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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Substrate effects on phase formation and interfacial stability in superconducting vanadium silicide thin films

Thin films of vanadium silicide (V-silicide) in the A15 cubic phase (V 3 Si) are promising for superconducting quantum devices due to their high transition temperature and potential compatibility with scalable semiconductor fabrication. However, solid-phase synthesis often yields secondary silicide phases that degrade performance. Here, in this study, we investigate the influence of substrate properties using two silicon-on-insulator architectures: one with a polycrystalline HfO 2 buried layer (group A) and the other with amorphous SiO 2 (group B). Both systems exhibit superconductivity consistent with V 3 Si formation, yet structural analysis reveals mixed-phase films in both cases. Crucially, only group A maintains an atomically sharp and chemically stable interface, a prerequisite for phase purity. Prolonged annealing in group A reduces the unwanted V 5 Si 3 phase but also leads to the emergence of Si-rich VSi 2 , likely due to localized substrate degradation. Preliminary atomic-resolution imaging suggests that HfO 2 crystallinity may promote local phase-selective nucleation. These findings highlight the importance of substrate design in promoting phase control and maintaining interfacial integrity in superconducting silicides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2026

Quadratic magnetoresistance across the insulator–metal transition in V4O7 thin films

We present a comparative magnetotransport study of V4O7 thin films grown simultaneously on single-crystal Al2O3 (r-cut) and amorphous SiO2 substrates, to examine substrate-induced effects on electronic transport across the insulator–metal transition (IMT). Temperature-dependent resistivity reveals a broad electronic ordering regime below the IMT, with both films exhibiting similar transition temperatures but differing by nearly an order of magnitude in absolute resistivity. Despite this strong substrate dependence of the resistivity scale, the magnetoresistance remains predominantly quadratic in magnetic field over wide temperature intervals for both substrates. Analysis of the quadratic magnetoresistance defines an effective mobility scale that evolves systematically across the IMT and exhibits a similar temperature dependence for the two films. Structural characterization, including atomic-resolution scanning transmission electron microscopy of the V4O7/Al2O3 interface and azimuthal X-ray diffraction measurements, reveals a sharp interface and well-defined in-plane crystallographic registry for the r-cut film, in contrast to the rotationally averaged in-plane structure expected for films grown on amorphous SiO2. These results indicate that while substrate-controlled structural registry modifies the resistivity scale, the quadratic magnetotransport response across the IMT remains largely robust, providing a consistent diagnostic of electronic transport in V4O7 thin films.

25 ENERGY STORAGE↗
DOE OSTI2020

Vip1 is a kinase and pyrophosphatase switch that regulates inositol diphosphate signaling

Inositol diphosphates (PP-IPs), also known as inositol pyrophosphates, are high-energy cellular signaling codes involved in nutrient and regulatory responses. We report that the evolutionarily conserved gene product, Vip1, possesses autonomous kinase and pyrophosphatase domains capable of synthesis and destruction of D-1 PP-IPs. Our studies provide atomic-resolution structures of the PP-IP products and unequivocally define that the Vip1 gene product is a highly selective 1-kinase and 1-pyrophosphatase enzyme whose activities arise through distinct active sites. Kinetic analyses of kinase and pyrophosphatase parameters are consistent with Vip1 evolving to modulate levels of 1-IP 7 and 1,5-IP 8 . Individual perturbations in kinase and pyrophosphatase activities in cells result in differential effects on vacuolar morphology and osmotic responses. Analogous to the dual-functional key energy metabolism regulator, phosphofructokinase 2, Vip1 is a kinase and pyrophosphatase switch whose 1-PP-IP products play an important role in a cellular adaptation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a di-heptamer macromolecular assembly

Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in addition to the enterotoxins TsdA and TsdB. The C. difficile toxin has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single-particle cryoelectron microscopy, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, 2 di-heptamer structures for activated CDTb (1.0 MDa) were solved at atomic resolution, including a symmetric ( Sym CDTb; 3.14 Å) and an asymmetric form ( Asym CDTb; 2.84 Å). Roles played by 2 receptor-binding domains of activated CDTb were of particular interest since the receptor-binding domain 1 lacks sequence homology to any other known toxin, and the receptor-binding domain 2 is completely absent in other well-studied heptameric toxins (i.e., anthrax). For Asym CDTb, a Ca 2+ binding site was discovered in the first receptor-binding domain that is important for its stability, and the second receptor-binding domain was found to be critical for host cell toxicity and the di-heptamer fold for both forms of activated CDTb. Together, these studies represent a starting point for developing structure-based drug-design strategies to target the most severe strains of C. difficile .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural elucidation of the cis -prenyltransferase NgBR/DHDDS complex reveals insights in regulation of protein glycosylation

Cis-prenyltransferase (cis-PTase) catalyzes the rate-limiting step in the synthesis of glycosyl carrier lipids required for protein glycosylation in the lumen of endoplasmic reticulum. Here, we report the crystal structure of the human NgBR/DHDDS complex, which represents an atomic resolution structure for any heterodimeric cis-PTase. The crystal structure sheds light on how NgBR stabilizes DHDDS through dimerization, participates in the enzyme’s active site through its C-terminal -RXG- motif, and how phospholipids markedly stimulate cis-PTase activity. Comparison of NgBR/DHDDS with homodimeric cis-PTase structures leads to a model where the elongating isoprene chain extends beyond the enzyme’s active site tunnel, and an insert within the α3 helix helps to stabilize this energetically unfavorable state to enable long-chain synthesis to occur. These data provide unique insights into how heterodimeric cis-PTases have evolved from their ancestral, homodimeric forms to fulfill their function in long-chain polyprenol synthesis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Layer-dependent topological phase in a two-dimensional quasicrystal and approximant

The electronic and topological properties of materials are derived from the interplay between crystalline symmetry and dimensionality. Simultaneously introducing “forbidden” symmetries via quasiperiodic ordering with low dimensionality into a material system promises the emergence of new physical phenomena. Here, we isolate a two-dimensional (2D) chalcogenide quasicrystal and approximant, and investigate their electronic and topological properties. The 2D layers of the materials with a composition close to Ta 1.6 Te, derived from a layered transition metal dichalcogenide, are isolated with standard exfoliation techniques, and investigated with electron diffraction and atomic resolution scanning transmission electron microscopy. Density functional theory calculations and symmetry analysis of the large unit cell crystalline approximant of the quasicrystal, Ta 21 Te 13 , reveal the presence of symmetry-protected nodal crossings in the quasicrystalline and approximant phases, whose presence is tunable by layer number. Our study provides a platform for the exploration of physics in quasicrystalline, low-dimensional materials and the interconnected nature of topology, dimensionality, and symmetry in electronic systems.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Protein folds vs. protein folding: Differing questions, different challenges

We report protein fold prediction using deep-learning artificial intelligence (AI) has transformed the field of protein structure prediction. By combining physical and geometric constraints—and especially patterns extracted from the Protein Data Bank —these machine learning algorithms can predict protein structures at or near atomic resolution and do so in seconds. Today, these computational methods have now solved more than 200 million protein structures, which are accessible from the AlphaFold Protein Structure Database. This accomplishment seems all the more remarkable because few thought it possible or saw it coming. Deservedly, deep-learning AI was named Science magazine’s 2021 “breakthrough of the year”. Clearly, deep-learning AI represents a major advance in protein fold prediction.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Structural basis of transcription: RNA polymerase II substrate binding and metal coordination using a free-electron laser

Catalysis and translocation of multisubunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near-atomic resolution and precise arrangement of key active site components have been elusive. Here, we present the free-electron laser (FEL) structures of a matched ATP-bound Pol II and the hyperactive Rpb1 T834P bridge helix (BH) mutant at the highest resolution to date. The radiation-damage-free FEL structures reveal the full active site interaction network, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg 2+ , and, more importantly, a putative third (site C) Mg 2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structures indicate that the third Mg 2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/BH interactions induce conformational changes that could allow translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the T834P mutant reveal rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.

