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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Neutron-proton pairing correction in the extended isovector and isoscalar pairing model

An extended O ST (8) model with multi j-orbits is constructed based on the angular momentum decomposition with “pseudo”-spin S for valence nucleons in a j-orbit. It is shown that the isovector S = 0 and T=1 pairs are exactly the J=0 and T=1 pairs in a given j-orbit, while the isoscalar S = 1 pairs are linear combinations of J=odd pairs, with which the pairing Hamiltonian can be used to estimate isovector and isoscalar pairing interactions. As an example of the model application, some low-lying J = 0 + level energies of even-even and odd-odd A=18 – 28 nuclei up to the half-filling in the ds-shell above the 16 O core are fit by the model and compared with the fitting results of the same Hamiltonian in the O LST (8) form. It has been verified from the fitting of both the models that the isoscalar pairing interaction can be neglected in the lower energy part of the spectra of these ds-shell nuclei as far as binding energies and a few J=0 + excited levels of these nuclei are concerned. With the mean-field plus isovector pairing interaction only, neutron-neutron, proton-proton, and neutron-proton pairing contributions at the ground or the lowest J=0 + state of these nuclei are estimated. It is shown that the isovector np-pairing contribution to the binding in the odd-odd N=Z nuclei is systematically larger than that in the even-even nuclei. Furthermore, the isoscalar np-pair content at the lowest J=0+ state of these nuclei is also estimated. In both the O ST (8) and O LST (8) models, it is clearly shown that the isoscalar-pair content in the lowest J=0 + state of the N=Z and N=Z±2 nuclei increases with increasing of the valence nucleons, especially in those even-even nuclei, which indicates the isoscalar pairing correlation to be of importance at low-lying states of N=Z and N=Z±2 nuclei, especially in those even-even nuclei with more valence nucleons up to the half-filling, even though the isoscalar pairing interaction is negligible.

20 ≤ A ≤ 38↗
DOE OSTI2026

Localization and functional exploration of leiomodin-2’s C-terminal binding sites

Striated muscle contraction occurs through interactions between overlapping myosin-based thick and actin-based thin filaments within the sarcomere. For effective contraction to occur, the length of the thin filament must be maintained to allow for sufficient overlap with the thick filament. The proteins leiomodin and tropomodulin compete for binding at the pointed end of thin filaments to regulate their length, utilizing their homologous N-terminal actin and tropomyosin binding sites. Leiomodin also has a region called the C-terminal extension, absent in tropomodulin. In this region, the cardiac isoform (leiomodin-2) contains additional actin-binding sites that enable it to bind along the sides of thin filaments in a Ca2+-dependent manner. Here, using nuclear magnetic resonance spectroscopy, we localize the regions of the C-terminal extension that contain residues involved in thin filament side-binding. Using co-sedimentation assays, we reveal that these regions can independently bind thin filaments and discover that the poly-proline region plays a role as a linker, maintaining an adequate distance between two of the regions required for effective interaction to occur. In addition to its role in side-binding, we provide direct evidence that the poly-proline region interacts with profilin and propose a new mechanism by which leiomodin-2 may assist in the polymerization of profilin-bound actin at thin filament pointed ends.

ACTIN-BINDING PROTEINS↗
DOE OSTI2020

Garcinoic Acid Is a Natural and Selective Agonist of Pregnane X Receptor

Pregnane X receptor (PXR) is a master xenobiotic-sensing transcription factor and a validated target for immune and inflammatory diseases. The identification of chemical probes to investigate the therapeutic relevance of the receptor is still highly desired. In fact, currently available PXR ligands are not highly selective and can exhibit toxicity and/or potential off-target effects. In this study, we have identified garcinoic acid as a selective and efficient PXR agonist. The properties of this natural molecule as a specific PXR agonist were demonstrated by the screening on a panel of nuclear receptors, the assessment of the physical and thermodynamic binding affinity, and the determination of the PXR-garcinoic acid complex crystal structure. Cytotoxicity, transcriptional, and functional properties were investigated in human liver cells, and compound activity and target engagement were confirmed in vivo in mouse liver and gut tissue. In conclusion, garcinoic acid is a selective natural agonist of PXR and a promising lead compound toward the development of new PXR-regulating modulators.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A Review of Advanced Characterization Methods and Techniques for Amorphous and Poorly Crystalline Materials Applicable to Cementitious Waste Forms

