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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

A Trichomonas vaginalis C2-XYPPX-repeat protein with a structured C2 domain displaying dampened flexibility upon binding calcium

C2 domains are ubiquitous membrane-binding modules of ∼130 residues in eukaryotes that are often associated with proteins involved in membrane trafficking and lipid modification. The genome of Trichomonas vaginalis, the most common, non-viral, sexually transmitted human pathogen, encodes eight genes that contain a N-terminal C2 module linked to a XYPPX-repeat domain of more than four XYPPX repeats (C2-XYPPX). While the function of the XYPPX-repeat domain remains unknown, its multiple association with C2 domains in T. vaginalis suggests it is important. Here, the C2 domain from one of these C2-XYPPX-repeat proteins, Tv-C2-1, was structurally and physically characterized using X-ray crystallography and NMR spectroscopy. The crystal structure for Tv-C2-1 shows that this domain shares a fold common to all C2 domains, a compact Greek-key motif composed of eight anti-parallel β-strands in the type-2 topology. An NMR chemical shift perturbation study with Ca 2+ showed that Tv-C2-1 bound two Ca 2+ atoms primarily via two loops (loop-1 and loop-3) on the predicted calcium binding face of the protein with K d s of 58.0 ± 0.1 μM and 232 ± 6 μM. Estimations of the overall rotational correlation time, τ c , in the apo (11.1 ns) and Ca 2+ -bound (9.2 ns) state suggests the protein becomes more compact upon Ca 2+ binding, consistent with a decrease in dynamics in loop-3 and marginally in loop-1 suggested by amide 15 N heteronuclear steady-state { 1 H}- 15 N NOEs. Showing Tv-C2-1 binds calcium and adopts a compact Greek-key motif structure, two primary features of C2 domains, suggests understanding the function of the XYPPX-repeat domain may be warranted.

NMR spectroscopy↗
DOE OSTI2024

Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR

Nuclear receptors are ligand-activated transcription factors that can often be useful drug targets. Unfortunately, ligand promiscuity leads to two-thirds of receptors remaining clinically untargeted. PXR is a nuclear receptor that can be activated by diverse compounds to elevate metabolism, negatively impacting drug efficacy and safety. This presents a barrier to drug development because compounds designed to target other proteins must avoid PXR activation while retaining potency for the desired target. This problem could be avoided by using PXR antagonists, but these compounds are rare, and their molecular mechanisms remain unknown. Here, we report structurally related PXR-selective agonists and antagonists and their corresponding co-crystal structures to describe mechanisms of antagonism and selectivity. Structural and computational approaches show that antagonists induce PXR conformational changes incompatible with transcriptional coactivator recruitment. These results guide the design of compounds with predictable agonist/antagonist activities and bolster efforts to generate antagonists to prevent PXR activation interfering with other drugs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Molecular dynamics simulations of uranyl and plutonyl cations in a task-specific ionic liquid

Ionic liquids (ILs) are a unique class of solvents with potential applications in advanced separation technologies relevant to the nuclear industry. ILs are salts with low melting points and a wide range of tunable physical properties, such as viscosity, hydrophobiciy, conductivity, and liquidus range. ILs have negligible vapor pressure, are often non-flammable, and can have high thermal stability and a wide electrochemical window, making them attractive for use in separations processes relevant to the nuclear industry. Metal salts generally have a low solubility in ILs; however, by incorporating new functional groups into the IL cation or anion that promote complexation with the metal, the solubility can be greatly increased. One such task-specific ionic liquid (TSIL) is 1-carboxy-N, N, N-trimethylglycine bis(trifluoromethylsulfonyl)imide ([Hbet][Tf 2 N]). Water, which is detrimental for electrochemical separations, is a common impurity in ILs and can coordinate with actinyl cations, particularly in ILs containing only weakly coordinating components. Understanding the behavior of actinides in TSIL/water mixtures on a molecular level is vital for designing improved separations processes. Classical molecular dynamics simulations of uranyl(VI) and plutonyl(VI) in 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf 2 N]) with deprotonated Hbet (betaine) and water have been performed to understand the coordination and dynamics of the actinyl cations. We find that betaine is a much stronger ligand than water and prefers to coordinate the metal in a bidentate manner. Potential of mean force simulations yield a relative free energy for betaine coordination of approximately -120 to -90 kJ/mol in mixtures with water. As the amount of betaine coordinated to the actinide increases, the diffusion coefficient of the actinyl cation decreases. Moreover, the betaine ligand is able to bridge between two metal centers, resulting in dimeric complexes with actinide–actinide distances of ~5 Å. Potential of mean force simulations show that these structures are stable, with relative free energies of up to -40 kJ/mol. The crystal structure for [(UO 2 ) 2 (bet) 6 (H 2 O) 2 ][Tf 2 N] 4 shows that the betaine bridges between two uranium atoms to form dimeric complexes similar to those found in our simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Vibrio MARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy

