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At least 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Nucleic acid mediated activation of a short prokaryotic Argonaute immune system

A short prokaryotic Argonaute (pAgo) TIR-APAZ (SPARTA) defense system, activated by invading DNA to unleash its TIR domain for NAD(P) + hydrolysis, was recently identified in bacteria. We report the crystal structure of SPARTA heterodimer in the absence of guide-RNA/target-ssDNA (2.66 Å) and a cryo-EM structure of the SPARTA oligomer (tetramer of heterodimers) bound to guide-RNA/target-ssDNA at nominal 3.15–3.35 Å resolution. The crystal structure provides a high-resolution view of SPARTA, revealing the APAZ domain as equivalent to the N, L1, and L2 regions of long pAgos and the MID domain containing a unique insertion (insert57). Cryo-EM structure reveals regions of the PIWI (loop10-9) and APAZ (helix αN) domains that reconfigure for nucleic-acid binding and decrypts regions/residues that reorganize to expose a positively charged pocket for higher-order assembly. The TIR domains amass in a parallel-strands arrangement for catalysis. We visualize SPARTA before and after RNA/ssDNA binding and uncover the basis of its active assembly leading to abortive infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Fabrication of Advanced Nanocarbon-Metal Composites for Improved Energy Efficiency

We fabricated nanocarbon metal composites (NCMC) of Al alloys with a process called “electrocharging assisted process” (EAP). This method consists of the application of a high current to a mixture of liquid metal and carbon particles. We investigated aluminum alloys (6061 and 1350) and used activated carbon and graphite powder as the source of carbon. The high current induces the formation of carbon chains and ribbons in the liquid metal. Upon solidification of the metal an epitaxial relation between the carbon nanostructures and the metal lattice is produced. The purpose of the project was to find the parameters during the reaction that would give rise to a high density of nanoribbons extending throughout the metal such that the electrical conductivity and the mechanical strength of the composite increased and that the method could be extended to large scale manufacturing. For this purpose, we designed two reactors for the incorporation of nanocarbon ribbons in aluminum metal. The first reactor was designed to have more control of the region with the high current density. However, there were problems with getting good mixing of the carbon in small volumes. A second reactor was designed with a stirrer that allowed for better mixing of the carbon by the introduction of argon gas through the shaft of the stirrer. NCMC were fabricated with a series of parameters to understand the role of current, time of applied current, type and shape of the cathode electrode and stirring speed of the mixture. We analyzed the composites by Raman scattering to gain information on the crystallite size of the nanocarbon, XRD to obtain the crystal structure of the composite, SEM and TEM to characterize the grain size of the aluminum grains and the quality of the crystal structure. We also measured the electrical conductivity and mechanical properties of selected samples. The nanocomposites showed increase in crystallite size of the nanocarbon with a linear dependence of the crystallite size on the duration of the applied current. There is a minimum current density necessary for the crystallite size to increase compared to the ~ 10 nm size of the activated carbon source used in the fabrication. The electrical conductivity of the nanocomposites increased with crystallite size of the nanocarbon and with the concentration of converted carbon. The maximum increase in electrical conductivity was 5.7% above the baseline for samples with ~ 4 wt % nanocarbon with crystallite size larger than 30 nm. These samples presented a hardness ~ 8% higher than the baseline samples with no carbon.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

Rapid Laser Reactive Sintering of Garnet Li 6.1 La 3 Zr 2 Al 0.3 O 12 Solid-State Electrolyte

