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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 469 records · Page 26
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Crystal structure of the CoV-Y domain of SARS-CoV-2 nonstructural protein 3

Abstract Replication of the coronavirus genome starts with the formation of viral RNA-containing double-membrane vesicles (DMV) following viral entry into the host cell. The multi-domain nonstructural protein 3 (nsp3) is the largest protein encoded by the known coronavirus genome and serves as a central component of the viral replication and transcription machinery. Previous studies demonstrated that the highly-conserved C-terminal region of nsp3 is essential for subcellular membrane rearrangement, yet the underlying mechanisms remain elusive. Here we report the crystal structure of the CoV-Y domain, the most C-terminal domain of the SARS-CoV-2 nsp3, at 2.4 Å-resolution. CoV-Y adopts a previously uncharacterized V-shaped fold featuring three distinct subdomains. Sequence alignment and structure prediction suggest that this fold is likely shared by the CoV-Y domains from closely related nsp3 homologs. NMR-based fragment screening combined with molecular docking identifies surface cavities in CoV-Y for interaction with potential ligands and other nsps. These studies provide the first structural view on a complete nsp3 CoV-Y domain, and the molecular framework for understanding the architecture, assembly and function of the nsp3 C-terminal domains in coronavirus replication. Our work illuminates nsp3 as a potential target for therapeutic interventions to aid in the on-going battle against the COVID-19 pandemic and diseases caused by other coronaviruses.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Controlling superconductivity of CeIrIn 5 microstructures by substrate selection

Superconductor/metal interfaces are usually fabricated in heterostructures that join these dissimilar materials. A conceptually different approach has recently exploited the strain sensitivity of heavy-fermion superconductors, selectively transforming regions of the crystal into the metallic state by strain gradients. The strain is generated by differential thermal contraction between the sample and the substrate. Here, we present an improved finite-element model that reliably predicts the superconducting transition temperature in CeIrIn 5 even in complex structures. Different substrates are employed to tailor the strain field into the desired shapes. Using this approach, both highly complex and strained as well as strain-free microstructures are fabricated to validate the model. This enables a high degree of control over the microscopic strain fields and forms the basis for more advanced structuring of superconductors as in Josephson junctions yet also finds natural use cases in any material class in which a modulation of the physical properties on a chip is desirable.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Czochralski Growth and Characterization of a Compositionally Complex Rare Earth Aluminum Garnet Scintillator: (Gd 1/4 Y 1/4 Tb 1/4 Lu 1/4 ) 3 Al 5 O 12 :Ce

Compositionally complex oxides have garnered increasing interest for their enhanced phase stability and tunable functional properties, yet their development as bulk single crystal scintillators remains limited. Herein, we report the Czochralski growth and characterization of (Gd 1/4 Y 1/4 Tb 1/4 Lu 1/4 ) 3 Al 5 O 12 :Ce (GYTLAG), a compositionally complex garnet incorporating four dodecahedrally coordinated principal rare earth elements. The garnet phase was confirmed by powder and single crystal X-ray diffraction, and macroscopic defects are described. X-ray absorption near-edge structure measurements confirm the 3+ oxidation state of all rare earths and support their occupation of the same crystallographic site; white line intensity variations correlate with the anticipated segregation behavior. Elemental segregation is quantified by SEM/EDS and ICP-OES, and a linear trend was established between the segregation coefficient and the difference between each rare earth’s ionic radius (r) and the average ionic radius (AIR) of the dodecahedral site. This trend offers a predictive framework for compositional control in future REAG crystals grown by the Czochralski method. Photoluminescence and radioluminescence measurements reveal both Ce 3+ and Tb 3+ emission. Scintillation pulses exhibit four-component decay with dominant ~230 µs and ~1.2 ms components, and the light yield is estimated to be up to 43,000 ph/MeV under 137Cs γ-ray excitation. GYTLAG also demonstrates a strong radioluminescence efficiency and 50% lower afterglow at 20 ms compared to a LuAG:Ce reference, underscoring its promise for scintillator applications.

