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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 1,747 records · Page 97
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

RNA quaternary structure and global symmetry

Many proteins associate into symmetric multisubunit complexes. Structural analyses suggested that, by contrast, virtually all RNAs with complex 3D structures function as asymmetric monomers. Recent crystal structures revealed that several biological RNAs exhibit global symmetry at the level of their tertiary and quaternary structures. Here we survey known examples of global RNA symmetry, including the true quaternary symmetry of the bacteriophage Φ29 prohead RNA (pRNA) and the internal pseudosymmetry of the single-chain flavin mononucleotide (FMN), glycine, and cyclic di-AMP (c-di-AMP) riboswitches. For these RNAs, we report global symmetry stabilizes the RNA fold, coordinates ligand–RNA interactions, and facilitates association with symmetric binding partners.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Chemical Kinetics for the Oxidation of Californium(III) Ions with Select Radiation-Induced Inorganic Radicals (Cl 2 •– and SO 4 •– )

Despite the availability of transuranic elements increasing in recent years, our understanding of their most basic and inherent radiation chemistry is limited and yet essential for accurate interpretation of their physical and chemical properties. Here, in this work, we explore the transient interactions between trivalent californium ions (Cf 3+ ) and select inorganic radicals arising from the radiolytic decomposition of common anions and functional group constituents, specifically the dichlorine (Cl 2 •- ) and sulfate (SO 4 •- ) radical anions. Chemical kinetics, as measured by integrated electron pulse radiolysis and transient absorption spectroscopy techniques, are presented for the reactions of these two oxidizing radicals with Cf 3+ ions. The derived and ionic strength corrected second-order rate coefficients (k) for these radiation-induced processes are k(Cf 3+ + Cl 2 •- ) = (8.28 ± 0.61) × 10 5 M -1 s -1 and k(Cf 3+ + SO 4 •- ) = (9.50 ± 0.43) × 10 8 M -1 s -1 under ambient temperature conditions (22 ± 1 °C).

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2012

Near quantitative agreement of model free DFT- MD predictions with XAFS observations of the hydration structure of highly charged transition metal ions

DFT-MD simulations (PBE96 and PBE0) with MD-XAFS scattering calculations (FEFF9) show near quantitative agreement with new and existing XAFS measurements for a comprehensive series of transition metal ions which interact with their hydration shells via complex mechanisms (high spin, covalency, charge transfer, etc.). This work was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. Pacific Northwest National Laboratory (PNNL) is operated for the U.S. DOE by Battelle. A portion of the research was performed using EMSL, a national scientific user facility sponsored by the U.S. DOE's Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2015

A thermodynamical analysis of rf current drive with fast electrons

The problem of rf current drive (CD) by pushing fast electrons with high-parallel-phase-velocity waves, such as lower-hybrid (LH) or electron-cyclotron (EC) waves, is revisited using the first and second laws, the former to retrieve the well-known one-dimensional (1D) steady-state CD efficiency, and the latter to calculate a lower bound for the rate of entropy production when approaching steady state. The laws of thermodynamics are written in a form that explicitly takes care of frictional dissipation and are thus applied to a population of fast electrons evolving under the influence of a dc electric field, rf waves, and collisions while in contact with a thermal, Maxwellian reservoir with a well-defined temperature. Besides the laws of macroscopic thermodynamics, there is recourse to basic elements of kinetic theory only, being assumed a residual dc electric field and a strong rf drive, capable of sustaining in the resonant region, where waves interact with electrons, a raised fast-electron tail distribution, which becomes an essentially flat plateau in the case of the 1D theory for LHCD. Within the 1D model, particularly suited for LHCD as it solely retains fast-electron dynamics in velocity space parallel to the ambient magnetic field, an H theorem for rf CD is also derived, which is written in different forms, and additional physics is recovered, such as the synergy between the dc and rf power sources, including the rf-induced hot conductivity, as well as the equation for electron-bulk heating. As much as possible 1D results are extended to 2D, to account for ECCD by also considering fast-electron velocity-space dynamics in the direction perpendicular to the magnetic field, which leads to a detailed discussion on how the definition of an rf-induced conductivity may depend on whether one works at constant rf current or power. Moreover, working out the collisional dissipated power and entropy-production rate written in terms of the fast-electron distribution, it is shown that the well-known formula for the steady-state CD efficiency, usually obtained from the first law in the form of power balance between the external sources and collisional losses, emerges as a lower bound for that CD figure of merit, in what can be interpreted as an instance of the second law.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2016