All solid-state lithium-ion batteries (ASSLIBs) have gained significant interest in recent years due to their wide range of applications, including mobile devices, electric vehicles, and grid storage. Garnet-type Li 7 La 3 Zr 2 O 12 (LLZO) solid-state electrolyte (SSE) continues to be a significant player in the fabrication of ASSLIBs with excellent ionic conductivity on the order of 10 -3 S•cm -1 with the integration of dopants and sintering aids to assist conductivity and structural evolution during the sintering procedure. Traditional sintering techniques, such as solid-state sintering (SSS), have been proven to yield desirable crystal structures. However, the low ionic conductivity results from inferior microstructure, and lithium loss is a significant challenge. Recently, a relatively novel sintering process called rapid laser reactive sintering (RLRS) has shown great potential for achieving fully dense solid oxide electrolytes with less surface element loss, resulted in high ionic conductivity. Here, we applied the same RLRS method to fabricate LLZO dense electrolyte with different amounts of aluminum dopants. We hope the rapid high-temperature sintering can densify the electrolyte and avoid the lithium loss for achieving high lithium-ion conductivity. In this work, we optimized multiple combinations of laser parameters (speed, power, and defocus distance), initial precursor composition, and controlled atmospheres to discover the optimal conditions for reaching the efficacious crystal structure, microstructure, and ionic conductivity.

25 ENERGY STORAGE↗
DOE OSTI2023

Quantification of the light output anistropy in deuterated stilbene

Deuterated stilbene is an organic scintillator that is a desirable material for fast neutron spectroscopy using spectrum unfolding techniques without requiring time-of-flight information. Due to the crystal structure of the material, some anisotropy of the light output exists, which is dependent on the direction of heavy charged particle recoil relative to the crystal structure. The anisotropy of trans-stilbene (hereafter referred to as stilbene) has been well characterized in previous work, but for deuterated stilbene, the anisotropy has only been partially characterized along the a and b crystal axes, while the artificial c' axis, which shows the largest anisotropy in stilbene, has not been characterized until this publication. Here, in this work, two deuterated stilbene crystals were characterized with neutron energies up to 35 MeV at the Los Alamos Neutron Science Center. For one of the crystals, the response is characterized along the a, b, and c' axes. This characterization shows a distinct anisotropy along the axes in deuterated stilbene, which is very similar to that found in regular stilbene, such that the a axis is the brightest, while the b' and c' axes are approximately 3% and 20%–35% lower relative to the a axis.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Rapid Laser Reactive Sintering of Garnet Li 6.4 La 3 Zr 1.4 Ta 0.6 O 12 and Li 6.1 La 3 Zr 2 Al 0.3 O 12 and Solid-State Electrolytes

All solid-state lithium-ion batteries (ASSLIBs) have gained significant interest in recent years due to their wide range of applications, including mobile devices, electric vehicles, and grid storage. Garnet-type Li 7 La 3 Zr 2 O 12 (LLZO) solid-state electrolyte (SSE) continues to be a significant player in the fabrication of ASSLIBs with excellent ionic conductivity on the order of 10 -3 S•cm -1 with the integration of dopants and sintering aids to assist conductivity and structural evolution during the sintering procedure. Traditional sintering techniques, such as solid-state sintering (SSS), have been proven to yield desirable crystal structures. However, the low ionic conductivity results from inferior microstructure, and lithium loss is a significant challenge. Recently, a relatively novel sintering process called rapid laser sintering (RLS) has shown great potential for achieving fully dense solid oxide electrolytes with less lithium loss, resulting in high ionic conductivity [1] [2] [3] [4]. Here, we applied a modified RLS method using precursor powders instead of pre-synthesized LLZO powders to fabricate Al-doped LLZO (Li 6.1 La 3 Zr 2 Al 0.3 O 12 + 13 wt% Li 2 CO 3 ) and Ta-doped LLZO (Li 6.4 La 3 Zr 1.4 Ta 0.6 O 12 + 5 wt% LiOH•H 2 O) dense electrolytes. This rapid laser reactive sintering (RLRS) could potentially reduce the number of processing steps and therefore lower the manufacturing cost. We hope the rapid high-temperature sintering can densify the electrolyte and avoid the lithium loss for achieving high lithium-ion conductivity. In this work, we optimized a combination of laser parameters (speed and power), initial precursor composition, and controlled atmospheres to discover the optimal conditions for reaching the efficacious crystal structure, microstructure, and ionic conductivity.