Compositionally complex oxide, high entropy oxide,↗
DOE OSTI2022

First-Principles Phonon Quasiparticle Theory Applied to a Strongly Anharmonic Halide Perovskite

Understanding and predicting lattice dynamics in strongly anharmonic crystals is one of the long-standing challenges in condensed matter physics. Here we propose a first-principles method that gives accurate quasiparticle (QP) peaks of the phonon spectrum with strong anharmonic broadening. On top of the conventional first-order self-consistent phonon (SC1) dynamical matrix, the proposed method incorporates frequency renormalization effects by the bubble self-energy within the QP approximation. We apply the developed methodology to the strongly anharmonic α-CsPbBr 3 that displays phonon instability within the harmonic approximation in the whole Brillouin zone. While the SC1 theory significantly underestimates the cubic-to-tetragonal phase transition temperature (T c ) by more than 50%, we show that our approach yields T c = 404–423 K, in excellent agreement with the experimental value of 403 K. Furthermore, we also demonstrate that an accurate determination of QP peaks is paramount for quantitative prediction and elucidation of phonon linewidth.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Structures and Mechanisms of a Novel Bacterial Transport System for Fatty Acids

Abstract Bacterial acquisition of metabolites is largely facilitated by transporters with unique substrate scopes. The tripartite ATP‐independent periplasmic (TRAP) transporters comprise a large family of bacterial proteins that facilitate the uptake of a variety of small molecules. It has been reported that some TRAP systems encode a fourth protein, the T component. The T‐component, or TatT, is predicted to be a periplasmic‐facing lipoprotein that enables the uptake of metabolites from the outer membrane. However, no substrates were revealed for any TatT and their functional role(s) remained enigmatic. We recently identified a homolog in Methylococcus capsulatus that binds to sterols, and herein, we report two additional homologs that demonstrate a preference for long‐chain fatty acids. Our bioinformatics, quantitative analyses of protein‐ligand interactions, and high‐resolution crystal structures suggest that TatTs might facilitate the trafficking of hydrophobic or lipophilic substrates and represent a new class of bacterial lipid and fatty acid transporters.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Enhancing Paraoxon Binding to Organophosphorus Hydrolase Active Site

Organophosphorus hydrolase (OPH) is a metalloenzyme that can hydrolyze organophosphorus agents resulting in products that are generally of reduced toxicity. The best OPH substrate found to date is diethyl p-nitrophenyl phosphate (paraoxon). Most structural and kinetic studies assume that the binding orientation of paraoxon is identical to that of diethyl 4-methylbenzylphosphonate, which is the only substrate analog co-crystallized with OPH. In the current work, we used a combined docking and molecular dynamics (MD) approach to predict the likely binding mode of paraoxon. Then, we used the predicted binding mode to run MD simulations on the wild type (WT) OPH complexed with paraoxon, and OPH mutants complexed with paraoxon. Additionally, we identified three hot-spot residues (D253, H254, and I255) involved in the stability of the OPH active site. We then experimentally assayed single and double mutants involving these residues for paraoxon binding affinity. The binding free energy calculations and the experimental kinetics of the reactions between each OPH mutant and paraoxon show that mutated forms D253E, D253E-H254R, and D253E-I255G exhibit enhanced substrate binding affinity over WT OPH. Interestingly, our experimental results show that the substrate binding affinity of the double mutant D253E-H254R increased by 19-fold compared to WT OPH.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

The E. coli L‐asparaginase V27T mutant: structural and functional characterization and comparison with theoretical predictions

Bacterial L‐asparaginases have been used for over 40 years as anticancer drugs. Ardalan et al. ( Medical Hypotheses 112, 7–17, 2018) proposed that the V27T mutant of Escherichia coli type II L‐asparaginase, EcAII(V27T), should display altered biophysical and catalytic properties compared to the wild‐type enzyme, EcAII(wt), rendering it more favourable as a pharmaceutical. They postulated that EcAII(V27T) would exhibit reduced glutaminolytic activity and be more stable compared to EcAII(wt). Their postulates, however, were purely theoretical. Here, we characterized experimentally selected properties of EcAII(V27T). We found asparaginolytic activity of this mutant unchanged, whereas its glutaminolytic activity was fourfold lower compared with EcAII(wt). We did not observe significant differences in stabilities of EcAII(wt) and EcAII(V27T). Crystal structures of the complexes with L‐Asp and L‐Glu showed considerable differences in binding modes of both substrates.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Evolution of Structure and Magnetism in FeCl 2 and FeCl 3 : From Clusters to Monolayers