This review covers advanced characterization methods of cementitious materials. The particular focus is to understand cementitious compositions with amorphous content because conventional techniques such as X-ray diffraction are more applicable to materials with long range order. Also of interest is advanced characterization that provides deeper insights into properties such as porosity. There are five groups of characterization methods discussed in this review which are: electron beam/microscopy, X-ray, neutron diffraction and scattering, nuclear magnetic resonance, and optical techniques. The techniques can be further grouped by the categories of nanoscale structural understanding (transmission electron microscopy and pair distribution function), microscale structural understanding (focused ion beam and x-ray tomography), microscopic elemental distributions (energy dispersive spectroscopy and X-ray fluorescence), and chemical binding information (electron energy loss spectroscopy, x-ray absorption spectroscopy, nuclear magnetic resonance, Raman spectroscopy, and infrared spectroscopy), with advantages and disadvantages of each method discussed. The recommendation for further research is to begin with techniques that are easier to prepare samples for, measure, and analyze, such as the optical techniques of Raman and infrared spectroscopy. If more information is needed, pursue collaborations, other techniques, or proposals for beam time at the synchrotron sources.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Exploring competitive metal binding and crystallization of UO 2 2+ and Cu 2+ tetrahydrofuran-2,3,4,5-tetracarboxylic acid complexes

Solvent extractions are used to separate actinide elements from fission products in nuclear waste streams and the successful isolation of specific species utilize subtle differences in metal ligand binding. Metal ligand binding is also important in crystallization of metal organic materials and herein we explore the importance of competitive binding in the tetrahydrofuran-2,3,4,5-tetracarboxylic acid (THFTCA) system. This ligand has been previously evaluated for the selective extraction of uranium from other lanthanides and actinides and in the current research, we evaluate the crystallization of uranyl-THFTCA complexes in the presence of Cu 2+ , Sr 2+ , Th 4+ , and Ce 3+ . Three major phases were formed in the crystallization experiments and characterized with single crystal X-ray diffraction, powder X-ray diffraction, thermogravimetric analysis, and Raman spectroscopy. Two of the resulting phases were novel (UTHF1 ((C 4 H 10 N 2 )[UO 2 (C 8 H 8 O 9 ) 2 ]∙2H 2 O) and UTHF2 (Na[(UO 2 )(C 8 H 5 O 9 )(H 2 O)]∙ 3.5 H 2 O)), whereas the third (CuTHF1) was previously reported in the literature. Raman spectroscopy was utilized to evaluate spectral changes in the mother liquor of UTHF1, UTHF2, and CuTHF1 over time to assess the crystallization process. Further, isothermal titration calorimetry was used to determine the binding constants for UO 2 2+ and Cu 2+ to the THFTCA ligand in solution and evaluate the role of competitive metal binding in this system. The thermodynamic parameters and the crystallographic data were used to justify the formation of a weaker UO 2 2+ -THFTCA complex. Formation of a weaker UO 2 2+ -THFTCA complex supports our findings that UTHF1 only forms in homomeric systems, but suggests that the crystallization of UTHF2 and CuTHF1 is reliant on the presence of additional counter ions and ligands to change the amount of available THFTCA ligand.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Mechanistic studies of small molecule ligands selective to RNA single G bulges

Abstract Small-molecule RNA binders have emerged as an important pharmacological modality. A profound understanding of the ligand selectivity, binding mode, and influential factors governing ligand engagement with RNA targets is the foundation for rational ligand design. Here, we report a novel class of coumarin derivatives exhibiting selective binding affinity towards single G RNA bulges. Harnessing the computational power of all-atom Gaussian accelerated molecular dynamics simulations, we unveiled a rare minor groove binding mode of the ligand with a key interaction between the coumarin moiety and the G bulge. This predicted binding mode is consistent with results obtained from structure-activity relationship studies and transverse relaxation measurements by nuclear magnetic resonance spectroscopy. We further generated 444 molecular descriptors from 69 coumarin derivatives and identified key contributors to the binding events, such as charge state and planarity, by lasso (least absolute shrinkage and selection operator) regression. Our work deepened the understanding of RNA-small molecule interactions and integrated a new framework for the rational design of selective small-molecule RNA binders.