25 ENERGY STORAGE↗
DOE OSTI2020

Crystal and magnetic structure of polar oxide HoCrWO 6

In this study, polar magnetic oxide HoCrWO 6 is synthesized and its crystal structure, magnetic structure, and thermodynamic properties are investigated. HoCrWO 6 forms the polar crystal structure (space group Pna 2 1 (#33)) due to the cation ordering of W 6+ and Cr 3+ . There is an antiferromagnetic transition at T N = 24.5 K along with the magnetic entropy change (~5 J.Kg. –1 K –1 at 70 kOe). Neutron diffraction measurement indicates that both Cr and Ho sublattices are ordered with the moment of 2.32(5)μ B and 8.7(4)μ B at 2 K, respectively. While Cr forms A-type collinear antiferromagnetic (AFM) structure with magnetic moment along the b axis, Ho sublattice orders in a non-coplanar AFM arrangement. A comparison with isostructural DyFeWO 6 and DyCrWO 6 indicates that the magnetic structure of this family of compounds is controlled by the presence or absence of e g electrons in the transition metal sublattice.

42 ENGINEERING↗
DOE OSTI2026

Identification of a key water molecule involved in the macrophage migration inhibitory factor‐catalyzed tautomerization of para ‐hydroxyphenylpyruvate using neutron crystallography

Abstract Neutron crystallography was used to determine a 2.5‐Å resolution all‐atom structure of macrophage migration inhibitory factor (MIF) interacting with 3‐(4‐hydroxyphenyl)‐pyruvate (HPP). MIF is a pro‐inflammatory, pro‐tumorigenic protein that may be an attractive therapeutic target. MIF catalyzes the interconversion of the keto and enol forms of HPP by a tautomerase reaction. Although HPP is evidently not a physiological substrate of MIF, many compounds that inhibit this activity in enzymatic assays have been found also to inhibit physiological activities of MIF. Therefore, the MIF‐catalyzed HPP tautomerization reaction is used in initial screening of compounds in the search for inhibitors of MIF physiological activity. The neutron diffraction‐derived crystal structure reveals the position of a water molecule involved in the tautomerization reaction, and also confirms the charged state of lysine‐32 in the active site. The structure confirms the previously proposed catalytic mechanism of MIF, with the N‐terminal Pro‐1 abstracting a proton to generate an HPP enolate intermediate which is subsequently protonated. The structure reported herein reveals that this proton is supplied by a neighboring water molecule. Along with the neutron structure, a room‐temperature synchrotron x‐ray crystal structure reveals a covalent adduct between HPP and MIF. While this adduct is a result of radiation‐induced chemistry, its formation confirms the catalytic role of the active site residue because a covalent complex could only form if the reactive carbon of the substrate is correctly positioned by the enzyme.

Schröder, Gabriela C. [Department of Molecular and↗
DOE OSTI2020

Thermodynamic properties of metaschoepite predicted from density functional perturbation theory

Density functional perturbation theory (DFPT) calculations of the thermodynamic properties of metaschoepite, (UO 2 ) 8 0 2 (OH) 12 •10H 2 0, are reported. Using a recently revised crystal structure of metaschoepite, the predicted molar entropy and isobaric heat capacity are overall significantly smaller than previous calculations using an earlier orthorhombic crystal structure model. The present DFPT calculations also show large differences between the thermo-dynamic functions of metaschoepite and schoepite, which might reflect the change in phonon properties upon removal of two H 2 0 molecules per formula unit and alteration of the H-bonded interlayer water network from schoepite to metaschoepite.

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

Controlling the symmetry of cadmium arsenide films by epitaxial strain

Epitaxial strains offer unique opportunities to obtain topological states in thin films and heterostructures that do not exist in their bulk counterparts. Here, we investigate the point group symmetries of coherently strained films of cadmium arsenide (Cd 3 As 2 ), a prototype three-dimensional Dirac semimetal, by convergent beam electron diffraction. We report a loss of the fourfold rotational axis and adoption of the orthorhombic mmm point group in (112)-oriented films under biaxial compressive stress. (001)-oriented Cd 3 As 2 films that are under a small biaxial tensile stress retain the fourfold rotational symmetry that protects the bulk nodes but adopt the non-centrosymmetric 4mm point group symmetry. This, in turn, suggests that (001) films adopt a different crystal structure in biaxial tension, one that differs in the arrangement of the ordered Cd vacancies that are an inherent feature of the crystal structure of Cd 3 As 2 and that are key to its nodal electronic structure. Density functional theory calculations confirm the experimental findings of the stability of the non-centrosymmetric structure under biaxial tension, whereas the centrosymmetric structure is stable under biaxial compression. The results show that bulk Cd 3 As 2 is already close to structural instability and showcase the extraordinary tunability of the topological states of Cd 3 As 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2023

