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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 793 records · Page 44
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism

Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome consists of transposable elements (TEs). Of these, 94% are affected by repeat-induced point mutations (RIP), a genome defense mechanism that acts during the sexual reproduction phase, indicating cryptic or ancient sexual reproduction in this putatively asexual fungus. Long terminal repeat retrotransposons, LINEs, and DNA transposons dominate, with three TE families (Ty3, Ty1, and Tad1) contributing over 60% of the genome size, indicating recent transposition bursts. Screening of 15 additional C. geophilum strains revealed recent and lineage-specific TE expansions, implying that several TEs escaped the RIP machinery and retained potential activity. Supporting TE activity in the context of symbiosis, we found 56 TEs differentially transcribed between ectomycorrhizal and free-living mycelium tissues. An even higher number (n = 66) of TEs were differentially expressed between stress resistance morphology (i.e. sclerotia) and free-living mycelium. This supports that TEs are differentially regulated as a response to symbiotic and stress-related conditions. Our results demonstrate that the C. geophilum genome expansion was driven by a few lineage-specific TE families in recent history, with high RIP activity attesting to sexual reproduction. We also provide insights how TEs could respond to lifestyle transitions and traits associated with desiccation resistance.

Cenococcum geophilum↗
DOE OSTI2024

Hard jet substructure in a multistage approach

We present predictions and postdictions for a wide variety of hard jet-substructure observables using a multistage model within the framework. The details of the multistage model and the various parameter choices are described in []. A novel feature of this model is the presence of two stages of jet modification: a high-virtuality phase [modeled using the modular all twist transverse-scattering elastic-drag and radiation model ()], where modified coherence effects diminish medium-induced radiation, and a lower virtuality phase [modeled using the linear Boltzmann transport model ()], where parton splits are fully resolved by the medium as they endure multiple scattering induced energy loss. Energy-loss calculations are carried out on event-by-event viscous fluid dynamic backgrounds constrained by experimental data. The uniform and consistent descriptions of multiple experimental observables demonstrate the essential role of modified coherence effects and the multistage modeling of jet evolution. Using the best choice of parameters from [], and with no further tuning, we present calculations for the medium modified jet fragmentation function, the groomed jet momentum fraction z g and angular separation r g distributions, as well as the nuclear modification factor of groomed jets. These calculations provide accurate descriptions of published data from experiments at the Large Hadron Collider. Furthermore, we provide predictions from the multistage model for future measurements at the BNL Relativistic Heavy Ion Collider. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Landau-Pomeranchuk-Midgal effect and charm production in p p collisions at energies available at the CERN Large Hadron Collider using the parton cascade model

We study the impact of the Landau-Pomeranchuk-Midgal (LPM) effect on the dynamics of parton interactions in proton-proton collisions at energies available at the CERN Large Hadron Collider. For our investigation we utilize a microscopic kinetic theory based on the Boltzmann equation. The calculation traces the space-time evolution of the cascading partons interacting via semihard pQCD scatterings and fragmentations. We focus on the impact of the LPM effect on the production of charm quarks, since their production is exclusively governed by processes well described in our kinetic theory. Furthermore, the LPM effect is found to become more prominent as the collision energy rises and at central rapidities, and may significantly affect the model's predicted charm distributions at low momenta.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2014

Magnetic fields and massive star formation

Massive stars (M > 8 M {sub ☉}) typically form in parsec-scale molecular clumps that collapse and fragment, leading to the birth of a cluster of stellar objects. We investigate the role of magnetic fields in this process through dust polarization at 870 μm obtained with the Submillimeter Array (SMA). The SMA observations reveal polarization at scales of ≲0.1 pc. The polarization pattern in these objects ranges from ordered hour-glass configurations to more chaotic distributions. By comparing the SMA data with the single dish data at parsec scales, we found that magnetic fields at dense core scales are either aligned within 40° of or perpendicular to the parsec-scale magnetic fields. This finding indicates that magnetic fields play an important role during the collapse and fragmentation of massive molecular clumps and the formation of dense cores. We further compare magnetic fields in dense cores with the major axis of molecular outflows. Despite a limited number of outflows, we found that the outflow axis appears to be randomly oriented with respect to the magnetic field in the core. This result suggests that at the scale of accretion disks (≲ 10{sup 3} AU), angular momentum and dynamic interactions possibly due to close binary or multiple systems dominate over magnetic fields. With this unprecedentedly large sample of massive clumps, we argue on a statistical basis that magnetic fields play an important role during the formation of dense cores at spatial scales of 0.01-0.1 pc in the context of massive star and cluster star formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Single- and multi-photon-induced ultraviolet excitation and photodissociation of CH 3 I probed by coincident ion momentum imaging

