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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Microstructural development in DED stainless steels: applying welding models to elucidate the impact of processing and alloy composition

Austenitic stainless steel microstructures produced by directed energy deposition (DED)are analogous to those developed during welding, particularly high energy density welding. To better understand microstructural development during DED, theories of microstructural evolution,which have been established to contextualize weld microstructures, are applied in this study to microstructural development in DED austenitic stainless steels. Phenomenological welding models that describe the development of oxide inclusions, compositional microsegregation, ferrite,matrix austenite grains, and dislocation substructures are utilized to clarify microstructural evolution during deposition of austenitic stainless steels. Two different alloys, 304L and 316L, arecompared to demonstrate the broad applicability of this framework for understanding microstmctural development during the DED process. Despite differences in grain morphology and solidification mode for these two alloys (which can be attributed to compositional differences),similar tensile properties are achieved. It is the fine-scale compositional segregation and dislocation structures that ultimately determine the strength of these materials. The evolution of microsegregation and dislocation structures is shown to be dependent on the rapid solidification and thermomechanical history of the DED processing method and not the composition of the starting material.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Electronic reconstruction at the polar (111)-oriented oxide interface

Atomically flat (111) interfaces between insulating perovskite oxides provide a landscape for new electronic phenomena. For example, the graphene-like coordination between interfacial metallic ion layer pairs can lead to topologically protected states [Xiao et al., Nat. Commun. 2, 596 (2011) and A. Rüegg and G. A. Fiete, Phys. Rev. B 84, 201103 (2011)]. The metallic ion/metal oxide bilayers that comprise the unit cell of the perovskite (111) heterostructures require the interface to be polar, generating an intrinsic polar discontinuity [Chakhalian et al., Nat. Mater. 11, 92 (2012)]. Here, we investigate epitaxial heterostructures of (111)-oriented LaAlO 3 /SrTiO 3 (LAO/STO). We find that during heterostructure growth, the LAO overlayer eliminates the structural reconstruction of the STO (111) surface with an electronic reconstruction, which determines the properties of the resulting two-dimensional conducting gas. This is confirmed by transport measurements, direct determination of the structure and atomic charge from coherent Bragg rod analysis, and theoretical calculations of electronic and structural characteristics. Interfacial behaviors of the kind discussed here may lead to new growth control parameters useful for electronic devices.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Crystal and Electronic Structures of A 2 NaIO 6 Periodate Double Perovskites (A = Sr, Ca, Ba): Candidate Wasteforms for I-129 Immobilization

The synthesis, structure, and thermal stability of the periodate double perovskites A 2 NaIO 6 (A= Ba, Sr, Ca) were investigated in the context of potential application for the immobilization of radioiodine. A combination of X-ray diffraction and neutron diffraction, Raman spectroscopy, and DFT simulations were applied to determine accurate crystal structures of these compounds and understand their relative stability. The compounds were found to exhibit rock-salt ordering of Na and I on the perovskite B-site; Ba 2 NaIO 6 was found to adopt the Fm- 3 m aristotype structure, whereas Sr 2 NaIO 6 and Ca 2 NaIO 6 adopt the P 2 1 / n hettotype structure, characterized by cooperative octahedral tilting. DFT simulations determined the Fm- 3 m and P 2 1 / n structures of Ba 2 NaIO 6 to be energetically degenerate at room temperature, whereas diffraction and spectroscopy data evidence only the presence of the Fm- 3 m phase at room temperature, which may imply an incipient phase transition for this compound. The periodate double perovskites were found to exhibit remarkable thermal stability, with Ba 2 NaIO 6 only decomposing above 1050 °C in air, which is apparently the highest recorded decomposition temperature so far recorded for any iodine bearing compound. As such, these compounds offer some potential for application in the immobilization of iodine-129, from nuclear fuel reprocessing, with an iodine incorporation rate of 25–40 wt%. The synthesis of these compounds, elaborated here, is also compatible with both current conventional and future advanced processes for iodine recovery from the dissolver off-gas.

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

Epitope topography of agonist antibodies to the checkpoint inhibitory receptor BTLA

B and T lymphocyte attenuator (BTLA) is an attractive target for a new class of therapeutics that attempt to rebalance the immune system by agonizing checkpoint inhibitory receptors (CIRs). Herpesvirus entry mediator (HVEM) binds BTLA in both trans- and cis-orientations. We report here the development and structural characterization of three humanized BTLA agonist antibodies, 22B3, 25F7, and 23C8. We determined the crystal structures of the antibody-BTLA complexes, showing that these antibodies bind distinct and non-overlapping epitopes of BTLA. While all three antibodies activate BTLA, 22B3 mimics HVEM binding to BTLA and shows the strongest agonistic activity in functional cell assays and in an imiquimod-induced mouse model of psoriasis. 22B3 is also capable of modulating HVEM signaling through the BTLA-HVEM cis-interaction. The data obtained from crystal structures, biochemical assays, and functional studies provide a mechanistic model of HVEM and BTLA organization on the cell surface and informed the discovery of a highly active BTLA agonist.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Hyperfine spectroscopy and laser cooling of the fermionic isotopes 47 Ti and 49 Ti

