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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 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Mutation-driven RRE stem-loop II conformational change induces HIV-1 nuclear export dysfunction

Abstract The Rev response element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 (human immunodeficiency virus type 1) infection. However, the structures and mechanisms underlying this process remain largely unknown. Here, we determined the crystal structure of the HIV-1 RRE stem-loop II (SLII), revealing a unique three-way junction architecture in which the base stem (IIa) bifurcates into the stem-loops (IIb and IIc) to compose Rev binding sites. The crystal structures of various SLII mutants demonstrated that while some mutants retain the same “compact” fold as the wild type, other single-nucleotide mutants induce drastic conformational changes, forming an “extended” SLII structure. Through in vitro Rev binding assays and Rev activity measurements in HIV-1-infected cells using structure-guided SLII mutants designed to favor specific conformers, we showed that while the compact fold represents a functional SLII, the alternative extended conformation inhibits Rev binding and oligomerization and consequently stimulates HIV-1 RNA nuclear export dysfunction. The propensity of SLII to adopt multiple conformations as captured in crystal structures and their influence on Rev oligomerization illuminate emerging perspectives on RRE structural plasticity-based regulation of HIV-1 nuclear export and provide opportunities for developing anti-HIV drugs targeting specific RRE conformations.

Biochemistry & Molecular Biology↗
DOE OSTI2026

59 Co(p,X) spallation reaction cross sections for 250 MeV to 2 GeV protons

Cobalt is an advantageous target for probing the physics of nuclear spallation, because it is a naturally mono-isotopic element ( 59 Co), and its per-nucleon binding energy (BE/A = 8.768 MeV) is near the maximum value for all nuclei. We measured nuclear spallation cross sections for the 59 Co(p,X) reaction at five kinetic energies ranging from 250 MeV to 2 GeV. Cross sections for the production of 58 Co, 57 Co, 57 Mn, 56 Co, 56 Mn, 56 Cr, 55 Fe, 53 Fe, 54 Mn, 52 Mn, 51 Cr, 49 Cr, 48 V, 47 Sc, 46 Sc, 44 Sc, and 44 Scm are reported. Where comparable data exist in the EXFOR reaction database, we find that our measured cross sections generally agree. In many cases, we provide data for reactions or energies not currently reported in EXFOR. Our cross sections also provide evidence for the presence of α-clusters within the 59 Co nucleus, a surprising result given the asymmetry in Z (27) and N (32) for this nucleus. Finally, we use our measurements to evaluate the accuracy of spallation cross section simulations from GEANT4-based radiation transport toolkit, performed with the INCLXX-, Bertini-, and Binary-ion-cascade (BIC) based physics lists. This benchmarking activity revealed that the simulations overestimated the cross sections by a factor of ∼2–4 on average, and that the INCL-XX physics list provides the most reliable results. This evaluation informs the selection of the GEANT4 physics lists used for the analysis of data from NASA’s Psyche mission, which will measure γ rays and neutrons resulting from spallation reactions occurring on the surface of an asteroid whose surface is thought to be rich in iron-nickel metal.

43 PARTICLE ACCELERATORS↗
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 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 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 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 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 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 OSTI2025

Defining the Antitumor Mechanism of Action of a Clinical-stage Compound as a Selective Degrader of the Nuclear Pore Complex

Cancer cells are acutely dependent on nuclear transport due to elevated transcriptional activity, suggesting an unrealized opportunity for selective therapeutic inhibition of the nuclear pore complex (NPC). Through large-scale phenotypic profiling of cancer cell lines, genome-scale functional genomic modifier screens, and mass spectrometry–based proteomics, we discovered that the clinical drug PRLX-93936 is a molecular glue that binds and reprograms the TRIM21 ubiquitin ligase to degrade the NPC. Upon compound-induced TRIM21 recruitment, the nuclear pore is ubiquitylated and degraded, resulting in the loss of short-lived cytoplasmic mRNA transcripts and the induction of cancer cell apoptosis. Direct compound binding to TRIM21 was confirmed via surface plasmon resonance and X-ray crystallography, whereas compound-induced TRIM21–nucleoporin complex formation was demonstrated through multiple orthogonal approaches in cells and in vitro. Phenotype-guided optimization yielded compounds with 10-fold greater potency and drug-like properties, along with robust pharmacokinetics and efficacy against pancreatic cancer xenografts and patient-derived organoids.

