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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
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↗
NASA NTRS2003

Photonic Interrogation and Control of Nano Processes

My research activities for the summer of 2003 consisted of two projects: One project was concerned with determining a method for predicting the static and dynamic assembly properties of nano-structures using laser tweezers. The other project was to investigate the generation of Laguerre-Gaussian modes using a spatial light modulator incorporated into an optical tweezers system. Concerning the first project, I initially pursued the approach suggested by my NASA colleague Dr. Art Decker. This approach involved mimicking the model of the structure of atomic nucleus for the assembly of 1 to 100 atoms using allowed quadruple transitions induced by orbital angular momentums of a Laguerre- Gaussian (Doughnut) laser mode. After realizing the inaptness of the nuclear model with the nanostructure model as far as the binding forces and transitions were concerned, I focused on using quantum dot modei. This model was not attuned also for the host lattice influences the electronic structure of the quantum dot. Thus one other option that I decided to pursue was the approach of molecular quantum mechanics. In this approach the nanostructure is treated as a large (10-100 nm) molecule constructed from single element or multi-elements. Subsequent to consultation with Dr. Fred Morales, a chemical engineer at NASA GRC, and Dr. David Ball, a computational chemist at Cleveland State University, I acquired a molecular-quantum computation software, Hyperchem 7.0. This software allows simulation of different molecular structures as far as their static and dynamic behaviors are concerned. The time that I spent on this project was about eight weeks. Once this suitable approach was identified, I realized the need to collaborate with a computational quantum chemist to pursue searching for stable nanostructures in the range of 10-100 nm that we can be assembled using laser tweezers. The second project was about generating laser tweezers that possess orbital angular momentum. As shown, we were able to generate laser tweezers modes of different orbital angular momentum using a spatial light modulator incorporated into a laser tweezers system. The motivation for investigating these types of modes stems from being able to spin particles at high speeds and also to orient two particles in separate traps and then join them together. Also, there has been recent intense interest on fundamental physics research on orbital angular momentum of light. The fact that circularly polarized light may have associated with it angular momentum that relates to the spin of individual photons (spin 0 for the plane polarized light, spin +1 for the right-circularly polarized light and spin -1 for the left-circularly polarized light) was first demonstrated by Beth in 1936. Orbital angular momentum is, however, distinct from spin in that the spin angular momentum of light is intrinsically linked to the behavior of the electric field in the light whereas orbital angular momentum is a consequence of inclined wavefronts. In 1992 L. Allen, et al showed that the Laguerre-Gaussian (LG) modes could possess well-defined orbital angular momentum that can exceed 1 planck's constant, i.e. l plancks constant per photon, where l is the azimuthal index of the mode.

Jassemnejad, Baha↗
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↗
DOE OSTI2021

Nucleon-pair coupling scheme in Elliott's SU(3) model

Elliott's SU(3) model is at the basis of the shell-model description of rotational motion in atomic nuclei. Here we demonstrate that SU(3) symmetry can be realized in a truncated shell-model space if constructed in terms of a sufficient number of collective S, D, G,...pairs (i.e., with angular momentum zero, two, four,...) and if the structure of the pairs is optimally determined either by a conjugate-gradient minimization method or from a Hartree-Fock intrinsic state. We illustrate the procedure for six protons and six neutrons in the pf (sdg) shell and exactly reproduce the level energies and electric quadrupole properties of the ground-state rotational band with SDG (SDGI) pairs. The SD-pair approximation without significant renormalization, on the other hand, cannot describe the full SU(3) collectivity. A mapping from Elliott's fermionic SU(3) model to systems with s, d, g,... bosons provides insight into the existence of a decoupled collective subspace in terms of S, D, G,... pairs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

An evolutionarily conserved tryptophan cage promotes folding of the extended RNA recognition motif in the hnRNPR ‐like protein family

Abstract The heterogeneous nuclear ribonucleoprotein (hnRNP) R‐like family is a class of RNA binding proteins in the hnRNP superfamily with diverse functions in RNA processing. Here, we present the 1.90 Å X‐ray crystal structure and solution NMR studies of the first RNA recognition motif (RRM) of human hnRNPR. We find that this domain adopts an extended RRM (eRRM1) featuring a canonical RRM with a structured N‐terminal extension (N ext ) motif that docks against the RRM and extends the β‐sheet surface. The adjoining loop is structured and forms a tryptophan cage motif to position the N ext motif for docking to the RRM. Combining mutagenesis, solution NMR spectroscopy, and thermal denaturation studies, we evaluate the importance of residues in the N ext –RRM interface and adjoining loop on eRRM folding and conformational dynamics. We find that these sites are essential for protein solubility, conformational ordering, and thermal stability. Consistent with their importance, mutations in the N ext –RRM interface and loop are associated with several cancers in a survey of somatic mutations in cancer studies. Sequence and structure comparison of the human hnRNPR eRRM1 to experimentally verified and predicted hnRNPR‐like proteins reveals conserved features in the eRRM.

Biochemistry & Molecular Biology↗
DOE OSTI2022

Angular momentum eigenstates of the isotropic 3-D harmonic oscillator: Phase-space distributions and coalescence probabilities

The isotropic 3-dimensional harmonic oscillator potential can serve as an approximate description of many systems in atomic, solid state, nuclear, and particle physics. In particular, the question of 2 particles binding (or coalescing) into angular momentum eigenstates in such a potential has interesting applications. Here we compute the probabilities for coalescence of two distinguishable, non-relativistic particles into such a bound state, where the initial particles are represented by generic wave packets of given average positions and momenta. We use a phase-space formulation and hence need the Wigner distribution functions of angular momentum eigenstates in isotropic 3-dimensional harmonic oscillators. These distribution functions have been discussed in the literature before but we utilize an alternative approach to obtain these functions. Along the way, we derive a general formula that expands angular momentum eigenstates in terms of products of 1-dimensional harmonic oscillator eigenstates.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