CoSn{sub 1.5}Te{sub 1.5} shows mixed conduction, with n-type carriers dominating the Seebeck coefficient and light, high mobility holes dominating the Hall coefficient. zT values of up to 0.35 were obtained, and further improvement is expected upon optimization of the carrier concentration or with n-type doping.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

How substrate specificity is imposed on a histone demethylase—lessons from KDM2A

Histone lysine methylation and demethylation regulate histone methylation dynamics, which impacts chromatin structure and function. To read and erase the methylated histone residues, lysine demethylases must specifically recognize the histone sequences and methylated sites and discriminate the degree of these methylations. In this issue of Genes & Development, Cheng and colleagues (pp. 1758–1771) determine a crystal structure of histone lysine demethylase KDM2A that specifically targets lower degrees of H3K36 methylation. The results reveal the structural basis for H3K36 substrate specificity and suggest mechanisms of Lys36 demethylation. This KDM2A– H3K36 complex structure, coupled with functional studies, provides needed insight into the process and regulation of histone demethylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Response of Pseudomonas putida to Complex, Aromatic-Rich Fractions from Biomass

There is strong interest in the valorization of lignin to produce valuable products; however, its structural complexity has been a conversion bottleneck. Chemical pretreatment liberates lignin-derived soluble fractions that may be upgraded by bioconversion. Here, cholinium ionic liquid pretreatment of sorghum produced soluble, aromatic-rich fractions that were converted by Pseudomonas putida (P. putida), a promising host for aromatic bioconversion. Growth studies and mutational analysis demonstrated that P. putida growth on these fractions was dependent on aromatic monomers but unknown factors also contributed. Proteomic and metabolomic analyses indicated that these unknown factors were amino acids and residual ionic liquid; the oligomeric aromatic fraction derived from lignin was not converted. A cholinium catabolic pathway was identified, and the deletion of the pathway stopped the ability of P. putida to grow on cholinium ionic liquid. This work demonstrates that aromatic-rich fractions obtained through pretreatment contain multiple substrates; conversion strategies should account for this complexity.

09 BIOMASS FUELS↗
DOE OSTI2016

High power microwave source with a three dimensional printed metamaterial slow-wave structure

For over the last decade, the concept of metamaterials has led to new approaches for considering the interaction of radiation with complex structures. However, practical manifestations of such a device operating at high power densities have proven difficult to achieve due to the resonant nature of metamaterials and the resultant high electric fields, which place severe constraints on manufacturing the slow wave structures. In this paper, we describe the first experimental manifestation of a high power microwave device utilizing a metallic slow wave structure (metamaterial-like) fabricated using additive manufacturing. The feasibility of utilizing additive manufacturing as a technique for building these relatively complicated structures has thus been demonstrated. The MW class microwave source operates in the C-band and shows frequency tunablility with electron beam voltage. The basic electromagnetic characteristics of this device, the construction using additive manufacturing, and the basic performance as a microwave oscillator are considered. Due to the tunable nature of the device, it shows promise not only as an oscillator but also as a microwave amplifier. Therefore, the dispersive characteristics and a discussion of the anticipated gain is included as it relates to an amplifier configuration.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2025

Asymmetric loading of TnsE regulates Tn7 targeting of DNA replication structures

Abstract Tn7 transposable elements are known for their sophisticated target-site selection mechanisms. For the prototypical Tn7 element, dedicated transposon-encoded proteins direct insertions to either a conserved site in the chromosome or replicating DNA structures in conjugal plasmids, ensuring the vertical and horizontal spread of the element. While the pathway targeting the attTn7 site in the bacterial chromosome has been extensively studied, the pathway targeting DNA replication structures remains poorly understood. We have used an integrative structural biology approach to elucidate how the Tn7-encoded protein TnsE recognizes replication sites. Using native mass spectrometry, we found that TnsE forms 1:1 and 2:1 (TnsE:DNA) complexes on 3′-recessed DNA, with gain-of-function TnsE variants favoring the formation of 2:1 complexes. Structural characterization confirms that two TnsE molecules bind to DNA with the C-terminal domain of the protein recognizing duplex DNA, leaving the N-terminal domain to impose DNA substrate specificity and recruit the core transposition machinery. Collectively, our work is consistent with a model where TnsE-mediated target-site selection relies on the formation of an asymmetric TnsE:DNA complex to recruit the Tn7 transposase to DNA replication structures.