One-dimensionality signature in optical conductivity of heavy-fermion CeIr 3 B 2

In low dimensions, the combined effects of interactions and quantum fluctuations can lead to dramatically new physics distinct from that existing in higher dimensions. Here, we investigate the electronic and optical properties of CeIr 3 ⁢B 2 , a quasione-dimensional (1D) Kondo lattice system, using ab initio calculations. The Ce atoms in the hexagonal crystal structure form 1D chains along the c axis, with extremely short Ce-Ce distances. The quasi-1D nature of the crystal structure is well reflected in its electronic structure. Extremely flat bands emerge within the ab plane of the Brillouin zone, yielding sharp optical transitions in the corresponding optical conductivity. Further, our calculations indicate that these prominent peaks in the optical conductivity provide a clear signature of quasi-1D heavy fermion systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro )

The COVID-19 pandemic, instigated by the SARS-CoV-2 coronavirus, continues to plague the globe. The SARS-CoV-2 main protease, or M pro , is a promising target for the development of novel antiviral therapeutics. Previous X-ray crystal structures of M pro were obtained at cryogenic temperature or room temperature only. Here we report a series of high-resolution crystal structures of unliganded M pro across multiple temperatures from cryogenic to physiological, and another at high humidity. We interrogate these data sets with parsimonious multiconformer models, multi-copy ensemble models, and isomorphous difference density maps. Our analysis reveals a perturbation-dependent conformational landscape for M pro , including a mobile zinc ion interleaved between the catalytic dyad, mercurial conformational heterogeneity at various sites including a key substrate-binding loop, and a far-reaching intramolecular network bridging the active site and dimer interface. Our results may inspire new strategies for antiviral drug development to aid preparation for future coronavirus pandemics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Wurtzite materials in alloys of rock salt compounds

Materials with crystal structures containing tetrahedral motifs are preferable for optoelectronic applications because they often have direct band gaps and low electron effective masses. However, crystal structures of manganese chalcogenides typically contain octahedral motifs, such as in rocksalt (RS) MnS and MnSe materials. Here we experimentally show that MnS 1-x Se x alloys with tetrahedrally-bonded wurtzite (WZ) structure can form between MnSe and MnS parent compounds with octahedral RS structures, at S-rich compositions (x<0.4) and low synthesis temperatures (~300°C). The calculated mixing enthalpies of MnS1-xSex alloys in RS and WZ structures cannot explain this experimental observation, so we hypothesize that WZ stabilization may be related to smaller structure density and lower surface energy compared to RS. The resulting WZ MnS 1-x Se x alloys have 3.0-3.2 eV optical absorption onset and lower electrical conductivity (<0.0001 S/cm) compared to the parent RS compounds. These experimental measurement result are consistent with computationally predicted band gaps and effective masses.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A Positive Charge in the Outer Coordination Sphere of an Artificial Enzyme Increases CO 2 Hydrogenation