The UV-induced photodissociation dynamics of iodomethane (CH 3 I) in its A-band are investigated by time-resolved coincident ion momentum imaging using strong-field ionization as a probe. The delay-dependent kinetic energy distribution of the photofragments resulting from double ionization of the molecule maps the cleavage of the carbon–iodine bond and shows how the existence of a potential well in the di-cationic potential energy surfaces shapes the observed distribution at small pump–probe delays. Furthermore, the competition between single- and multi-photon excitation and ionization of the molecule is studied as a function of the intensity of the UV-pump laser pulse. Two-photon excitation to Rydberg states is identified by tracking the transformation of the delay-dependent singly-charged iodomethane yield from a pure Gaussian distribution at low intensity to a Gaussian with an exponentially decaying tail at higher intensities. In conclusion, dissociative ionization induced by absorption of three UV photons is resolved as an additional delay-dependent feature in the kinetic energy of the fragment ions detected in coincidence.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Fluorescence Quenching of Dyes by Graphene Oxide

Fluorescence quenching of four dyes [acridine orange (AO), rhodamine B (Rd B), rhodamine 110 (Rd 110), and rhodamine 640 (Rd 640)] by colloidal graphene oxide (GO) in phosphate buffer (pH 6.0) was studied. Dynamic and static quenching were analyzed using the Stern–Volmer equation. Static quenching by graphene oxide was observed for AO, Rd 640, and Rd B whereas mixed dynamic and static quenching was characteristic of Rd 110. The Stern–Volmer constant of dynamic quenching was 10 times less than that of static quenching. The measured association constants of the dyes with GO fell in the order 2540 (AO) > 495 (Rd 640) > 260 (Rd 110) > 144 L/g (Rd B). The value of the π–π-stacking interaction was strongly influenced by the phthalic fragment oriented perpendicular to the xanthene in the rhodamine dyes and the four alkyl groups of Rd B as a result of their torsional vibrations and rotational motions.

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

Field-Coupled Water Splitting with Metal-Free Donor–Acceptor Covalent Organic-Framework Junctions

Advancing metal-free electrocatalysts for hydrogen and oxygen evolution reactions (HER/OER) across acidic and alkaline media requires coordinated control of intermediate binding thermodynamics, interfacial charge delivery, and near-electrode transport dynamics. Here, we design amide-linked benzene–triazine covalent organic frameworks (BTA/TzTA-Hz COFs) and integrate them with carbon nanotubes (CNTs) to form COF–CNT junctions that establish a built-in interfacial electric field. Density functional theory (DFT) and electrostatic potential maps indicate complementary active motifs, with benzene-proximal fragments associated with HER and triazine-proximal motifs associated with OER. CNT integration shifts the contact-potential difference by ≈0.20 V, while operando electrochemical impedance spectroscopy suggests partially separable high-frequency junction-charging and lower-frequency Faradaic/transport responses. A 300 mT static magnetic field lowers the HER and OER overpotentials by tens of millivolts. Under anodic bias, the effective interfacial charging capacitance increases, and Mott–Schottky analysis shows an apparent ∼0.15 V flat-band shift with an essentially unchanged slope. Together, these observations are consistent with field-perturbed interfacial charging and altered bias partitioning. Field-dependent impedance and bubble imaging are consistent with magnetohydrodynamic convection that promotes bubble detachment and near-electrode mass transport for both half-reactions, and they reveal an OER-specific high-frequency perturbation under anodic bias. Under field, the heterostructure reaches an OER onset overpotential of ∼261 mV and requires an overpotential of 366 mV at 10 mA cm –2 in alkaline electrolyte. These results illustrate how reticular-framework chemistry, junction engineering, and both built-in and applied fields can program reactivity through interfacial electrostatics and near-electrode transport in organic-framework electrocatalysts.

Garcia-Enriquez, Lissette [Univ. of Texas at El Pa↗
DOE OSTI2022

Structural basis of R-loop recognition by the S9.6 monoclonal antibody

R-loops are ubiquitous, dynamic nucleic-acid structures that play fundamental roles in DNA replication and repair, chromatin and transcription regulation, as well as telomere maintenance. The DNA-RNA hybrid–specific S9.6 monoclonal antibody is widely used to map R-loops. Here, we report crystal structures of a S9.6 antigen-binding fragment (Fab) free and bound to a 13-bp hybrid duplex. We demonstrate that S9.6 exhibits robust selectivity in binding hybrids over double-stranded (ds) RNA and in categorically rejecting dsDNA. S9.6 asymmetrically recognizes a compact epitope of two consecutive RNA nucleotides via their 2'-hydroxyl groups and six consecutive DNA nucleotides via their backbone phosphate and deoxyribose groups. Recognition is mediated principally by aromatic and basic residues of the S9.6 heavy chain, which closely track the curvature of the hybrid minor groove. These findings reveal the molecular basis for S9.6 recognition of R-loops, detail its binding specificity, identify a new hybrid-recognition strategy, and provide a framework for S9.6 protein engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Mapping the magnetic field in the Taurus/B211 filamentary cloud with SOFIA HAWC + and comparing with simulation