Biochemistry & Molecular Biology↗
DOE OSTI2017

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

The metabolism of carbohydrate polymers drives microbial diversity in the human gut microbiota. It is unclear, however, whether bacterial consortia or single organisms are required to depolymerize highly complex glycans. Here in this paper we show that the gut bacterium Bacteroides thetaiotaomicron uses the most structurally complex glycan known: the plant pectic polysaccharide rhamnogalacturonan-II, cleaving all but 1 of its 21 distinct glycosidic linkages. The deconstruction of rhamnogalacturonan-II side chains and backbone are coordinated to overcome steric constraints, and the degradation involves previously undiscovered enzyme families and catalytic activities. The degradation system informs revision of the current structural model of rhamnogalacturonan-II and highlights how individual gut bacteria orchestrate manifold enzymes to metabolize the most challenging glycan in the human diet.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Synchrotron x-Ray Study of Heterostructured Materials: A Review

Heterostructured materials (HSMs) have shown great potential for breaking the strength-ductility tradeoff. HSMs consist of heterogeneous zones that may have different sizes, shapes, compositions, structures, etc. Interactions and competitions among them often lead to unprecedented properties. However, due to the complex structures in a broad range of length scales, it is challenging to unravel deformation physics and strengthening mechanisms underlying extraordinary mechanical properties. Synchrotron x-rays provide powerful techniques and indispensable tools for investigating HSMs at various length scales. Here, we will present in situ high-energy x-ray diffraction and Laue x-ray microdiffraction techniques and their application in studying the HSMs. In this study, the principles of these techniques will be briefly introduced. We will focus on their application in studying stress partitioning and plastic accommodation during tensile deformation, thermo-driven and/or stress-driven phase transformations and various deformation microstructures like geometrically necessary dislocations and local stress/strain distributions, etc., in HSMs. Some important findings will be summarized. Challenging issues remain in studying HSMs and will be discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Theoretical study of photodetachment processes of anionic boron cluster. III. B{sub 7}{sup −}

Photodetachment spectroscopy of B{sub 7}{sup −} is theoretically studied in this paper. Calculated photodetachment bands are compared with the available experimental results and assigned to the vibronic structure of the electronic ground and excited states of the neutral B{sub 7} cluster. The complex structure of photodetachment bands is found to arise from many stable isomers of B{sub 7}{sup −} of different symmetry point group. In this study we focus on three most stable isomers of B{sub 7}{sup −} and examine their photodetachment bands. Extensive quantum chemistry calculations are carried out to establish the potential energy surfaces and the coupling surfaces of the electronic states of neutral B{sub 7} originating from each of the three isomers. A diabatic electronic ansatz is employed and the nuclear dynamics is studied both by time-independent and time-dependent quantum mechanical methods. Both agreements and discrepancies of the theoretical results with the experimental findings are discussed.

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

Structural basis of HIV inhibition by translocation-defective RT inhibitor 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)

4'-Ethynyl-2-fluoro-2'-deoxyadenosine (EFdA) is the most potent nucleoside analog inhibitor of HIV reverse transcriptase (RT). It retains a 3'-OH yet acts as a chain-terminating agent by diminishing translocation from the pretranslocation nucleotide-binding site (N site) to the posttranslocation primer-binding site (P site). Also, facile misincorporation of EFdA-monophosphate (MP) results in difficult-to-extend mismatched primers. To understand the high potency and unusual inhibition mechanism of EFdA, we solved RT crystal structures (resolutions from 2.4 to 2.9 Å) that include inhibition intermediates ( i ) before inhibitor incorporation (catalytic complex, RT/DNA/EFdA-triphosphate), ( ii ) after incorporation of EFdA-MP followed by dT-MP (RT/DNA EFdA-MP P • dT-MP N ), or ( iii ) after incorporation of two EFdA-MPs (RT/DNA EFdA-MP P • EFdA-MP N ); ( iv ) the latter was also solved with EFdA-MP mismatched at the N site (RT/DNA EFdA-MP P • EFdA-MP *N ). We report that the inhibition mechanism and potency of EFdA stem from interactions of its 4'-ethynyl at a previously unexploited conserved hydrophobic pocket in the polymerase active site. Furthermore, the high resolution of the catalytic complex structure revealed a network of ordered water molecules at the polymerase active site that stabilize enzyme interactions with nucleotide and DNA substrates. Finally, decreased translocation results from favorable interactions of primer-terminating EFdA-MP at the pretranslocation site and unfavorable posttranslocation interactions that lead to observed localized primer distortions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Atomic-Scale Understanding of Structure and Properties of Complex Pyrophosphate Crystals by First-Principles Calculations