Here, we report on magneto-optical trapping of the two fermionic isotopes of atomic titanium, 47 Ti and 49 Ti . Unlike the even mass-number isotopes, which were recently laser cooled, 47 Ti and 49 Ti have nonzero nuclear spins and, consequently, their atomic levels are split by hyperfine structure. Combining and comparing theoretical calculations and atomic beam-spectroscopy measurements, we determine the hyperfine structures and isotope shifts of the 3⁢𝑑 2 ⁢4⁢𝑠 2 𝑎 3 ⁢𝐹 4 → 3⁢𝑑 2 ⁢( 3 𝑃)⁢4⁢𝑠⁢4⁢𝑝⁢( 3 𝑃 𝑜 ) 𝑦 5 ⁢𝐷$^o_4$ optical-pumping transition at optical wavelength 391 nm and the 3⁢𝑑 3 ⁢(4𝐹)⁢4⁢𝑠 𝑎 5 ⁢𝐹 5 → 3⁢𝑑 3 ⁢( 4 𝐹)⁢4⁢𝑝 𝑦 5 ⁢𝐺$^𝑜_6$ laser-cooling transition at wavelength 498 nm. With this information, we produce magneto-optical traps of both 47 Ti and 49 Ti by applying two additional tones of light to repump atoms to the maximum-spin states on the laser-cooling transition. Directly loading from the atomic flux of a titanium sublimation pump, we produce 47 Ti and 49 Ti traps with 731(190) and 1142(240) atoms, and with lifetimes of 330⁢(15) and 310⁢(8)⁢ ms, respectively.

atomic spectra↗
DOE OSTI2021

Structural basis for antibody binding to adenylate cyclase toxin reveals RTX linkers as neutralization-sensitive epitopes

RTX leukotoxins are a diverse family of prokaryotic virulence factors that are secreted by the type 1 secretion system (T1SS) and target leukocytes to subvert host defenses. T1SS substrates all contain a C-terminal RTX domain that mediates recruitment to the T1SS and drives secretion via a Brownian ratchet mechanism. Neutralizing antibodies against the Bordetella pertussis adenylate cyclase toxin, an RTX leukotoxin essential for B . pertussis colonization, have been shown to target the RTX domain and prevent binding to the α M β 2 integrin receptor. Knowledge of the mechanisms by which antibodies bind and neutralize RTX leukotoxins is required to inform structure-based design of bacterial vaccines, however, no structural data are available for antibody binding to any T1SS substrate. Here, we determine the crystal structure of an engineered RTX domain fragment containing the α M β 2 -binding site bound to two neutralizing antibodies. Notably, the receptor-blocking antibodies bind to the linker regions of RTX blocks I–III, suggesting they are key neutralization-sensitive sites within the RTX domain and are likely involved in binding the α M β 2 receptor. As the engineered RTX fragment contained these key epitopes, we assessed its immunogenicity in mice and showed that it elicits similar neutralizing antibody titers to the full RTX domain. The results from these studies will support the development of bacterial vaccines targeting RTX leukotoxins, as well as next-generation B . pertussis vaccines.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Single-Cell Metabolomics with Rapid Determination of Chemical Formulas from Isotopic Fine Structures

Metabolomic measurements can provide functional readouts of cellular states and phenotypes. Here, we present a protocol for single-cell metabolomics that permits direct untargeted detection of a broad number of metabolites under ambient conditions, without the need for sample processing, and with high confidence in the discovery and identification of the molecular formulas for detected metabolites. This protocol describes combining fiber-based laser ablation electrospray ionization (f-LAESI) with a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer (21T-FTICR-MS) to obtain high confidence molecular formula information about detected metabolites. The f-LAESI source utilizes mid-infrared laser ablation through a sharp optical fiber tip, affording direct ambient analysis of cells without the need for sample processing. Using the 21T-FTICR-MS as a mass analyzer enabled measurement of the isotopic fine structure (IFS) for numerous metabolites simultaneously from single cells, and the IFSs were in turn computationally processed to rapidly determine the corresponding elemental compositions. This metabolomics technique complements other single cell omics measurement methods, helping to resolve complex molecular interactions that take place within cells unattainable from single cell transcriptomic and proteomics methods.

mass spectrometry, FTICR, FTMS, ultrahigh mass res↗
DOE OSTI2021

Optimized structure and electronic band gap of monolayer GeSe from quantum Monte Carlo methods

Here, we have used highly accurate quantum Monte Carlo methods to determine the chemical structure and electronic band gaps of monolayer GeSe. Two-dimensional (2D) monolayer GeSe has received a great deal of attention due to its unique thermoelectric, electronic, and optoelectronic properties with a wide range of potential applications. Density functional theory (DFT) methods have usually been applied to obtain optical and structural properties of bulk and 2D GeSe. For the monolayer, DFT typically yields a larger band-gap energy than for bulk GeSe but cannot conclusively determine if the monolayer has a direct or indirect gap. Moreover, the DFT-optimized lattice parameters and atomic coordinates for monolayer GeSe depend strongly on the choice of approximation for the exchange-correlation functional, which makes the ideal structure-and its electronic properties-unclear. In order to obtain accurate lattice parameters and atomic coordinates for the monolayer, we use a surrogate Hessian-based parallel line search within diffusion Monte Carlo to fully optimize the GeSe monolayer structure. The DMC-optimized structure is different from those obtained using DFT, as are calculated band gaps. The potential energy surface has a shallow minimum at the optimal structure. This, combined with the sensitivity of the electronic structure to strain, suggests that the optical properties of monolayer GeSe are highly tunable by strain.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Ni( II )-binding affinity of Cc NikZ-II and its homologs: the role of the HH -prong and variable loop revealed by structural and mutational studies