Green functions of currents in the odd-intrinsic parity sector of QCD

The independent operator basis of the most important resonances in the odd-intrinsic parity sector of QCD allows us to construct Lagrangians for corresponding Feynman diagrams of several types of interaction channels of the mesons and resonances. Here, we will discuss all three-point current correlators non-trivial for this sector. We briefly summarize their basic properties and high energy behaviour via the operator product expansion (OPE) framework. We also show that the vector field formalism is not compatible with the OPE, and for this reason the antisymmetric field formalism is a more suitable choice. We also briefly introduce some fundamental phenomological aspects that could be useful in the next studies.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Stochastic modelling of intermittent fluctuations in the scrape-off layer: Correlations, distributions, level crossings, and moment estimation

A stochastic model is presented for intermittent fluctuations in the scrape-off layer of magnetically confined plasmas. The fluctuations in the plasma density are modeled by a super-position of uncorrelated pulses with fixed shape and duration, describing radial motion of blob-like structures. In the case of an exponential pulse shape and exponentially distributed pulse amplitudes, predictions are given for the lowest order moments, probability density function, auto-correlation function, level crossings, and average times for periods spent above and below a given threshold level. Also, the mean squared errors on estimators of sample mean and variance for realizations of the process by finite time series are obtained. These results are discussed in the context of single-point measurements of fluctuations in the scrape-off layer, broad density profiles, and implications for plasma–wall interactions due to the transient transport events in fusion grade plasmas. The results may also have wide applications for modelling fluctuations in other magnetized plasmas such as basic laboratory experiments and ionospheric irregularities.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2020

Phenological responses of temperate and boreal trees to warming depend on ambient spring temperatures, leaf habit, and geographic range

Changes in plant phenology associated with climate change have been observed globally. What is poorly known is whether and how phenological responses to climate warming will differ from year to year, season to season, habitat to habitat, or species to species. Here, we present 5 y of phenological responses to experimental warming for 10 subboreal tree species. Research took place in the open-air B4WarmED experiment in Minnesota. The design is a two habitat (understory and open) × three warming treatments (ambient, +1.7 °C, +3.4 °C) factorial at two sites. Phenology was measured twice weekly during the growing seasons of 2009 through 2013. We found significant interannual variation in the effect of warming and differences among species in response to warming that relate to geographic origin and plant functional group. Moreover, responses to experimental temperature variation were similar to responses to natural temperature variation. Warming advanced the date of budburst more in early compared to late springs, suggesting that to simulate interannual variability in climate sensitivity of phenology, models should employ process-based or continuous development approaches. Differences among species in timing of budburst were also greater in early compared to late springs. Our results suggest that climate change—which will make most springs relatively “early”—could lead to a future with more variable phenology among years and among species, with consequences including greater risk of inappropriately early leafing and altered interactions among species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Disruption of evolutionarily correlated tRNA elements impairs accurate decoding

Bacterial transfer RNAs (tRNAs) contain evolutionarily conserved sequences and modifications that ensure uniform binding to the ribosome and optimal translational accuracy despite differences in their aminoacyl attachments and anticodon nucleotide sequences. In the tRNA anticodon stem-loop, the anticodon sequence is correlated with a base pair in the anticodon loop (nucleotides 32 and 38) to tune the binding of each tRNA to the decoding center in the ribosome. Disruption of this correlation renders the ribosome unable to distinguish correct from incorrect tRNAs. The molecular basis for how these two tRNA features combine to ensure accurate decoding is unclear. In this work, we solved structures of the bacterial ribosome containing either wild-type tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ or tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ containing a reversed 32–38 pair on cognate and near-cognate codons. Structures of wild-type tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ bound to the ribosome reveal 23S ribosomal RNA (rRNA) nucleotide A1913 positional changes that are dependent on whether the codon-anticodon interaction is cognate or near cognate. Further, the 32–38 pair is destabilized in the context of a near-cognate codon-anticodon pair. Reversal of the pairing in tRNA$^{\mathrm{Ala}}_{\mathrm{GGC}}$ ablates A1913 movement regardless of whether the interaction is cognate or near cognate. These results demonstrate that disrupting 32–38 and anticodon sequences alters interactions with the ribosome that directly contribute to misreading.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

KINETIC EVOLUTION OF CORONAL HOLE PROTONS BY IMBALANCED ION-CYCLOTRON WAVES: IMPLICATIONS FOR MEASUREMENTS BY SOLAR PROBE PLUS