ABSTRACT Optical and infrared polarization mapping and recent Planck observations of the filametary cloud L1495 in Taurus show that the large-scale magnetic field is approximately perpendicular to the long axis of the cloud. We use the HAWC + polarimeter on SOFIA to probe the complex magnetic field in the B211 part of the cloud. Our results reveal a dispersion of polarization angles of 36°, about five times that measured on a larger scale by Planck. Applying the Davis–Chandrasekhar–Fermi (DCF) method with velocity information obtained from Institut de Radioastronomie Millimétrique 30 m C18O(1-0) observations, we find two distinct sub-regions with magnetic field strengths differing by more than a factor 3. The quieter sub-region is magnetically critical and sub-Alfv$\acute{\rm e}$nic; the field is comparable to the average field measured in molecular clumps based on Zeeman observations. The more chaotic, super-Alfv$\acute{\rm e}$nic sub-region shows at least three velocity components, indicating interaction among multiple substructures. Its field is much less than the average Zeeman field in molecular clumps, suggesting that the DCF value of the field there may be an underestimate. Numerical simulation of filamentary cloud formation shows that filamentary substructures can strongly perturb the magnetic field. DCF and true field values in the simulation are compared. Pre-stellar cores are observed in B211 and are seen in our simulation. The appendices give a derivation of the standard DCF method that allows for a dispersion in polarization angles that is not small, present an alternate derivation of the structure function version of the DCF method, and treat fragmentation of filaments.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2015

Transient β-hairpin formation in α-synuclein monomer revealed by coarse-grained molecular dynamics simulation

Parkinson’s disease, originating from the intrinsically disordered peptide α-synuclein, is a common neurodegenerative disorder that affects more than 5% of the population above age 85. It remains unclear how α-synuclein monomers undergo conformational changes leading to aggregation and formation of fibrils characteristic for the disease. In the present study, we perform molecular dynamics simulations (over 180 μs in aggregated time) using a hybrid-resolution model, Proteins with Atomic details in Coarse-grained Environment (PACE), to characterize in atomic detail structural ensembles of wild type and mutant monomeric α-synuclein in aqueous solution. The simulations reproduce structural properties of α-synuclein characterized in experiments, such as secondary structure content, long-range contacts, chemical shifts, and {sup 3}J(H{sub N}H{sub C{sub α}})-coupling constants. Most notably, the simulations reveal that a short fragment encompassing region 38-53, adjacent to the non-amyloid-β component region, exhibits a high probability of forming a β-hairpin; this fragment, when isolated from the remainder of α-synuclein, fluctuates frequently into its β-hairpin conformation. Two disease-prone mutations, namely, A30P and A53T, significantly accelerate the formation of a β-hairpin in the stated fragment. We conclude that the formation of a β-hairpin in region 38-53 is a key event during α-synuclein aggregation. We predict further that the G47V mutation impedes the formation of a turn in the β-hairpin and slows down β-hairpin formation, thereby retarding α-synuclein aggregation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Hetero-site-specific X-ray pump-probe spectroscopy for femtosecond intramolecular dynamics

New capabilities at X-ray free-electron laser facilities allow the generation of two-colour femtosecond X-ray pulses, opening the possibility of performing ultrafast studies of X-ray-induced phenomena. Specifically, the experimental realization of hetero-site-specific X-ray-pump/X-ray-probe spectroscopy is of special interest, in which an X-ray pump pulse is absorbed at one site within a molecule and an X-ray probe pulse follows the X-ray-induced dynamics at another site within the same molecule. In this paper, we show experimental evidence of a hetero-site pump-probe signal. By using two-colour 10-fs X-ray pulses, we are able to observe the femtosecond time dependence for the formation of F ions during the fragmentation of XeF 2 molecules following X-ray absorption at the Xe site.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Microexplosions and ignition dynamics in engineered aluminum/polymer fuel particles

