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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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
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↗
NASA NTRS1997

Mechanical continuity and reversible chromosome disassembly within intact genomes removed from living cells

Chromatin is thought to be structurally discontinuous because it is packaged into morphologically distinct chromosomes that appear physically isolated from one another in metaphase preparations used for cytogenetic studies. However, analysis of chromosome positioning and movement suggest that different chromosomes often behave as if they were physically connected in interphase as well as mitosis. To address this paradox directly, we used a microsurgical technique to physically remove nucleoplasm or chromosomes from living cells under isotonic conditions. Using this approach, we found that pulling a single nucleolus or chromosome out from interphase or mitotic cells resulted in sequential removal of the remaining nucleoli and chromosomes, interconnected by a continuous elastic thread. Enzymatic treatments of interphase nucleoplasm and chromosome chains held under tension revealed that mechanical continuity within the chromatin was mediated by elements sensitive to DNase or micrococcal nuclease, but not RNases, formamide at high temperature, or proteases. In contrast, mechanical coupling between mitotic chromosomes and the surrounding cytoplasm appeared to be mediated by gelsolin-sensitive microfilaments. Furthermore, when ion concentrations were raised and lowered, both the chromosomes and the interconnecting strands underwent multiple rounds of decondensation and recondensation. As a result of these dynamic structural alterations, the mitotic chains also became sensitive to disruption by restriction enzymes. Ion-induced chromosome decondensation could be blocked by treatment with DNA binding dyes, agents that reduce protein disulfide linkages within nuclear matrix, or an antibody directed against histones. Fully decondensed chromatin strands also could be induced to recondense into chromosomes with pre-existing size, shape, number, and position by adding anti-histone antibodies. Conversely, removal of histones by proteolysis or heparin treatment produced chromosome decondensation which could be reversed by addition of histone H1, but not histones H2b or H3. These data suggest that DNA, its associated protein scaffolds, and surrounding cytoskeletal networks function as a structurally-unified system. Mechanical coupling within the nucleoplasm may coordinate dynamic alterations in chromatin structure, guide chromosome movement, and ensure fidelity of mitosis.

NASA Discipline Cell Biology↗
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↗
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 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↗
NASA NTRS2000

Cardiac tissue enriched factors serum response factor and GATA-4 are mutual coregulators

Combinatorial interaction among cardiac tissue-restricted enriched transcription factors may facilitate the expression of cardiac tissue-restricted genes. Here we show that the MADS box factor serum response factor (SRF) cooperates with the zinc finger protein GATA-4 to synergistically activate numerous myogenic and nonmyogenic serum response element (SRE)-dependent promoters in CV1 fibroblasts. In the absence of GATA binding sites, synergistic activation depends on binding of SRF to the proximal CArG box sequence in the cardiac and skeletal alpha-actin promoter. GATA-4's C-terminal activation domain is obligatory for synergistic coactivation with SRF, and its N-terminal domain and first zinc finger are inhibitory. SRF and GATA-4 physically associate both in vivo and in vitro through their MADS box and the second zinc finger domains as determined by protein A pullout assays and by in vivo one-hybrid transfection assays using Gal4 fusion proteins. Other cardiovascular tissue-restricted GATA factors, such as GATA-5 and GATA-6, were equivalent to GATA-4 in coactivating SRE-dependent targets. Thus, interaction between the MADS box and C4 zinc finger proteins, a novel regulatory paradigm, mediates activation of SRF-dependent gene expression.

NASA Discipline Musculoskeletal↗
NASA NTRS2000

Skeletal muscle Ca(2+)-independent kinase activity increases during either hypertrophy or running

Spikes in free Ca(2+) initiate contractions in skeletal muscle cells, but whether and how they might signal to transcription factors in skeletal muscles of living animals is unknown. Since previous studies in non-muscle cells have shown that serum response factor (SRF) protein, a transcription factor, is phosphorylated rapidly by Ca(2+)/calmodulin (CaM)-dependent protein kinase after rises in intracellular Ca(2+), we measured enzymatic activity that phosphorylates SRF (designated SRF kinase activity). Homogenates from 7-day-hypertrophied anterior latissimus dorsi muscles of roosters had more Ca(2+)-independent SRF kinase activity than their respective control muscles. However, no differences were noted in Ca(2+)/CaM-dependent SRF kinase activity between control and trained muscles. To determine whether the Ca(2+)-independent and Ca(2+)/CaM-dependent forms of Ca(2+)/CaM-dependent protein kinase II (CaMKII) might contribute to some of the SRF kinase activity, autocamtide-3, a synthetic substrate that is specific for CaMKII, was employed. While the Ca(2+)-independent form of CaMKII was increased, like the Ca(2+)-independent form of SRF kinase, no alteration in CaMKII occurred at 7 days of stretch overload. These observations suggest that some of SRF phosphorylation by skeletal muscle extracts could be due to CaMKII. To determine whether this adaptation was specific to the exercise type (i.e., hypertrophy), similar measurements were made in the white vastus lateralis muscle of rats that had completed 2 wk of voluntary running. Although Ca(2+)-independent SRF kinase was increased, no alteration occurred in Ca(2+)/CaM-dependent SRF kinase activity. Thus any role of Ca(2+)-independent SRF kinase signaling has downstream modulators specific to the exercise phenotype.