Extracytoplasmic Ni(II)-binding proteins (NiBPs) are molecular shuttles involved in cellular nickel uptake. Here, we determined the crystal structure of apo CcNikZ-II at 2.38 Å, which revealed a Ni(II)-binding site comprised of the double His (HH-)prong (His511, His512) and a short variable (v-)loop nearby (Thr59-Thr64, TEDKYT). Mutagenesis of the site identified Glu60 and His511 as critical for high affinity Ni(II)-binding. Phylogenetic analysis showed 15 protein clusters with two groups containing the HH-prong. Metal-binding assays with 11 purified NiBPs containing this feature yielded higher Ni(II)-binding affinities. Replacement of the wild type v-loop with those from other NiBPs improved the affinity by up to an order of magnitude. This work provides molecular insights into the determinants for Ni(II) affinity and paves way for NiBP engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

RCSB protein data Bank: Next‐generation advanced search for exploration of experimental structures and computed structure models

Abstract The Protein Data Bank (PDB), established in 1971, is the primary global, open‐access archive for experimentally determined 3D macromolecular structures (proteins, RNA, DNA). The research‐focused RCSB.org web‐portal provides access to these data alongside more than one million machine‐learning‐predicted structure models, greatly expanding the available structural landscape. Rapid growth of both experimental and computational structures has increased the need for powerful yet accessible search tools that serve a broad and diverse scientific community. Herein, we describe a redesigned RCSB Protein Data Bank RCSB.org Advanced Search capability that supports intuitive discovery of 3D structures through a unified interface. This interface integrates annotation‐, sequence‐, and 3D structure‐based searches, embeds an interactive 3D viewer, and incorporates curated biological knowledge, such as catalytic site definitions from Mechanism and Catalytic Site Atlas and ligand‐guided structural motifs, for constructing geometry‐driven queries. A new Chemical Search tool allows definition of chemical queries via an integrated drawing tool or standard identifiers, seamlessly combining them with annotation filters. By allowing query definition directly within spatial and chemical contexts, these search interfaces reduce the need for detailed knowledge of residue numbering, chain identifiers, or external cheminformatics software. This capability enables efficient exploration of structures, chemical diversity, and structure–function relationships across all life domains. The redesigned interfaces can be accessed directly at rcsb.org/search/advanced for Advanced Search and rcsb.org/search/chemical for Chemical Search.

Rose, Yana [Research Collaboratory for Structural ↗
DOE OSTI2022

The crystal structure of Vibrio cholerae (6-4) photolyase reveals interactions with cofactors and a DNA-binding region

Photolyases (PLs) reverse UV-induced DNA damage using blue light as an energy source. Of these PLs, (6-4) PLs repair (6-4)-lesioned photoproducts. We recently identified a gene from Vibrio cholerae (Vc) encoding a (6-4) PL, but structural characterization is needed to elucidate specific interactions with the chromophore cofactors. Here, we determined the crystal structure of Vc (6-4) PL at 2.5 Å resolution. Our high-resolution structure revealed that the two well-known cofactors, flavin adenine dinucleotide and the photoantenna 6,7-dimethyl 8-ribityl-lumazin (DMRL), stably interact with an α-helical and an α/β domain, respectively. Additionally, the structure has a third cofactor with distinct electron clouds corresponding to a [4Fe-4S] cluster. Moreover, we identified that Asp106 makes a hydrogen bond with water and DMRL, which indicates further stabilization of the photoantenna DMRL within Vc (6-4) PL. Further analysis of the Vc (6-4) PL structure revealed a possible region responsible for DNA binding. The region located between residues 478 to 484 may bind the lesioned DNA, with Arg483 potentially forming a salt bridge with DNA to stabilize further the interaction of Vc (6-4) PL with its substrate. Our comparative analysis revealed that the DNA lesion could not bind to the Vc (6-4) PL in a similar fashion to the Drosophila melanogaster (Dm, (6-4)) PL without a significant conformational change of the protein. The 23rd helix of the bacterial (6-4) PLs seems to have remarkable plasticity, and conformational changes facilitate DNA binding. In conclusion, our structure provides further insight into DNA repair by a (6-4) PL containing three cofactors.

(6-4) lesioned photoproduct↗
DOE OSTI2022

Structure of maize BZR1-type β-amylase BAM8 provides new insights into its noncatalytic adaptation

Plant β-amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (β/α) 8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. Further, the noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of β-amylase domain of Zea mays BAM8/BES1/BZR1-5 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.

59 BASIC BIOLOGICAL SCIENCES↗