We extend the kinetic guiding-center model of collisionless coronal hole protons presented in Isenberg and Vasquez to consider driving by imbalanced spectra of obliquely propagating ion-cyclotron waves. These waves are assumed to be a small by-product of the imbalanced turbulent cascade to high perpendicular wavenumber, and their total intensity is taken to be 1% of the total fluctuation energy. We also extend the kinetic solutions for the proton distribution function in the resulting fast solar wind to heliocentric distances of 20 solar radii, which will be attainable by the Solar Probe Plus spacecraft. We consider three ratios of outward-propagating to inward-propagating resonant intensities: 1, 4, and 9. The self-consistent bulk flow speed reaches fast solar wind values in all cases, and these speeds are basically independent of the intensity ratio. The steady-state proton distribution is highly organized into nested constant-density shells by the resonant wave-particle interaction. The radial evolution of this kinetic distribution as the coronal hole plasma flows outward is understood as a competition between the inward- and outward-directed large-scale forces, causing an effective circulation of particles through the (v{sub ∥}, v{sub ⊥}) phase space and a characteristic asymmetric shape to the distribution. These asymmetries are substantial and persist to the outer limit of the model computation, where they should be observable by the Solar Probe Plus instruments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Regulation of FANCD2 and FANCI monoubiquitination by their interaction and by DNA

FANCD2 and FANCI function together in the Fanconi anemia network of deoxyribonucleic acid (DNA) crosslink repair. These proteins form the dimeric ID2 complex that binds DNA and becomes monoubiquitinated upon exposure of cells to DNA crosslinking agents. The monoubiquitinated ID2 complex is thought to facilitate DNA repair via recruitment of specific nucleases, translesion DNA polymerases and the homologous recombination machinery. Using the ubiquitin conjugating enzyme (E2) UBE2T and ubiquitin ligase (E3) FANCL, monoubiquitination of human FANCD2 and FANCI was examined. The ID2 complex is a poor substrate for monoubiquitination, consistent with the published crystal structure showing the solvent inaccessibility of the target lysines. Importantly, FANCD2 monoubiquitination within the ID2 complex is strongly stimulated by duplex or branched DNA, but unstructured singlestranded DNA or chromatinized DNA is ineffective. Interaction of FANCL with the ID2 complex is indispensable for its E3 ligase efficacy. Interestingly, mutations in FANCI that impair its DNA binding activity compromise DNA-stimulated FANCD2 monoubiquitination. Moreover, we demonstrate that in the absence of FANCD2, DNA also stimulates FANCI monoubiquitination, but in a FANCL-independent manner. These results implicate the role of a proper DNA ligand in FANCD2 and FANCI monoubiquitination, and reveal regulatory mechanisms that are dependent on protein–protein and protein–DNA interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Spectroscopy of Spinons in Coulomb Quantum Spin Liquids

We calculate the effect of the emergent photon on threshold production of spinons in U(1) Coulomb spin liquids such as quantum spin ice. The emergent Coulomb interaction modifies the threshold production cross-section dramatically, changing the weak turn-on expected from the density of states to an abrupt onset reflecting the basic coupling parameters. The slow photon typical in existing lattice models and materials suppresses the intensity at finite momentum and allows profuse Cerenkov radiation beyond a critical momentum. Furthermore, these features are broadly consistent with recent numerical and experimental results.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Weak gravity conjecture

The weak gravity conjecture holds that in a theory of quantum gravity any gauge force must mediate interactions stronger than gravity for some particles. This statement has surprisingly deep and extensive connections to many different areas of physics and mathematics. Several variations on the basic conjecture have been proposed, including statements that are much stronger but are nonetheless satisfied by all known consistent quantum gravity theories. These related conjectures and the evidence for their validity in the string theory landscape are reviewed. Also reviewed here are a variety of arguments for these conjectures, which tend to fall into two categories: qualitative arguments that claim the conjecture is plausible based on general principles and quantitative arguments for various special cases or analogs of the conjecture. The implications of these conjectures for particle physics, cosmology, general relativity, and mathematics are also outlined. Finally, important directions for future research are highlighted.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2017

Elucidation of complexity and prediction of interactions in microbial communities

Summary Microorganisms engage in complex interactions with other members of the microbial community, higher organisms as well as their environment. However, determining the exact nature of these interactions can be challenging due to the large number of members in these communities and the manifold of interactions they can engage in. Various omic data, such as 16S rRNA gene sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics and metabolomics, have been deployed to unravel the community structure, interactions and resulting community dynamics in situ . Interpretation of these multi‐omic data often requires advanced computational methods. Modelling approaches are powerful tools to integrate, contextualize and interpret experimental data, thus shedding light on the underlying processes shaping the microbiome. Here, we review current methods and approaches, both experimental and computational, to elucidate interactions in microbial communities and to predict their responses to perturbations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Identification of Adenovirus Serotype 5 Hexon Regions That Interact with Scavenger Receptors