Vibrio vulnificus causes life-threatening wound and gastrointestinal infections, mediated primarily by the production of a Multifunctional-Autoprocessing Repeats-In-Toxin (MARTX) toxin. The most commonly present MARTX effector domain, the Makes Caterpillars Floppy-like (MCF) toxin, is a cysteine protease stimulated by host adenosine diphosphate (ADP) ribosylation factors (ARFs) to autoprocess. Here, we show processed MCF then binds and cleaves host Ra s-related proteins in b rain (Rab) guanosine triphosphatases within their C-terminal tails resulting in Rab degradation. We demonstrate MCF binds Rabs at the same interface occupied by ARFs. Moreover, we show MCF preferentially binds to ARF1 prior to autoprocessing and is active to cleave Rabs only subsequent to autoprocessing. We then use structure prediction algorithms to demonstrate that structural composition, rather than sequence, determines Rab target specificity. We further determine a crystal structure of aMCF as a swapped dimer, revealing an alternative conformation we suggest represents the open, activated state of MCF with reorganized active site residues. The cleavage of Rabs results in Rab1B dispersal within cells and loss of Rab1B density in the intestinal tissue of infected mice. Collectively, our work describes an extracellular bacterial mechanism whereby MCF is activated by ARFs and subsequently induces the degradation of another small host guanosine triphosphatase (GTPase), Rabs, to drive organelle damage, cell death, and promote pathogenesis of these rapidly fatal infections.

Science & Technology - Other Topics↗
DOE OSTI2025

Effects of chemical disorder and spin-orbit coupling on the electronic-structure and Fermi-surface topology of YbSb-based monopnictides

Here, in this work, we study the influence of disorder on the electronic structure of YbSb—a rare-earth monopnictide featuring a simple rocksalt (B1) crystal structure and a well-defined Fermi-surface topology—by employing first-principles density-functional theory. We focus on chemical disorder introduced through Te and Al doping, selected based on their thermodynamic stability in alloyed configurations, to understand how such perturbations modify the electronic states of YbSb. Our results indicate that Te doping predominantly introduces electronlike states at the 𝑋 and 𝐿 points, while Al doping leads to a suppression of holelike states at Γ, effectively driving the system from a semimetallic state to one characterized by very narrow-gap behavior at Γ. This modulation of the Fermi surface, particularly the reduction of central hole pockets at Γ, plays a central role in altering interpocket scattering—a mechanism critical for tuning quantum transport properties, including superconductivity. This disorder-driven modulation of the Fermi surface, particularly the suppression of central hole pockets at Γ, controls interpocket scattering, which is essential for optimizing quantum transport properties, including superconductivity. Our results show that disorder can be effectively used for engineering band topology, thereby tuning quantum related response through a tailored electronic structure.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Effects of carbon substitution on magnetic properties and magnetocaloric effects in Mn 65-x Ga 17 C 18+x compounds

This study involved the tuning of the magnetic, magnetocaloric, and room-temperature structural properties of Mn 65-x Ga 17 C 18+x (0 ≤ x ≤ 4) compounds prepared using a high-energy ball milling (HEBM) technique. This study indicates that the crystal structure of all the compounds can be described as an anti-perovskite cubic structure with the Pm-3m space group and the crystal cell volume decreases with increasing carbon concentration. The system shows a first-order structural phase transition at a temperature T=T M between two cubic phases having different magnetic structures. The phases are characterized by antiferromagnetic (AFM) and ferromagnetic (FM) -like behavior at low (T < T M ) and high (T M > T) temperature regions, respectively. A suppression of the AFM phase was observed with increasing C concentration. The temperature-induced first-order transitions (FOTs) were found to possess a small thermal hysteresis in the magnetization (~2-3 K) in an applied magnetic field of H = 50 kOe. Magnetic entropy changes estimated from isothermal magnetization curves indicate that the largest value of the magnetic entropy change of |ΔS M | = 2.1 J kg -1 K -1 for x = 4 with ΔH = 50 kOe, with a relative cooling power (RCP) of ~190 J kg -1 . Furthermore, high-energy ball milling (HEBM), a scalable technique, has been demonstrated as a viable method to synthesize magnetocaloric materials with substantial RCP values.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Optical and photoelectric properties of surface barrier diodes based on n- Hg3In2Te6 crystals