The protein scaffold around the active site of enzymes is known to influence catalytic activity, but specific scaffold features responsible for favorable influences are often not known. This study focuses on using an artificial metalloenzyme to probe one specific feature of the scaffold, the position of a positive charge in the outer coordination sphere around the active site. Previous work showed that a small molecular complex, [Rh(P Et 2 N glycine P Et 2 )2 ] – , immobilized covalently within a protein scaffold was activated for CO 2 hydrogenation. In this work, using an iterative design where the effect of arginine, histidine, or lysine residues placed in the outer coordination sphere of the catalytic active site were evaluated, we tested the hypothesis that positively charged groups facilitate CO 2 hydrogenation with seven unique constructs. Single-, double-, and triple-point mutations were introduced to directly compare catalytic activity, as monitored by turnover frequencies (TOFs) measured in real time with 1 H NMR spectroscopy, and evaluate related structural and electronic properties. Two of the seven constructs showed a 2- and 3-fold increase relative to the wild type, with overall rates ranging from 0.2 to 0.7 h –1 , and a crystal structure of the fastest of these shows the positive charge positioned next to the active site. A crystal structure of the arginine-containing complex shows that the arginines are positioned near the metal. Molecular dynamics (MD) studies also suggest that the positive charge is oriented next to the active site in the two constructs with faster rates but not in the others and that the positive charge near the active site holds the CO 2 near the metal, all consistent with a positive charge appropriately positioned in the scaffold benefiting catalysis. The MD studies also suggest that changes in the water distribution around the active site may contribute to catalytic activity, while modest structural changes and movement of the complex within the scaffold do not.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Vacancy-tuned magnetism in LaMn x Sb 2

The layered AMP 2 (A = alkali-earth or rare-earth atom, M = transition metal, P = Sb, Bi) compounds are widely studied for their rich magnetism and electronic structure topology. We provide a detailed characterization of the magnetic and transport properties of LaMn x Sb 2 , an understudied member of the AMP 2 family. LaMn x Sb 2 forms with intrinsic Mn vacancies, and we demonstrate that by varying the starting ratio of La, Mn, and Sb, we can synthetically control the Mn occupancy and produce single crystals with x = 0.74 – 0.97. Magnetization and transport measurements indicate LaMn x Sb 2 has a rich temperature-composition (T–x) magnetic phase diagram with physical properties strongly influenced by the Mn occupancy. LaMn x Sb 2 orders antiferromagnetically at T 1 = 130–180 K, where T 1 increases with x. Below T 1 , the T–x phase diagram is complicated. At high x, there is a second transition T 2 that decreases in temperature as x is lowered, vanishing below x ≤ 0.85. A third, first-order, transition T 3 is detected at x ≈ 0.92, and the transition temperature increases as x is lowered, crossing above T 2 near x ≈ 0.9. On moving below x < 0.79, here we find the crystal structure changes from the P 4/nmm arrangement to an I$\bar{4}$2m structure with partially ordered Mn vacancies. The change in crystal structure results in the sudden appearance of two new low-temperature phases and a crossover between regimes of negative and positive magnetoresistance when x ≤ 0.78. Finally, we provide powder neutron diffraction for x = 0.93, and find that the high-x compositions first adopt a G-type antiferromagnetic structure with the Mn moments aligned within the ab plane, which is followed upon further cooling by a second transition to a different, noncollinear structure where the moments are rotated within the basal plane. Our results demonstrate that LaMn x Sb 2 is a highly tunable material with six unique magnetically ordered phases, depending on T and x.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Synthesis, structure, and transport properties of Ba 8 Cu 16 – x Au x P 30 clathrate solid solution

In this work, a new clathrate solid solution Ba 8 Cu 16 – x Au x P 30 ( x = 4, 8, 12) was synthesized by a high-temperature solid-state annealing method. The crystal structures of Ba 8 Cu 16 – x Au x P 30 were determined by single crystal x-ray diffraction. This clathrate solid solution crystallizes in the orthorhombic superstructure of clathrate-I type with 23 crystallographically independent framework sites, eight of them are occupied by Au/Cu and 15 are exclusively occupied by P atoms. The distribution of Au and Cu atoms over these eight framework sites is not random with a clear preference for Au to occupy the largest (Au/Cu)P 4 tetrahedra in the framework. The thermal stability and thermoelectric properties of the Ba 8 Cu 16 – x Au x P 30 solid solution were evaluated. Low thermal conductivity was achieved for Ba 8 Cu 16 – x Au x P 30 due to the combination of the host–guest crystal structure with rattling Ba atoms with the presence of heavy Au atoms and substitutional Cu/Au disorder in the clathrate framework.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Pyrolyzer Assisted Vapor Transport Deposition of Antimony-Doped Cadmium Telluride