In this work, we address one of the most fundamental questions in cluster science─how do the structure and properties evolve from clusters to crystals? Using density functional theory (DFT), we focus our study on the evolution of structure and magnetism in iron-chloride systems, from clusters to monolayers. The choice of this system is motivated by the recent experimental confirmation of one of the author’s earlier theoretical prediction that the FeCl 2 cluster is magnetic with a spin magnetic moment of 4 μ B localized at the Fe site, while its dimer, Fe 2 Cl 4 , is antiferromagnetic. Similarly, FeCl 3 cluster is magnetic with a total spin magnetic moment of 5 μ B , with 4 μ B localized at the Fe site and 1 μ B distributed over the Cl sites. The dimer clusters Fe 2 Cl 4 and Fe 2 Cl 6 have an antiferromagnetic ground state, and upon Li-functionalization, both can be magnetically transformed from antiferromagnetic to ferromagnetic states. In contrast, FeCl 2 and FeCl 3 monolayers exhibit different magnetic ground states in their periodic forms: FeCl 2 is ferromagnetic (FM), but in FeCl 3 , the antiferromagnetic (AFM) and FM states are energetically nearly degenerate. Such a difference arises due to the different chemical coordination of the Fe atoms with the Cl atoms, caused by their different oxidation states, which is +2 in FeCl 2 and +3 in FeCl 3 , respectively. Interestingly, Li-functionalization allows both FeCl 3 and FeCl 2 monolayers to be ferromagnetic. Our study highlights that several, but not all, electronic and magnetic characteristics of isolated clusters are preserved in the extended periodic structures. This systematic investigation of iron-halide clusters is expected to inspire further experimental and theoretical exploration into the magnetism of other transition metal halides.

cluster chemistry↗
DOE OSTI2022

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro

Abstract In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO 226–234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Low-dimensional physics of clay particle size distribution and layer ordering

Abstract Clays are known for their small particle sizes and complex layer stacking. We show here that the limited dimension of clay particles arises from the lack of long-range order in low-dimensional systems. Because of its weak interlayer interaction, a clay mineral can be treated as two separate low-dimensional systems: a 2D system for individual phyllosilicate layers and a quasi-1D system for layer stacking. The layer stacking or ordering in an interstratified clay can be described by a 1D Ising model while the limited extension of individual phyllosilicate layers can be related to a 2D Berezinskii–Kosterlitz–Thouless transition. This treatment allows for a systematic prediction of clay particle size distributions and layer stacking as controlled by the physical and chemical conditions for mineral growth and transformation. Clay minerals provide a useful model system for studying a transition from a 1D to 3D system in crystal growth and for a nanoscale structural manipulation of a general type of layered materials.

42 ENGINEERING↗
DOE OSTI2021

Pressure-induced superconductivity in the hydrogen-rich pseudobinary CaB - H n compounds

Here, the crystal structures of CaB – Hn compounds with n = 1 – 12 in a pressure range of 50–300 GPa were studied using the genetic algorithm method and first-principles density-function theory calculations. Stable structures with stoichiometry of CaB H 6 and CaB H 7 were predicted in different pressure range. BH 4 , BH 5 , and BH 6 units were found to be the main motifs in these compounds. Moreover, metastable Imm2 CaB H 7 is dynamically stable above 180 GPa, with the formation of tetrahedral BH 4 unit surrounded by Ca atom and H 3 unit. Electron-phonon coupling (EPC) calculations reveal that the superconducting properties are closely related to the strong hydrogen-boron bonding of the BH 4 unit in Imm2, and T c can reach ~200 K at 200 GPa. As the major units, BH 4 , BH 5 , and BH 6 units exist in the Imm2, P 2 , and P2 1 /m phases of CaB H 7 at 300 GPa, respectively; the corresponding EPC parameter λ decreases with the increase of hydrogen content in CaB H 7 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
NASA NTRS1974

Effect of Various Material Properties on the Adhesive Stage of Fretting

Various properties of metals and alloys were studied with respect to their effect on the initial stage of the fretting process, namely adhesion. Crystallographic orientation, crystal structure, interfacial binding energies of dissimiliar metal, segregation of alloy constituents and the nature and structure of surface films were found to influence adhesion. High atomic density, low surface energy grain orientations exhibited lower adhesion than other orientations. Knowledge of interfacial surface binding energies assists in predicting adhesive transfer and wear. Selective surface segregation of alloy constituents accomplishes both a reduction in adhesion and improved surface oxidation characteristics. Equivalent surface coverages of various adsorbed species indicate that some are markedly more effective in inhibiting adhesion than others.