The high radiation resistance of Hg3In2Te6 (MIT) single crystals to large doses of ionizing radiation makes devices quite attractive. Such a feature of the crystal structure has not only important advantages, but also causes serious technological difficulties in doping and controlling the specific resistance within the required limits and type of conductivity of single crystals. These technological difficulties create serious problems when creating structures with a potential barrier, especially with a p-n junction. At the moment, there are no publications on the creation of a p-n junction based on MIT. The only alternative is to create a potential barrier such as a Schottky diode or a metal-dielectric-semiconductor structure. This limits the use of MIT to produce, for example, rectifier diodes that can operate at relatively high reverse bias voltages. The typical resistivity of single crystals of MIT of n-type conductivity, which are used for the manufacture of diodes and photodiodes, is approximately equal to ρ≈103-104 Ω×cm. Such a specific resistance leads to a relatively large resistance of the neutral part of the single crystal, which in turn limits the direct currents of the rectifier diodes and significantly limits an important parameter of photodiodes - the dynamic range of the watt-ampere characteristic. This problem arises from the relatively high series resistance of the substrate. For rectifier diodes, this relatively large series resistance leads to a significant forward bias voltage drop, which reduces both the rectification factor and the amount of rectified current. We have already created diodes and photodiodes on Cr/MIT/Cr single crystals with a specific resistance of ρ≈103-104 Ω×cm. The diodes had relatively small dark currents but had the disadvantage of a relatively large specific resistance of the substrate, which we have already discussed above [1,2,3].

Sklyarchuk, V.↗
DOE OSTI2025

Structural determinants for pH-dependent activation of a plant metacaspase

Arabidopsis thaliana metacaspase 9 (AtMC9) plays roles in clearing dead cells, forming xylem vessels, and regulating immunity and programmed cell death in plants. The protease's activation is controlled by pH levels, but the exact structural mechanism behind this has not been elucidated. In this work, high-resolution crystal structures for AtMC9 at active (pH 5.5 and pH 4.2) and inactive (pH 7.5) conditions are reported. The three structures are similar except for local conformations where their hydrogen bonding interactions with solvents are mediated through the protonation of specific titratable amino acid residues' side chains. By combining structural analysis, molecular dynamics simulations under constant pHs, and biochemical assays coupled with site-directed mutagenesis, we show that the regulation of AtMC9 activation involves multiple titratable glutamate and histidine residues across the three domains of p20, linker, and p10. Specifically, deprotonated Glu112, His193, and His208 can suppress AtMC9 proteolytic activity, while protonation of Glu255 and His307 at acidic pH may promote it. This study provides valuable insights into the pH-dependent activation of AtMC9 and could potentially lead to improving crops with enhanced immunity and controlled cell death, ultimately increasing agricultural productivity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis for expanded substrate specificities of human long chain acyl-CoA dehydrogenase and related acyl-CoA dehydrogenases

Crystal structures of human long-chain acyl-CoA dehydrogenase (LCAD) and the catalytically inactive Glu291Gln mutant, have been determined. These structures suggest that LCAD harbors functions beyond its historically defined role in mitochondrial β-oxidation of long and medium-chain fatty acids. LCAD is a homotetramer containing one FAD per 43 kDa subunit with Glu291 as the catalytic base. The substrate binding cavity of LCAD reveals key differences which makes it specific for longer and branched chain substrates. The presence of Pro132 near the start of the E helix leads to helix unwinding that, together with adjacent smaller residues, permits binding of bulky substrates such as 3α, 7α, l2α-trihydroxy-5β-cholestan-26-oyl-CoA. This structural element is also utilized by ACAD11, a eucaryotic ACAD of unknown function, as well as bacterial ACADs known to metabolize sterol substrates. Sequence comparison suggests that ACAD10, another ACAD of unknown function, may also share this substrate specificity. These results suggest that LCAD, ACAD10, ACAD11 constitute a distinct class of eucaryotic acyl CoA dehydrogenases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A chemical bonding based descriptor for predicting the role of anharmonicity induced by quantum nuclear effects in hydride superconductors

Quantum nuclear effects (QNEs) can significantly alter a material’s crystal structure and phonon spectra, impacting properties such as thermal conductivity and superconductivity. However, predicting a priori whether these effects will enhance or suppress superconductivity, or destabilize a structure, remains a grand challenge. Herein, we address this unresolved problem by introducing two possible descriptors, based upon the integrated crystal orbital bonding index (iCOBI) or the bond valence function, to predict the influence of QNEs on a crystal lattice’s dynamic stability, phonon spectra and superconducting properties. We find that structures with atoms in symmetric chemical bonding environments exhibit greater resilience to structural perturbations induced by QNEs, while those with atoms in asymmetric bonding environments are more susceptible to structural alterations, resulting in enhanced superconducting critical temperatures.