Yuan, Linjie [Stanford School of Medicine, CA (Uni↗
DOE OSTI2024

Structural and biochemical analyses of the nuclear IκBζ protein in complex with the NF-κB p50 homodimer

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

Cell Biology↗
DOE OSTI2025

Ligand‐Directed Actinide Oxo‐Bond Manipulation in Actinyl Thiacalix[4]arene Complexes

Abstract Understanding the chemistry of the inert actinide oxo bond in actinyl ions AnO 2 2+ is important for controlling actinide behavior in the environment, during separations, and in nuclear waste (An=U, Np, Pu). The thioether calixarene TC4A (4‐ tert ‐butyltetrathiacalix[4]arene) binds equatorially to the actinyl cation forming a conical pocket that differentiates the two trans‐ oxo groups. The ‘ate’ complexes, [A] 2 [UO 2 (TC4A)] (A=[Li(DME) 2 ], HNEt 3 ) and [HNEt 3 ] 2 [AnO 2 (TC4A)] (An=U, Np, Pu), enable selective oxo chemistry. Silylation of the U VI oxo groups by bis(trimethylsilyl)pyrazine occurs first at only the unencapsulated exo oxo and only one silylation is needed to enable migration of the endo oxo out of the cone, whereupon a second silylation affords the stable U IV cis‐ bis(siloxide) [A] 2 [U(OSiMe 3 ) 2 (TC4A)]. Calculations confirm that only one silylation event is needed to initiate oxo rearrangement, and that the putative cis dioxo isomer of [UO 2 (TC4A)] 2− would be stable if it could be accessed synthetically, at only 23 kcal.mol −1 in energy above the classical trans dioxo. Calculations for the transuranic cis [AnO 2 (TC4A)] 2− (An=Np, Pu) are at higher energies, 30–35 kcal.mol −1 , retaining the U complexes as the more obvious target for a cis ‐dioxo actinyl ion. The aryloxide (OAr) groups of the macrocycle are essential in stabilizing this as‐yet unseen uranyl geometry as further bonding in the TC4A U‐O Ar groups stabilizes the U=O ‘yl’ bonds, explaining the stability of the putative cis [UO 2 (TC4A)] 2− in this ligand framework.

Pyrch, Mikaela M. [College of Chemistry University↗
DOE OSTI2025

Ligand‐Directed Actinide Oxo‐Bond Manipulation in Actinyl Thiacalix[4]arene Complexes

Understanding the chemistry of the inert actinide oxo bond in actinyl ions AnO2 2+ is important for controlling actinide behavior in the environment, during separations, and in nuclear waste (An=U, Np, Pu). The thioether calixarene TC4A (4-tert-butyltetrathiacalix[4]arene) binds equatorially to the actinyl cation forming a conical pocket that differentiates the two trans-oxo groups. The 'ate' complexes, [A]2[UO2(TC4A)] (A=[Li(DME)2], HNEt3) and [HNEt3]2[AnO2(TC4A)] (An=U, Np, Pu), enable selective oxo chemistry. Silylation of the UVI oxo groups by bis(trimethylsilyl)pyrazine occurs first at only the unencapsulated exo oxo and only one silylation is needed to enable migration of the endo oxo out of the cone, whereupon a second silylation affords the stable UIV cis-bis(siloxide) [A]2[U(OSiMe3)2(TC4A)]. Calculations confirm that only one silylation event is needed to initiate oxo rearrangement, and that the putative cis dioxo isomer of [UO2(TC4A)]2- would be stable if it could be accessed synthetically, at only 23 kcal.mol-1 in energy above the classical trans dioxo. Calculations for the transuranic cis[AnO2(TC4A)]2- (An=Np, Pu) are at higher energies, 30-35 kcal.mol-1, retaining the U complexes as the more obvious target for a cis-dioxo actinyl ion. The aryloxide (OAr) groups of the macrocycle are essential in stabilizing this as-yet unseen uranyl geometry as further bonding in the TC4A U-OAr groups stabilizes the U=O 'yl' bonds, explaining the stability of the putative cis[UO2(TC4A)]2- in this ligand framework.

Pyrch, Mikaela M↗
DOE OSTI2024

Investigating the effects of precise mass measurements of Ru and Pd isotopes on machine learning mass modeling

Atomic masses are a foundational quantity in our understanding of nuclear structure, astrophysics, and fundamental symmetries. The longstanding goal of creating a predictive global model for the binding energy of a nucleus remains a significant challenge, however, and prompts the need for precise measurements of atomic masses to serve as anchor points for model developments. We present precise mass measurements of neutron-rich Ru and Pd isotopes performed at the Californium Rare Isotope Breeder Upgrade facility at Argonne National Laboratory using the Canadian Penning Trap mass spectrometer. The masses of 108 Ru, 110 Ru, and 116 Pd were measured to a relative mass precision $\delta$⁢$m/m$ ≈ 10 -8 via the phase-imaging ion-cyclotron-resonance technique, and represent an improvement of approximately an order of magnitude over previous measurements. Further, these mass data were used in conjunction with the physically interpretable machine learning (PIML) model, which uses a mixture density neural network to model mass excesses via a mixture of Gaussian distributions. The effects of our new mass data on a Bayesian-updating of a PIML model are presented.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Electronic and Geometric Contributors to Hydrogen Binding in Uranium Oxide Grain Boundaries