Science & Technology - Other Topics↗
DOE OSTI2020

In situ laser reflectivity to monitor and control the nucleation and growth of atomically thin 2D materials*

The growth of atomically thin two-dimensional (2D) layered and other quantum materials is typically performed without in situ monitoring or control. Here, a simple laser reflectivity approach is demonstrated to provide in situ control over sub-monolayer thickness and growth kinetics during pulsed laser deposition (PLD) of MoSe 2 layers. First, the general technique is presented with emphasis on designing the maximum sensitivity of the optical contrast through consideration of Fresnel's equations with proper choice of layer thickness, substrate, and laser monitoring wavelength, incidence angle, and laser polarization. Then the 632.8 nm optical reflectivity of MoSe 2 layers on SiO 2 /Si substrates was predicted and compared with in situ monitoring of MoSe 2 growth by PLD under actual growth conditions using a probe HeNe laser beam. The measurements showed high sensitivity and excellent agreement with MoSe 2 surface coverages calculated from atomic resolution STEM analysis of 2D layers deposited in arrested growth experiments. Finally, growth kinetics revealed by these measurements showed sigmoidal nucleation and growth stages in the formation of the 2D MoSe 2 layers that are described by a simple model, indicating the promise of the laser reflectivity technique for in situ monitoring and control of 2D materials deposition.

2D materials↗
DOE OSTI2023

Automating STEM Aberration Correction via Bayesian Optimization

Multipole aberration correctors have given scanning transmission electron microscopes (STEM) the ability to produce high-quality, atomic-resolution images, enabling STEM to be a key tool in material sciences for characterizing the structure and composition of materials. However, the process of correcting these aberrations typically requires human input and is accomplished using scanned STEM or Ronchigram images at different focii and beam tilts. In this work, we demonstrate an automated on-sample aberration correction system using Bayesian Optimization. We have developed a Python-based server able to communicate with the CEOS DCOR aberration corrector and the Thermo Fischer microscope scripting interface. This server allows us to change aberrations, acquire images and perform basic image analysis.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI

Abstract Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural adaptation of oxygen tolerance in 4-hydroxybutyrl-CoA dehydratase, a key enzyme of archaeal carbon fixation

Abstract Autotrophic microorganisms that convert inorganic carbon into organic matter were key players in the evolution of life on Earth. As the early atmosphere became oxygenated, microorganisms needed to develop mechanisms for oxygen protection, especially those relying on enzymes containing oxygen-sensitive metal clusters (e.g., Fe-S). Here we investigated how 4-hydroxybutyryl-CoA dehydratase (4HBD) - the key enzyme of the 3-hydroxypropionate/4-hydroxybutyrate (HP/HB) cycle for CO 2 -fixation - adapted as conditions shifted from anoxic to oxic. 4HBD is found in both anaerobic bacteria and aerobic ammonia-oxidizing archaea (AOA). The oxygen-sensitive bacterial 4HBD and oxygen-tolerant archaeal 4HBD share 59 % amino acid identity. To examine the structural basis of oxygen tolerance in archaeal 4HBD, we determined the atomic resolution structure of the enzyme. Two tunnels providing access to the canonical [4Fe-4S] cluster in oxygen-sensitive bacterial 4HBD were closed with four conserved mutations found in all aerobic AOA and other archaea. Further biochemical experiments and molecular dynamics simulations support our findings that restricting access to the active site is the key to oxygen tolerance, explaining how active site evolution drove a major evolutionary transition. Significance statement Autotrophy (primary production) was the first life strategy on Earth. Before photosynthesis (using solar energy to fix carbon dioxide), life relied on chemical reactions for energy. These chemosynthetic reactions are present in all domains of life, including archaea possessing the most energy-efficient carbon fixation pathway - the 3-hydroxypropionate/4-hydroxybutyrate cycle. This efficiency results from enzyme modifications, including enhanced enzyme stability and catalysis of multiple reactions. We reveal the first structure of aerobic 4-hydroxybutyryl-CoA dehydratase (4HBD) from ammonia-oxidizing archaea. These archaea are among the most abundant organisms on the planet, and their 4HBD active site evolved oxygen tolerance to support aerobic metabolism. This modification can provide further insight into enzyme evolution on early earth, as photosynthesis developed and began oxygenating the atmosphere.