Physical chemistry↗
DOE OSTI2024

Evolution of structure and spectroscopic properties of a new 1,3-diacetylpyrene polymorph with temperature and pressure

A new polymorph of 1,3-diacetylpyrene has been obtained from its melt and thoroughly characterized using single-crystal X-ray diffraction, steady-state UV–Vis spectroscopy and periodic density functional theory calculations. Experimental studies covered the temperature range from 90 to 390 K and the pressure range from atmospheric to 4.08 GPa. Optimal sample placement in a diamond anvil cell according to our previously presented methodology ensured over 80% data coverage up to 0.8 Å for a monoclinic sample. Unrestrained Hirshfeld atom refinement of the high-pressure crystal structures was successful and anharmonic behavior of carbonyl oxygen atoms was observed. Unlike the previously characterized polymorph, the structure of 2°AP-β is based on infinite π-stacks of antiparallel 2°AP molecules. 2°AP-β displays piezochromism and piezofluorochromism which are directly related to the variation in interplanar distances within the π-stacking. The importance of weak intermolecular interactions is reflected in the substantial negative thermal expansion coefficient of -55.8 (57) MK -1 in the direction of C—H∙∙∙O interactions.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Generalized representative structures for atomistic systems

A new method is presented to generate atomic structures that reproduce the essential characteristics of arbitrary material systems, phases, or ensembles. Previous methods allow one to reproduce the essential characteristics (e.g. the chemical disorder) of a large random alloy within a small crystal structure. The ability to generate small representations of random alloys, along with the restriction to crystal systems, results from using the fixed-lattice cluster correlations to describe structural characteristics. A more general description of the structural characteristics of atomic systems is obtained using complete sets of atomic environment descriptors. These are used within for generating representative atomic structures without restriction to fixed lattices. A general data-driven approach is provided here utilizing the atomic cluster expansion (ACE) basis. The N-body ACE descriptors are a complete set of atomic environment descriptors that span both chemical and spatial degrees of freedom and are used within for describing atomic structures. The generalized representative structure (GRS) method presented within generates small atomic structures that reproduce ACE descriptor distributions corresponding to arbitrary structural and chemical complexity. It is shown that systematically improvable representations of crystalline systems on fixed parent lattices, amorphous materials, liquids, and ensembles of atomic structures may be produced efficiently through optimization algorithms. With the GRS method, we highlight reduced representations of atomistic machine-learning training datasets that contain similar amounts of information and small 40–72 atom representations of liquid phases. The ability to use GRS methodology as a driver for informed novel structure generation is also demonstrated. The advantages over other data-driven methods and state-of-the-art methods restricted to high-symmetry systems are highlighted.

atomic cluster expansion↗
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

Transition Metal Taggants in UO 2 from First Principles

The incorporation of transition metals into nuclear fuel has gained attention both to improve fuel properties and as a possible nuclear forensics tool. Recent experimental studies by Ulrich et al. and Adorno Lopes et al. have investigated Ni and Fe as candidate transition metal dopants for potential nuclear forensics purposes and found that there is minimal alteration to key UO 2 fuel properties. In the present work, we performed density functional theory (DFT) investigations into possible defect structures for Ni and Fe incorporation. The dynamic stability of these defect structures was validated by calculating the phonon density of states. We found that transition metal incorporation likely occurs via substitution at U sites in the fluorite crystal structure with a nearby O vacancy for charge-balancing, which agrees with experimentally proposed structures. Additionally, this defect structure does not cause long-range alterations to the crystal parameters—an important consideration for use as a nuclear fuel taggant. Future needed work involves computational investigation of additional defect concentrations using larger supercells, additional transition metal charge states, and thermal effects. Such investigations can be carried forward into sintering models for a more complete understanding of the suitability of Ni and Fe as fuel taggants.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2026

Structure-Aware Unsupervised, Transformational Machine Learning for Drug Discovery (DTRA Basic Research Final Report)