Most of an intravenous dose of species C adenovirus serotype 5 (Ad5) is destroyed by liver Kupffer cells. In contrast, another species C virus, Ad6, evades these cells to mediate more efficient liver gene delivery. Given that this difference in Kupffer cell interaction is mediated by the hypervariable (HVR) loops of the virus hexon protein, we genetically modified each of the seven HVRs of Ad5 with a cysteine residue to enable conditional blocking of these sites with polyethylene glycol (PEG). We show that these modifications do not affect in vitro virus transduction. In contrast, after intravenous injection, targeted PEGylation at HVRs 1, 2, 5, and 7 increased viral liver transduction up to 20-fold. Elimination or saturation of liver Kupffer cells did not significantly affect this increase in the liver transduction. In vitro, PEGylation blocked uptake of viruses via the Kupffer cell scavenger receptor SRA-II. These data suggest that HVRs 1, 2, 5, and 7 of Ad5 may be involved in Kupffer cell recognition and subsequent destruction. These data also demonstrate that this conditional genetic-chemical mutation strategy is a useful tool for investigating the interactions of viruses with host tissues.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Peptidoglycan Contribution to the B Cell Superantigen Activity of Staphylococcal Protein A

Staphylococcus aureus causes reiterative and chronic persistent infections. This can be explained by the formidable ability of this pathogen to escape immune surveillance mechanisms. Cells of S. aureus display the abundant staphylococcal protein A (SpA). SpA binds to immunoglobulin (Ig) molecules and coats the bacterial surface to prevent phagocytic uptake. SpA also binds and cross-links variable heavy 3 (V H 3) idiotype (IgM) B cell receptors, promoting B cell expansion and the secretion of nonspecific V H 3-IgM via a mechanism requiring CD4 + T cell help. SpA binding to antibodies is mediated by the N-terminal Ig-binding domains (IgBDs). The so-called region X, uncharacterized LysM domain, and C-terminal LPXTG sorting signal for peptidoglycan attachment complete the linear structure of the protein. Here, we report that both the LysM domain and the LPXTG motif sorting signal are required for the B cell superantigen activity of SpA in a mouse model of infection. SpA molecules purified from staphylococcal cultures are sufficient to exert B cell superantigen activity and promote immunoglobulin secretion as long as they carry intact LysM and LPXTG motif domains with bound peptidoglycan fragments. The LysM domain binds the glycan chains of peptidoglycan fragments, whereas the LPXTG motif is covalently linked to wall peptides lacking glycan. These findings emphasize the complexity of SpA interactions with B cell receptors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Identification of Effector Metabolites Using Exometabolite Profiling of Diverse Microalgae

Dissolved exometabolites mediate algal interactions in aquatic ecosystems, but microalgal exometabolomes remain understudied. We conducted an untargeted metabolomic analysis of nonpolar exometabolites exuded from four phylogenetically and ecologically diverse eukaryotic microalgal strains grown in the laboratory, freshwater Chlamydomonas reinhardtii, brackish Desmodesmus sp., marine Phaeodactylum tricornutum, and marine Microchloropsis salina, to identify released metabolites based on relative enrichment in the exometabolomes compared to cell pellet metabolomes. Exudates from the different taxa were distinct, but we did not observe clear phylogenetic patterns. We used feature-based molecular networking to explore the identities of these metabolites, revealing several distinct di- and tripeptides secreted by each of the algae, lumichrome, a compound that is known to be involved in plant growth and bacterial quorum sensing, and novel prostaglandin-like compounds. We further investigated the impacts of exogenous additions of eight compounds selected based on exometabolome enrichment on algal growth. Of these compounds, five (lumichrome, 5'-S-methyl-5'-thioadenosine, 17-phenyl trinor prostaglandin A2, dodecanedioic acid, and aleuritic acid) impacted growth in at least one of the algal cultures. Two of these compounds (dodecanedioic acid and aleuritic acid) produced contrasting results, increasing growth in some algae and decreasing growth in others. Together, our results reveal new groups of microalgal exometabolites, some of which could alter algal growth when provided exogenously, suggesting potential roles in allelopathy and algal interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2012

Structural Basis of Ets1 Cooperative Binding to Widely Separated Sites on Promoter DNA

Ets1 is a member of the Ets family of transcription factors. Ets1 is expressed in autoinhibited form and its DNA binding depends on partner proteins bound to adjacent sequences or the relative positioning of a second Ets-binding site (EBS). The autoinhibition of Ets1 is mediated by structural coupling of regions flanking the DNA-binding domain. The NMR structure of Ets1 revealed that the inhibitory regions comprised of helices HI1 and HI2 and H4 are packed together on the Ets domain to form an inhibitory module. The crystal structure of Ets1 unexpectedly revealed a homodimer in which homodimerisation occurs via swapping of HI1 helices. Modeling of DNA binding indicates that the Ets1 dimer can bind to two antiparallel pieces of DNA. To verify this, we crystallized and solved the structure of the complex comprised of Ets1 dimer and two pieces of DNA. DNA binding by Ets1 dimer resulted in formation of additional intermolecular protein - DNA interactions, implying that the complex formation is cooperative.

59 BASIC BIOLOGICAL SCIENCES↗