Biochemistry & Molecular Biology↗
DOE OSTI2021

Ground-state and decay properties of neutron-rich 106 Nb

The ground-state properties of neutron-rich 106 Nb and its β decay into 106 Mo have been studied using the CARIBU radioactive-ion-beam facility at Argonne National Laboratory. Niobium-106 ions were extracted from a 252 Cf fission source and mass separated before being delivered as low-energy beams to the Canadian Penning Trap, as well as the X-Array and SATURN β-decay-spectroscopy station. The measured 106 Nb ground-state mass excess of –66202.0(13) keV is consistent with a recent measurement but has three times better precision; this work also rules out the existence of a second long-lived, β-decaying state in 106 Nb above 5 keV in excitation energy. The decay half-life of 106 Nb was measured to be 1.097(21) s, which is 8% longer than the adopted value. Here, the level scheme of the decay progeny, 106 Mo, has been expanded up to ≈ 4 MeV. The distribution of decay strength and considerable population of excited states in 106 Mo of J ≥ 3 emphasizes the need to revise the adopted J π = 1 – ground-state spin-parity assignment of 106 Nb; it is more likely to be J ≥ 3.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Universal reduced basis for the calibration of covariant energy density functionals

The reduced basis method is used to construct a “universal” basis of Dirac orbitals that may be applicable throughout the nuclear chart to calibrate covariant energy density functionals. Relative to the successful development of a reduced basis emulator for the nonrelativistic Schrödinger equation, the Dirac equation adds an extra layer of complexity due to the existence of negative energy states, which complicates building an efficient reduced basis. However, once this problem is mitigated, the resulting reduced basis is able to accurately and efficiently reproduce the high-fidelity model at a fraction of the computational cost. We are confident that the resulting reduced basis will serve as a foundational element in developing rapid and accurate emulators. In turn, these emulators will play a critical role in the Bayesian optimization of covariant energy density functionals.

Bayesian methods↗
DOE OSTI2023

Trends of Neutron Skins and Radii of Mirror Nuclei from First Principles

The neutron skin of atomic nuclei impacts the structure of neutron-rich nuclei, the equation of state of nucleonic matter, and the size of neutron stars. Here we predict the neutron skin of selected light- and medium-mass nuclei using coupled-cluster theory and the auxiliary field diffusion Monte Carlo method with two- and three-nucleon forces from chiral effective field theory. We find a linear correlation between the neutron skin and the isospin asymmetry in agreement with the liquid-drop model and compare with data. We also extract the linear relationship that describes the difference between neutron and proton radii of mirror nuclei and quantify the effect of charge symmetry breaking terms in the nuclear Hamiltonian. In conclusion, our results for the mirror-difference charge radii and binding energies per nucleon agree with existing data.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural basis for heme-dependent NCoR binding to the transcriptional repressor REV-ERBβ

Heme is the endogenous ligand for the constitutively repressive REV-ERB nuclear receptors, REV-ERBα (NR1D1) and REV-ERBβ (NR1D2), but how heme regulates REV-ERB activity remains unclear. Cellular studies indicate that heme is required for the REV-ERBs to bind the corepressor NCoR and repress transcription. However, fluorescence-based biochemical assays suggest that heme displaces NCoR; here, we show that this is due to a heme-dependent artifact. Using ITC and NMR spectroscopy, we show that heme binding remodels the thermodynamic interaction profile of NCoR receptor interaction domain (RID) binding to REV-ERBβ ligand-binding domain (LBD). We solved two crystal structures of REV-ERBβ LBD cobound to heme and NCoR peptides, revealing the heme-dependent NCoR binding mode. ITC and chemical cross-linking mass spectrometry reveals a 2:1 LBD:RID stoichiometry, consistent with cellular studies showing that NCoR-dependent repression of REV-ERB transcription occurs on dimeric DNA response elements. Our findings should facilitate renewed progress toward understanding heme-dependent REV-ERB activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Rational design of a genetically encoded NMR zinc sensor