Hydrogen induced corrosion of uranium, which leads to the formation of toxic and pyrophoric UH 3 , raises significant safety concerns for long-term storage of nuclear materials. Previous work suggests hydrogen diffuses through the grain boundaries (GBs) of the passivating oxide layer to initiate hydriding reactions. However, the atomistic mechanisms underlying this phenomenon and the structural factors that control its initiation are not well understood. To address this knowledge gap, here we use a high-throughput density functional theory (DFT) workflow to investigate the adsorption of H and H 2 in the defective bulk UO 2 . Specifically, we have exhaustively investigated the adsorption of H (107 sites) and H 2 (26 sites) in three different coincident site lattice (CSL) GBs: Σ3, Σ5, and Σ9. Compared to the binding energies in pristine UO 2 , we observe significantly stronger hydrogen adsorption at these GB sites. Interestingly, we find that the trends in H and H 2 adsorption vary considerably across the three GB models. In particular, while a small number of sites in Σ5 and Σ9 show exothermic adsorption of H and H 2 , respectively, no such sites are found in Σ3. These results provide fundamental atomistic insights that could guide the development of future corrosion mitigation strategies for the storage of nuclear materials.

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

Loosely bound composite dark matter

We investigate loosely bound composite states made of dark matter, where the binding energy for constituent particles is considerably less than the constituent mass. We focus on models of nuclear and molecular dark matter, where constituents are separated by length scales larger than the inverse constituent mass, just like nuclei and atoms in the Standard Model. The cosmology, structure, and interactions at underground experiments are described. We find that loosely bound composites can have a very large cross section for scattering with nuclei that scales with nucleon number like ∼ A 4 . For some couplings, these composites produce extremely soft (≪ keV) individual atomic recoils while depositing a large amount of total recoil energy (≫ keV) in a single passage through a detector, implying an interesting new class of signatures for low threshold direct detection.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

Dual-Bed Radioiodine Capture from Complex Gas Streams with Zeolites: Regeneration and Reuse of Primary Sorbent Beds for Sustainable Waste Management

Dual-sorbent systems are proposed for radioiodine management with a regenerated primary bed for multiple cycles of use in complex conditions and a secondary bed for disposal with higher waste loadings. Sorbent approaches for the effective capture of gaseous radioiodine (isotopes 129 I and 131 I) produced from a range of nuclear processes have been studied for over half a century. (1−5) Whether or not a sorbent (e.g., molecular sieve) is required to physically screen/trap or chemically bind a radionuclide of interest through chemisorption, the complexity of the gas stream has a large impact on the performance (e.g., loading capacity, selectivity) and active life of a sorbent bed. (3) Silver mordenite (AgZ), the U.S. Department of Energy baseline sorbent for radioiodine capture from nuclear processes, performs well within acidic conditions and at elevated temperatures (6) and can be consolidated into a chemically durable waste form for long-term disposal. (7,8) However, new sorbents are being sought because optimal capture performance of AgZ significantly decreases in dynamic oxidizing environments with competing species, and it is expensive and it contains Ag (a toxic metal). (9) Until a new sorbent is found to replace AgZ, the regeneration and reuse of AgZ is an attractive alternative to a single-use primary sorbent bed. In this regard, a primary sorbent could be designed for enhanced capture in complex gas streams and the ability to be regenerated for reuse. Here, a secondary sorbent could then be tailored for maximum iodine loading in the gas stream and chemical durability within a disposal facility.

chemisorption↗
DOE OSTI2025

Ab initio calculations of the carbon and oxygen isotopes: Energies, correlations, and superfluid pairing

We perform ab initio nuclear lattice calculations of the neutron-rich carbon and oxygen isotopes using high-fidelity chiral interactions. We find good agreement with the observed binding energies and compute correlations associated with each two-nucleon interaction channel. For the isospin T = 1 channels, we show that the dependence on T z provides a measure of the correlations among the extra neutrons in the neutron-rich nuclei. For the spin-singlet S-wave channel, we observe that any paired neutron interacts with the nuclear core as well as its neutron pair partner, while any unpaired neutron interacts primarily with only the nuclear core. For the other partial waves, the correlations among the extra neutrons grow more slowly and smoothly with the number of neutrons. These general patterns are observed in both the carbon and oxygen isotopes and may be universal features that appear in many neutron-rich nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Ligand efficacy shifts a nuclear receptor conformational ensemble between transcriptionally active and repressive states

Abstract Nuclear receptors (NRs) are thought to dynamically alternate between transcriptionally active and repressive conformations, which are stabilized upon ligand binding. Most NR ligand series exhibit limited bias, primarily consisting of transcriptionally active agonists or neutral antagonists, but not repressive inverse agonists—a limitation that restricts understanding of the functional NR conformational ensemble. Here, we report a NR ligand series for peroxisome proliferator-activated receptor gamma (PPARγ) that spans a pharmacological spectrum from repression (inverse agonism) to activation (agonism) where subtle structural modifications switch compound activity. While crystal structures provide snapshots of the fully repressive state, NMR spectroscopy and conformation-activity relationship analysis reveals that compounds within the series shift the PPARγ conformational ensemble between transcriptionally active and repressive conformations that are natively populated in the apo/ligand-free ensemble. Our findings reveal a molecular framework for minimal chemical modifications that enhance PPARγ inverse agonism and elucidate their influence on the dynamic PPARγ conformational ensemble.

Science & Technology - Other Topics↗