DeMirci, Hasan (ORCID:0000000291355397)↗
DOE OSTI2022

Origin of insulating and nonferromagnetic SrRuO 3 monolayers

The electro-magnetic properties of ultrathin epitaxial ruthenate films have long been the subject of debate. Here we combine experimental with theoretical investigations of (SrTiO 3 ) 5 -(SrRuO 3 ) n -(SrTiO 3 ) 5 (STO 5 -SRO n -STO 5 ) heterostructures with n = 1 and 2 unit cells, including extensive atomic-resolution scanning-transmission-electron-microscopy imaging, electron-energy-loss-spectroscopy chemical mapping, as well as transport and magneto-transport measurements. The experimental data demonstrate that the STO 5 -SRO 2 -STO 5 heterostructure is nearly stoichiometric, metallic, and ferromagnetic with T C ~ 128 K, even though it lacks the characteristic bulk-SRO octahedral tilts and matches the cubic STO structure. In contrast, the STO 5 -SRO 1 -STO 5 heterostructure features Ru-Ti intermixing in the RuO 2 layer, also without octahedral tilts, but is accompanied by a loss of metallicity and ferromagnetism. Density-functional-theory calculations show that stoichiometric n = 1 and n = 2 heterostructures are metallic and ferromagnetic with no octahedral tilts, while non-stoichiometry in the Ru sublattice in the n = 1 case opens an energy gap and induces antiferromagnetic ordering. Furthermore, the results indicate that the observed non-stoichiometry is the cause of the observed loss of metallicity and ferromagnetism in the n = 1 case.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Humble planar defects in SiGe nanopillars

We report a {001} planar defect found in SiGe nanopillars. The defect structure, determined by atomic-resolution electron microscopy, matches the Humble defect model proposed for diamond. We also investigate several possible variants of the Humble structure using first-principles calculations and find that the one lowest in energy is in agreement with the scanning transmission electron microscope images. The pillar composition has been analyzed with electron energy loss spectroscopy, which hints at how the defect is formed. Our results show that the structure and formation process of defects in nanostructured group IV semiconductors can be different from their bulk counterparts.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Emergence of Topologically Nontrivial Spin-Polarized States in a Segmented Linear Chain

The synthesis of new materials with novel or useful properties is one of the most important drivers in the fields of condensed matter physics and materials science. Discoveries of this kind are especially significant when they point to promising future basic research and applications. Van der Waals bonded materials comprised of lower-dimensional building blocks have been shown to exhibit emergent properties when isolated in an atomically thin form. Here, we report the discovery of a transition metal chalcogenide in a heretofore unknown segmented linear chain form, where basic building blocks each consisting of two hafnium atoms and nine tellurium atoms (Hf 2 Te 9 ) are van der Waals bonded end-to-end. First-principle calculations based on density functional theory reveal striking crystal-symmetry-related features in the electronic structure of the segmented chain, including giant spin splitting and nontrivial topological phases of selected energy band states. In this work, atomic-resolution scanning transmission electron microscopy reveals single segmented Hf 2 Te 9 chains isolated within the hollow cores of carbon nanotubes, with a structure consistent with theoretical predictions. Van der Waals-bonded segmented linear chain transition metal chalcogenide materials could open up new opportunities in low-dimensional, gate-tunable, magnetic and topological crystalline systems.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Inversion of Many-Beam Bragg Intensities for Phasing by Iterated Projections: Removal of Multiple Scattering Artifacts from Diffraction Data