Elucidating the biochemical roles of the essential metal ion, Zn 2+ , motivates detection strategies that are sensitive, selective, quantitative, and minimally invasive in living systems. Fluorescent probes have identified Zn 2+ in cells but complementary approaches employing nuclear magnetic resonance (NMR) are lacking. Recent studies of maltose binding protein (MBP) using ultrasensitive 129 Xe NMR spectroscopy identified a switchable salt bridge which causes slow xenon exchange and elicits strong hyperpolarized 129 Xe chemical exchange saturation transfer (hyper-CEST) NMR contrast. To engineer the first genetically encoded, NMR-active sensor for Zn 2+ , we converted the MBP salt bridge into a Zn 2+ binding site, while preserving the specific xenon binding cavity. The zinc sensor (ZS) at only 1 μM achieved ‘turn-on’ detection of Zn 2+ with pronounced hyper-CEST contrast. This made it possible to determine different Zn 2+ levels in a biological fluid via hyper-CEST. ZS was responsive to low-micromolar Zn 2+ , only modestly responsive to Cu 2+ , and nonresponsive to other biologically important metal ions, according to hyper-CEST NMR spectroscopy and isothermal titration calorimetry (ITC). Protein X-ray crystallography confirmed the identity of the bound Zn 2+ ion using anomalous scattering: Zn 2+ was coordinated with two histidine side chains and three water molecules. Penta-coordinate Zn 2+ forms a hydrogen-bond-mediated gate that controls the Xe exchange rate. Metal ion binding affinity, 129 Xe NMR chemical shift, and exchange rate are tunable parameters via protein engineering, which highlights the potential to develop proteins as selective metal ion sensors for NMR spectroscopy and imaging.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Tritium adsorption and absorption on (100) and (001) surfaces of pure and tin defective zirconium

Zirconium alloys such as zircaloy-4 are used as tritium (T) getter materials in tritium-producing burnable absorber rods (TPBARs) due to their ability to capture T, thereby forming metal hydrides. Developing an understanding of T adsorption onto zircaloy prior to diffusion into the subsurface is relevant for rational tritium getter and TPBAR design, to improve material properties for nuclear applications. Herein, density functional theory calculations revealed the preferred binding sites for T adsorption on Zr(001) and Zr(100). The energy barriers of T transfer, along the surface and from the surface to the subsurface were computed. The adsorption properties of Zr(001) were found to be superior to those of Zr(100). Surface tin impurities were found to strongly repel T. The presence of subsurface and surface tin resulted in higher absorption energy barriers for both the forward and reverse processes. Based on the calculated energy barriers, a surface to surface T diffusion coefficient of 9.53 × 10 -10 m 2 s -1 is expected for pristine Zr(001). Finally, a surface to subsurface T diffusion coefficient on the order of 10 -13 m 2 s -1 is predicted in pristine Zr, decreasing to 10 -19 m 2 s -1 for the transfer with a subsurface tin impurity.