In this study, we developed a new method for in situ Sb doping of CdTe thin films combining vapor transport deposition with a Group V pyrolyzer to address Sb doping concentration and doping efficiency. The Sb doped CdSeTe (CdSeTe:Sb) films were deposited in solar cell structures under variations of Sb dopant source heater, vapor pyrolyzer temperature, and Cd vapor excess. Results indicate that although these parameters do not affect the CdTe morphology or crystal structure, they critically influence doping efficiency and trap concentration. Capacitance-voltage measurements show that a higher dopant heater (TD) or pyrolyzer (TP) temperature leads to higher net carrier concentration, achieving a net carrier concentration of 1016 cm-3 and 20% doping efficiency with a TD/TP combination of 600 degrees C/1100 degrees C. By tuning the Cd/Sb flux ratio during CdSeTe:Sb deposition, the lowest defect concentration is achieved at Cd/Sb of 1.4:1, which produced the best VOC CdSeTe:Sb cell. This demonstrates a path to produce high net carrier concentration polycrystalline CdTe thin film with a low concentration of dopant-induced defects.

14 SOLAR ENERGY↗
NASA NTRS2001

The gating mechanism of the large mechanosensitive channel MscL

The mechanosensitive channel of large conductance, MscL, is a ubiquitous membrane-embedded valve involved in turgor regulation in bacteria. The crystal structure of MscL from Mycobacterium tuberculosis provides a starting point for analysing molecular mechanisms of tension-dependent channel gating. Here we develop structural models in which a cytoplasmic gate is formed by a bundle of five amino-terminal helices (S1), previously unresolved in the crystal structure. When membrane tension is applied, the transmembrane barrel expands and pulls the gate apart through the S1-M1 linker. We tested these models by substituting cysteines for residues predicted to be near each other only in either the closed or open conformation. Our results demonstrate that S1 segments form the bundle when the channel is closed, and crosslinking between S1 segments prevents opening. S1 segments interact with M2 when the channel is open, and crosslinking of S1 to M2 impedes channel closing. Gating is affected by the length of the S1-M1 linker in a manner consistent with the model, revealing critical spatial relationships between the domains that transmit force from the lipid bilayer to the channel gate.

Non-NASA Center↗
DOE OSTI2023

Floating zone crystal growth, structure, and properties of a cubic Li 5.5 La 3 Nb 1.5 Zr 0.5 O 12 garnet-type lithium-ion conductor

As a promising candidate for solid-state electrolytes in Li-ion batteries, the garnet-type Li-ion conductor series Li 5+x La 3 Nb 2-x Zr x O 12 (LLNZO) (0 ≤ x ≤ 2) exhibits high ionic conductivity at room temperature. However, no previous single-crystal growth or characterization has been reported for LLNZO compositions 0 ≤ x ≤ 1. To obtain a complete understanding of the trend in the structure–property relationship in this class of materials, we used the floating zone (FZ) method to grow a single crystal of Li 5.5 La 3 Nb 1.5 Zr 0.5 O 12 that was 4 mm in diameter and 10 mm in length. Using Laue neutron single-crystal diffraction, two distinct Li sites were observed: tetrahedral 24d and octahedral 96h sites. The maximum entropy method (MEM) based on neutron single-crystal diffraction data was used to map Li nuclear density and estimate that the bottleneck of Li transport exists between neighboring tetrahedral and octahedral sites, and that Li is delocalized between split octahedral sites. Room-temperature Li-ion conductivity in Li 5.5 La 3 Nb 1.5 Zr 0.5 O 12 measured with electrochemical impedance spectroscopy (EIS) was 1.37 × 10 -4 S cm -1 . The Li migration activation energy was estimated to be 0.50 eV from EIS and 0.47 eV from dielectric relaxation measurements. The Li-ion jump attempt rate was estimated to be 1.47 × 10 12 Hz while the time scale of successful migration is 10 -7 to 10 -6 s.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