Buckley, D. H.↗
DOE OSTI2024

Grain boundary self-diffusion and point defect interactions in α -U via molecular dynamics

Though metallic U-Zr fuel has been used in nuclear reactors since the 1960s, many of its fundamental and thermodynamic properties are still unknown. The a-U phase, which has a highly anisotropic crystal structure and physical properties, is present in U-Zr fuel. The character and behavior of a-U grain boundaries will strongly impact fuel thermophysical performance under irradiation. Here, we study the interaction of point defects with grain boundaries, diffusion along grain boundaries, and the predicted diffusional creep behavior of a-U via molecular dynamics. We calculate the segregation energy of vacancies and interstitials to grain boundaries and quantify the biased sink strength of the grain boundaries, and observe that this sink strength is not strongly dependent on the grain boundary orientation. We also find that grain boundary diffusivity is strongly dependent on the grain boundary energy and grain boundary orientation. The presence of point defects within the grain boundary can induce diffusion in grain boundaries with low formation energies and can enhance diffusion in high-energy grain boundaries. We also find that diffusional creep of a-U at prototypical metallic fuel operation conditions is extremely high and could help explain observed metallic fuel swelling behaviors.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2023

Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin

The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub 2 ) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub 2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub 2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub 2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

DONUT: physics-aware machine learning for real-time X-ray nanodiffraction analysis

Coherent X-ray scattering techniques are critical for investigating the fundamental structural properties of materials at the nanoscale. While advancements have made these experiments more accessible, real-time analysis remains a significant bottleneck, often hindered by artifacts and computational demands. In scanning X-ray nanodiffraction microscopy, which is widely used to spatially resolve structural heterogeneities, this challenge is compounded by the convolution of the divergent beam with the sample’s local structure. To address this, we introduce DONUT (Diffraction with Optics for Nanobeam by Unsupervised Training), a physics-aware neural network designed for the rapid and automated analysis of nanobeam diffraction data. By incorporating a differentiable geometric diffraction model directly into its architecture, DONUT learns to predict crystal lattice strain and orientation in real-time. Crucially, this is achieved without reliance on labeled datasets or pre-training, overcoming a fundamental limitation for supervised machine learning in X-ray science. We demonstrate experimentally that DONUT accurately extracts all features within the data over 200 times more efficiently than conventional fitting methods.

Materials science↗
DOE OSTI2022

A high-dimensional neural network potential for molecular dynamics simulations of condensed phase nickel and phase transitions

A high-dimensional neural network interatomic potential was developed and used in molecular dynamics simulations of condensed phase Ni and Ni systems with liquid–solid phase coexistence. The reference data set was generated by sampling the potential energy surface over a broad temperature-pressure domain using ab initio MD simulations to train a unified potential. Excellent agreement was achieved between bulk face-centered cubic nickel thermal expansion simulations and relevant experimental data. The same potential also yields accurate structures and diffusivities in the liquid state. The phase transition between liquid and solid phases was simulated using the two-phase interface method. The predicted melting point temperature is within a few kelvins of the literature value. Here, the general methodology could be applied to describe crystals with much more complex phase behaviors.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Functional soft materials from blue phase liquid crystals

Blue phase (BP) liquid crystals are chiral fluids wherein millions of molecules self-assemble into cubic lattices that are on the order of hundred nanometers. As the unit cell sizes of BPs are comparable to the wavelength of light, they exhibit selective Bragg reflections in the visible. The exploitation of the photonic properties of BPs for technological applications is made possible through photopolymerization, a process that renders mechanical robustness and thermal stability. We review here the preparation and characterization of stimuli-responsive, polymeric photonic crystals based on BPs. We highlight recent studies that demonstrate the promise that polymerized BP photonic crystals hold for colorimetric sensing and dynamic light control. We review using Landau–de Gennes simulations for predicting the self-assembly of BPs and the potential for using theory to guide experimental design. Finally, opportunities for using BPs to synthesize new soft materials, such as highly structured polymer meshes, are discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2025

DONUT: Physics-aware Machine Learning for Real-time X-ray Nanodiffraction Analysis

SF-25-088 Coherent X-ray scattering techniques are critical for investigating the fundamental structural properties of materials at the nanoscale. While advancements have made these experiments more accessible, real-time analysis remains a significant bottleneck, often hindered by artifacts and computational demands. In scanning X-ray nanodiffraction microscopy, which is widely used to spatially resolve structural heterogeneities, this challenge is compounded by the convolution of the divergent beam with the sample’s local structure. To address this, we introduce DONUT (Diffraction with Optics for Nanobeam by Unsupervised Training), a physics-aware neural network designed for the rapid and automated analysis of nanobeam diffraction data. By incorporating a differentiable geometric diffraction model directly into its architecture, DONUT learns to predict crystal lattice strain and orientation in real-time. Crucially, this is achieved without reliance on labeled datasets or pre-training, overcoming a fundamental limitation for supervised machine learning in X-ray science. We demonstrate experimentally that DONUT accurately extracts all features within the data over 200 times more efficiently than conventional fitting methods.

Zhou, Tao [Argonne National Laboratory (ANL), Argo↗