An iterated projection algorithm (N-Phaser) is developed that reconstructs a scattering potential from N-beam multiple Bragg scattered intensities. The method may be used to eliminate multiple scattering artifacts from electron diffraction data, solving the phase problem and increasing the thicknesses of samples used in materials science, solid-state chemistry, and small molecule crystallography. For high-energy transmission electron diffraction, we show that the algorithm recovers accurate complex structure factors from a wide range of thicknesses, orientations, and relativistic beam energies, and does not require known thickness or atomic-resolution data if sufficient multiple scattering occurs. Furthermore, extensions to Cryo-electron microscopy and Micro-electron diffraction are suggested.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Local strain-dependent electronic structure and perpendicular magnetic anisotropy of a MnGaN 2D magnetic monolayer

Local strain-dependent spin-polarized electronic structure of a two-dimensional (2D) magnetic layer is an exciting property for practical applications. For example, it holds the promise for advanced ultrathin spintronic nanodevices with customized electronic and magnetic properties by local strain engineering. Here, we demonstrate that the spin-polarized electronic structure of a 2D manganese gallium nitride (MnGaN-2D) magnetic monolayer is sensitive to intrinsic local lattice strain, as proven by first-principles calculations and indicated by scanning tunneling spectroscopy measurements. Atomic resolution images reveal a highly non-Gaussian lattice spacing/strain distribution, while the spectroscopy reveals variations in the electronic density of states. Simulations of the MnGaN-2D monolayer based on first-principles calculations, including both isotropic and anisotropic strains, confirm a highly strain-dependent manganese partial density of states. Spin-orbit coupling is included which indicates either out-of-plane perpendicular magnetic anisotropy (PMA) or in-plane magnetic anisotropy, dependent on the type of strain whether compressive or tensile, suggesting that MnGaN-2D is magnetoelastic. The MnGaN-2D PMA is further supported by superconducting quantum interference device magnetometry measurements which reveal a high spin polarization of ~ 79 % at room temperature.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2021

Interplay between charge ordering and geometric ferroelectricity in LuFe 2 O 4 /LuFeO 3 superlattices

Oxide superlattices have drawn great attentions owing to the intriguing coupling among elastic, electrical, and magnetic orderings at the interfaces and the emerging of improper ferroelectricity. Here, superlattices composed of hexagonal LuFeO 3 (h-LuFeO 3 ) and LuFe 2 O 4 are investigated via density functional theory calculations. h-LuFeO 3 is a well-known multiferroic material that is stable only in thin-film or doped bulk state, while LuFe 2 O 4 is a charge ordered material where the existence of ferroelectricity is still in controversy. We have found that the charge ordering (CO) induced polarizations in LuFe 2 O 4 layers coexist with the geometric polarizations in h-LuFeO 3 layers in the (LuFe 2 O 4 ) m /(LuFeO 3 ) n superlattices with different periodicities, and the ferroelectric states are generally preferred over the antiferroelectric states for LuFe 2 O 4 in superlattices. The out-of-plane polarizations in h-LuFeO 3 and LuFe 2 O 4 layers tend to be aligned in parallel, and the overall polarization increases with the ratio of h-LuFeO 3 . The influence of layered polarizations on the local electrostatic potential is not significant except the detected small trend caused by the CO-induced polarization within a FeO bilayer. Besides, the local electronic structures show that the Fermi level position in a certain layer can be tuned by the valences of Fe in this layer and the polarization distributions in neighboring layers. LuFe 2 O 4 layers sandwiched between thick h-LuFeO 3 layers are more susceptible. The calculated configurations of the superlattices are supported by atomic-resolution transmission electron microscopy experiments. Our results pave a way for tunable ferroelectricity in superlattice systems and create a new playground for manipulating the coupling between various degrees of freedom.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