The electronic structure and mechanical and optical properties of five pyrophosphate crystals with very complex structures are studied by first principles density functional theory calculations. The results show the complex interplay of the minor differences in specific local structures and compositions can result in large differences in reactivity and interaction that are rare in other classes of inorganic crystals. These are discussed by dividing the pyrophosphate crystals into three structural units. H 2 P 2 O 7 is the most important and dominating unit in pyrophosphates. The other two are the influential cationic group with metals and water molecules. The strongest P-O bond in P 2 O 5 is the strongest bond for crystal cohesion, but O-H and N-H bonds also play an important part. Different type of bonding between O and H atoms such as O-H, hydrogen bonding, and bridging bonds are present. Metallic cations such as Mg, Zn, and Cu form octahedral bonding with O. The water molecule provides the unique H∙∙∙O bonds, and metallic elements can influence the structure and bonding to a certain extent. The two Cu-containing phosphates show the presence of narrow metallic bands near the valence band edge. All this complex bonding affects their physical properties, indicating that fundamental understanding remains an open question.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2014

Structural and dynamical studies of acid-mediated conversion in amorphous-calcium-phosphate based dental composites

Our objective was to investigate the complex structural and dynamical conversion process of the amorphous-calcium-phosphate (ACP)-to-apatite transition in ACP based dental composite materials. Composite disks were prepared using zirconia hybridized ACP fillers (0.4 mass fraction) and photo-activated Bis-GMA/TEGDMA resin (0.6 mass fraction). We performed an investigation of the solution-mediated ACP-to-apatite conversion mechanism in controlled acidic aqueous environment with in situ ultra-small angle X-ray scattering based coherent X-ray photon correlation spectroscopy and ex situ X-ray diffraction, as well as other complementary techniques. We established that the ACP-to-apatite conversion in ACP composites is a two-step process, owing to the sensitivity to local structural changes provided by coherent X-rays. Initially, ACP undergoes a local microstructural rearrangement without losing its amorphous character. We established the catalytic role of the acid and found the time scale of this rearrangement strongly depends on the pH of the solution, which agrees with previous findings about ACP without the polymer matrix being present. In the second step, ACP is converted to an apatitic form with the crystallinity of the formed crystallites being poor. Separately, we also confirmed that in the regular Zr-modified ACP the rate of ACP conversion to hydroxyapatite is slowed significantly compared to unmodified ACP, which is beneficial for targeted slow release of functional calcium and phosphate ions from dental composite materials. Significantly, for the first time, we were able to follow the complete solution-mediated transition process from ACP to apatite in this class of dental composites in a controlled aqueous environment. A two-step process, suggested previously, was conclusively identified.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Uranyl/12-crown-4 Ether Complexes and Derivatives: Structural Characterization and Isomeric Differentiation

The following gas-phase uranyl/12-crown-4 (12C4) complexes were synthesized by electrospray ionization: [UO 2 (12C4) 2 ] 2+ and [UO 2 (12C4) 2 (OH)] + . Collision-induced dissociation (CID) of the dication resulted in [UO 2 (12C4-H)] + (12C4-H is a 12C4 that has lost one H), which spontaneously adds water to yield [UO 2 (12C4-H)(H 2 O)] + . The latter has the same composition as complex [UO 2 (12C4)(OH)] + produced by CID of [UO 2 (12C4) 2 (OH)] + but exhibits different reactivity with water. The postulated structures as isomeric [UO 2 (12C4-H)(H 2 O)] + and [UO 2 (12C4)(OH)] + were confirmed by comparison of infrared multiphoton dissociation (IRMPD) spectra with computed spectra. The structure of [UO 2 (12C4-H)] + corresponds to cleavage of a C-O bond in the 12C4 ring, with formation of a discrete U-O eq bond and equatorial coordination by three intact ether moieties. Comparison of IRMPD and computed IR spectra furthermore enabled assignment of the structures of the other complexes. Theoretical studies of the chemical bonding features of the complexes provide an understanding of their stabilities and reactivities. Finally, the results reveal bonding and structures of the uranyl/12C4 complexes and demonstrate the synthesis and identification of two different isomers of gas-phase uranyl coordination complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