The major goal of this project is to develop machine learning (ML) methods to enable improved predictive power on real drug discovery for novel targets. More specifically, we planned to demonstrate the capability and effectiveness of ML tools utilizing unlabeled large-volume protein-ligand datasets. We investigated multiple pre-training approaches for 3D protein-ligand structure-based foundation models, without relying on experimental binding data. We also addressed scenarios in which crystal structures are unavailable or binding data are limited. We also planned to develop a complete pipeline to screen novel compounds as well as to demonstrate the capability and effectiveness of the developed methods by testing on a realistic drug discovery task such as SARS-CoV-2. While the major goals and milestones remain consistent with the original proposal, certain technical details have been adjusted, based on the experimental results and related outcomes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Synthesizing intermetallic thermoelectric materials using metal flux growth method

With zero energy poverty by 2050 goals, exploring innovative energy technologies is essential. Thermoelectric materials (TEMs) have the potential to harness waste heat and convert it to electricity (e.g., for spacecraft power, sensors, and cryogenic cooling). Two limitations of thermoelectric compounds are their low efficiency and limited pool of materials. Optimizing the efficiency of TEMs is challenging due to the interdependent relationship between electrical and thermal conductivity. A deeper understanding of electronic properties and lattice thermal conductivity is necessary to “understand, predict and ultimately control” the thermoelectric properties of TEMs. Understanding the influence of light-atom-doping and intrinsic defects on the electronic properties of the f-element containing TEMs are important questions that need to be answered to design and synthesize TEMs with optimal parameters. The purpose of this work is to understand how doping f-element based TEMs with light elements, such as carbon and boron, would impact the crystal structure, bond lengths, band gaps, and thermoelectric characteristics. High-quality f¬-element containing intermetallic single crystals are grown in metal flux media. In molten metal flux growth method, one or more low-melting metals such as aluminum, gallium, tin, and bismuth are used in excess as the reaction medium. As these are solution-state reactions, we can use lower temperatures than solid-state reactions and isolate the kinetic products instead of the thermodynamically stable compound. Then these are characterized using X-ray diffraction, scanning electron microscopy, energy dispersive spectroscopy, magnetization, electrical and thermal conductivities, and thermoelectric power.

37 - INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL C↗
DOE OSTI2025

Structural Distortions and Uniaxial Negative Thermal Expansion in the Polar Dion–Jacobson Oxide RbNdTa 2 O 7

We provide deeper insight into the crystal structures, sequential structural phase transitions (I2cm → Cmce → I4/mcm → P4/mmm), thermal expansion, and electronic properties of the n = 2 Dion–Jacobson polar oxide RbNdTa 2 O 7 , through X-ray powder diffraction, neutron powder diffraction, Raman studies, and density functional theory calculations. We observed a uniaxial negative thermal expansion (NTE) across the first-order transition, I2cm → Cmce, where the unit cell contracts along the c-axis, which is driven by a contraction of the NdTa 2 O 6 layer. Here, this NTE occurs within the temperature range of the first-order phase transition and contrasts with the corkscrew mechanism typically observed in Ruddlesden–Popper phases. In RbNdTa 2 O 7 , the I2cm (hybrid improper ferroelectric) → Cmce (antipolar) transition involves crucial changes in the bond lengths of Nd and Ta polyhedra, coupled with polar to antipolar displacement of the Nd ions, leading to a net contraction in the NdTa 2 O 6 layer along the c-axis, while preserving the overall octahedral tilting magnitude. This transition highlights the intricate interplay between the Nd and Ta coordination and the associated TaO 6 distortions. Temperature-dependent Raman spectra analysis further confirms the first-order structural transition and associated NTE, providing evidence for increased bond stiffness across this transition. Additionally, using neutron powder diffraction, we have determined that the transition I4/mcm → P4/mmm occurs at approximately 1150 K. Finally, we have calculated from DFT + U, the partial density of states, the energy bandgaps, and effective masses of the charge carriers of the polar ground structure.

Chemical structure↗
DOE OSTI2026

i -Wave Symmetry Altermagnetism and Anomalous Hall Conductivity in Monolayer FeCl 3

In this work, the FeCl 3 monolayer is proposed to host a rare and exotic i -wave symmetry altermagnetism. Using first-principles calculations, we performed a detailed investigation of the structural stability and electronic, magnetic, and spintronic properties of monolayer FeCl 3 . Our results suggest the system is semiconducting in nature and exhibits i-wave symmetry nonrelativistic spin splitting (NRSS), originating from its hexagonal crystal structure with roto-inversion symmetries and anisotropic crystal field. The momentum-resolved spin-splitting further supports the presence of spin-dependent topological features. Further, the monolayer exhibits sizable conventional spin-Hall and anomalous Hall conductivities, highlighting its promise as a versatile platform for next-generation flexo-spintronic applications.

altermagnetism↗