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

Mass measurements of 60–63 Ga reduce x-ray burst model uncertainties and extend the evaluated T=1 isobaric multiplet mass equation

We report precision mass measurements of neutron-deficient gallium isotopes approaching the proton drip line. The measurements of 60–63 Ga performed with the TITAN multiple-reflection time-of-flight mass spectrometer provide a more than threefold improvement over the current literature mass uncertainty of 61 Ga and mark the first direct mass measurement of 60 Ga. The improved precision of the 61 Ga mass has important implications for the astrophysical rp process, as it constrains essential reaction Q values near the 60 Zn waiting point. Based on calculations with a one-zone model, we demonstrate the impact of the improved mass data on prediction uncertainties of x-ray burst models. The first-time measurement of the 60 Ga ground-state mass establishes the proton-bound nature of this nuclide, thus constraining the location of the proton drip line along this isotopic chain. Including the measured mass of 60 Ga further enables us to extend the evaluated T = 1 isobaric multiplet mass equation up to A = 60.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Applications of reduced-basis methods to the nuclear single-particle spectrum

Reduced-basis methods provide a powerful framework for building efficient and accurate emulators. Although widely applied in many fields to simplify complex models, reduced-basis methods have only been recently introduced into nuclear physics. In this Letter we build an emulator to study the single-particle structure of atomic nuclei. By scaling a suitable mean-field Hamiltonian, a “universal” reduced basis is constructed capable of accurately and efficiently reproduce the entire single-particle spectrum of a variety of nuclei. Indeed, the reduced-basis model reproduces both ground- and excited-state energies as well as the associated wave functions with remarkable accuracy. Here our results bode well for more demanding applications that use Bayesian optimization to calibrate nuclear energy density functionals.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Inhibition of FAM46/TENT5 activity by BCCIPα adopting a unique fold

The FAM46 (also known as TENT5) proteins are noncanonical poly(A) polymerases (PAPs) implicated in regulating RNA stability. The regulatory mechanisms of FAM46 are poorly understood. Here, we report that the nuclear protein BCCIPα, but not the alternatively spliced isoform BCCIPβ, binds FAM46 and inhibits their PAP activity. Unexpectedly, our structures of the FAM46A/BCCIPα and FAM46C/BCCIPα complexes show that, despite sharing most of the sequence and differing only at the C-terminal portion, BCCIPα adopts a unique structure completely different from BCCIPβ. The distinct C-terminal segment of BCCIPα supports the adoption of the unique fold but does not directly interact with FAM46. The β sheets in BCCIPα and FAM46 pack side by side to form an extended β sheet. A helix-loop-helix segment in BCCIPα inserts into the active site cleft of FAM46, thereby inhibiting the PAP activity. Our results together show that the unique fold of BCCIPα underlies its interaction with and functional regulation of FAM46.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Mechanism of RanGTP priming H2A-H2B release from Kap114 in an atypical RanGTP•Kap114•H2A-H2B complex

Previously, we showed that the nuclear import receptor Importin-9 wraps around the H2A-H2B core to chaperone and transport it from the cytoplasm to the nucleus. However, unlike most nuclear import systems where RanGTP dissociates cargoes from their importins, RanGTP binds stably to the Importin-9•H2A-H2B complex, and formation of the ternary RanGTP•Importin-9•H2A-H2B complex facilitates H2A-H2B release to the assembling nucleosome. It was unclear how RanGTP and the cargo H2A-H2B can bind simultaneously to an importin, and how interactions of the three components position H2A-H2B for release. Here, we show cryo-EM structures of Importin-9•RanGTP and of its yeast homolog Kap114, including Kap114•RanGTP, Kap114•H2A-H2B, and RanGTP•Kap114•H2A-H2B, to explain how the conserved Kap114 binds H2A-H2B and RanGTP simultaneously and how the GTPase primes histone transfer to the nucleosome. In the ternary complex, RanGTP binds to the N-terminal repeats of Kap114 in the same manner as in the Kap114/Importin-9•RanGTP complex, and H2A-H2B binds via its acidic patch to the Kap114 C-terminal repeats much like in the Kap114/Importin-9•H2A-H2B complex. Ran binds to a different conformation of Kap114 in the ternary RanGTP•Kap114•H2A-H2B complex. Here, Kap114 no longer contacts the H2A-H2B surface proximal to the H2A docking domain that drives nucleosome assembly, positioning it for transfer to the assembling nucleosome or to dedicated H2A-H2B chaperones in the nucleus.

59 BASIC BIOLOGICAL SCIENCES↗