NASA Program Fundamental Space Biology↗
NASA NTRS2004

Electron Spin Dephasing and Decoherence by Interaction with Nuclear Spins in Self-Assembled Quantum Dots

Electron spin dephasing and decoherence by its interaction with nuclear spins in self-assembled quantum dots are investigated in the framework of the empirical tight-binding model. Electron spin dephasing in an ensemble of dots is induced by the inhomogeneous precession frequencies of the electron among dots, while electron spin decoherence in a single dot arises from the inhomogeneous precession frequencies of nuclear spins in the dot. For In(x)Ga(1-x) As self-assembled dots containing ~30000 nuclei, the dephasing and decoherence times are predicted to be on the order of 100 ps and 1 (micro)s.

ensemble dephasing↗
NASA NTRS2002

Isolation and characterization of a novel calmodulin-binding protein from potato

Tuberization in potato is controlled by hormonal and environmental signals. Ca(2+), an important intracellular messenger, and calmodulin (CaM), one of the primary Ca(2+) sensors, have been implicated in controlling diverse cellular processes in plants including tuberization. The regulation of cellular processes by CaM involves its interaction with other proteins. To understand the role of Ca(2+)/CaM in tuberization, we have screened an expression library prepared from developing tubers with biotinylated CaM. This screening resulted in isolation of a cDNA encoding a novel CaM-binding protein (potato calmodulin-binding protein (PCBP)). Ca(2+)-dependent binding of the cDNA-encoded protein to CaM is confirmed by (35)S-labeled CaM. The full-length cDNA is 5 kb long and encodes a protein of 1309 amino acids. The deduced amino acid sequence showed significant similarity with a hypothetical protein from another plant, Arabidopsis. However, no homologs of PCBP are found in nonplant systems, suggesting that it is likely to be specific to plants. Using truncated versions of the protein and a synthetic peptide in CaM binding assays we mapped the CaM-binding region to a 20-amino acid stretch (residues 1216-1237). The bacterially expressed protein containing the CaM-binding domain interacted with three CaM isoforms (CaM2, CaM4, and CaM6). PCBP is encoded by a single gene and is expressed differentially in the tissues tested. The expression of CaM, PCBP, and another CaM-binding protein is similar in different tissues and organs. The predicted protein contained seven putative nuclear localization signals and several strong PEST motifs. Fusion of the N-terminal region of the protein containing six of the seven nuclear localization signals to the reporter gene beta-glucuronidase targeted the reporter gene to the nucleus, suggesting a nuclear role for PCBP.

NASA Discipline Plant Biology↗
NASA NTRS1984

Binding constants of phenylalanine for the four mononucleotides

Earlier work has shown that several properties of amino acids correlate directly with properties of their anticodonic nucleotides. Furthermore, in precipitation studies with thermal proteinoids and homopolyribonucleotides, an anticodonic preference was displayed between Lys-rich, Pro-rich and Gly-rich thermal proteinoids and their anticodonic polyribonucleotides. However, Phe-rich thermal proteinoid displayed a preference for its codonic nucleotide, poly U. This inconsistency seemed to be explained by a folding in of the hydrophobic residues of Phe causing the proteinoid to appear more hydrophilic. The present work used nuclear magnetic resonance techniques to resolve a limited question: to which of the four nucleotides does Phe bind most strongly? The results show quite clearly that Phe binds most strongly to its anticodonic nucleotide, AMP.

Khaled, M. A.↗
NASA NTRS1972

Deformed Brueckner-Hartree-Fock calculations

The renormalized Brueckner-Hartree-Fock (RBHF) theory for many-body nuclear systems is generalized to permit calculations for intrinsic states having permanent deformation. Both Hartree-Fock and Brueckner self-consistencies are satisfied, and details of the numerical techniques are discussed. The Hamada-Johnston interaction is used in a study of deformations, binding, size, and separation energies for several nuclei. Electromagnetic transition rates, moments, and electron scattering form factors are calculated using nuclear wave functions obtained by angular momentum projection. Comparison is made to experiment as well as to predictions of ordinary and density-dependent Hartree-Fock Theory.

Ford, W. F.↗
NASA NTRS1972

Deformed Brueckner-Hartree-Fock calculations.

The renormalized Brueckner-Hartree-Fock (RBHF) theory for many-body nuclear systems has been generalized to permit calculations for intrinsic states having permanent deformation. Both Hartree-Fock and Brueckner self-consistencies are satisfied, and details of the numerical techniques are discussed. The Hamada-Johnston interaction is used in a study of deformations, binding, size, and separation energies for several nuclei. Electromagnetic transition rates, moments, and electron scattering form factors are calculated using nuclear wave functions obtained by angular momentum projection. Comparison is made to experiment as well as to predictions of ordinary and density-dependent Hartree-Fock theory.

Ford, W. F.↗
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↗