Aluminum particles are widely used as a metal fuel in solid propellants. However, poor combustion efficiencies and two-phase flow losses result due in part to particle agglomeration. Engineered composite particles of aluminum (Al) with inclusions of polytetrafluoroethylene (PTFE) or low-density polyethylene (LDPE) have been shown to improve ignition and yield smaller agglomerates in solid propellants, recently. Reductions in agglomeration were attributed to internal pressurization and fragmentation (microexplosions) of the composite particles at the propellant surface. We explore the mechanisms responsible for microexplosions in order to better understand the combustion characteristics of composite fuel particles. Single composite particles of Al/PTFE and Al/LDPE with diameters between 100 and 1200 µm are ignited on a substrate to mimic a burning propellant surface in a controlled environment using a CO 2 laser in the irradiance range of 78–7700 W/cm 2 . Furthermore, the effects of particle size, milling time, and inclusion content on the resulting ignition delay, product particle size distributions, and microexplosion tendencies are reported. For example particles with higher PTFE content (30 wt%) had laser flux ignition thresholds as low as 77 W/cm 2 , exhibiting more burning particle dispersion due to microexplosions compared to the other materials considered. Composite Al/LDPE particles exhibit relatively high ignition thresholds compared to Al/PTFE particles, and microexplosions were observed only with laser fluxes above 5500 W/cm 2 due to low LDPE reactivity with Al resulting in negligible particle self-heating. However, results show that microexplosions can occur for Al containing both low and high reactivity inclusions (LDPE and PTFE, respectively) and that polymer inclusions can be used to tailor the ignition threshold. Furthermore, this class of modified metal particles shows significant promise for application in many different energetic materials that use metal fuels.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Photodissociation dynamics of superexcited O{sub 2}: Dissociation channels O({sup 5}S) vs. O({sup 3}S)

The photodissociation dynamics of O{sub 2}, O{sub 2} + hυ → O({sup 3}P) + O(2p{sup 3}({sup 4}S)3s, {sup 3}S/{sup 5}S), has been studied by combining the XUV laser pump / UV laser probe and velocity map imaging methods in the photon energy range 14.64–15.20 eV. The fragment yield spectra of O({sup 3}S) and O({sup 5}S) and their velocity map images have been recorded using the state-selective (1+1) REMPI method to detect the fragments. The fragment yield spectra show resolved fine structure that arises from the predissociated Rydberg states I, I{sup ′} and I{sup ″} ({sup 3}Π{sub Ω=0,1,2}). The branching ratios between the two decay channels have been measured by one-photon ionization of the fragments O({sup 3}S) and O({sup 5}S) simultaneously. It is surprising to find that the dissociation cross sections for the production of O({sup 5}S) are larger than, or comparable to, those of O({sup 3}S) for the I and I{sup ′} states, while the cross sections for the production of O({sup 5}S) are smaller than those of O({sup 3}S) for the I{sup ″} state. All fragments O({sup 5}S) arise from perpendicular transitions, which provides direct experimental evidence about the symmetry assignments of the states I, I{sup ′} and I{sup ″} excited in this energy region. Although most of the fragments O({sup 3}S) arise from perpendicular transitions, some of them are from parallel transitions. Based on the calculated ab initio potential energy curves, we propose that the neutral dissociation into O({sup 3}P) + O({sup 3}S) occurs mainly via the interaction of the Rydberg states I, I{sup ′}, and I{sup ″} with the vibrational continuum of the diabatic 8{sup 3}Π{sub u} state (1π{sub u}{sup −1}(a{sup 4}Π{sub u})3sσ{sub g},{sup 3}Π{sub u}), while the neutral dissociation into O({sup 3}P) + O({sup 5}S) occurs mainly via the interaction of Rydberg states I, I{sup ′}, and I{sup ″} with the diabatic 7{sup 3}Π{sub u} (1π{sub g}{sup −1}(X{sup 2}Π{sub g})3pσ{sub u},{sup 3}Π{sub u})

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Constraints on lepton asymmetry from nucleosynthesis in a linearly coasting cosmology

We study the effect of neutrino degeneracy on primordial nucleosynthesis in a universe in which the cosmological scale factor evolves linearly with time. The degeneracy parameter of electron type neutrinos (ξ{sub e}) determines the n/p (neutron to proton) ratio, which in turn determines the abundance of {sup 4}He in a manner quite distinct from the Standard Scenario. The observed abundances of {sup 4}He, Y{sub P} = 0.254 ± 0.003, and the minimum metallicity that is essential for fragmentation and cooling processes in star forming prestellar gas clouds (Z = Z{sub cr} = 10{sup −6}Z{sub ⊙}), constrain the baryon to photon ratio, η{sub B} = (3.927±0.292)10{sup −9}, corresponding to a baryonic matter density, Ω{sub B} = 0.263 ± 0.026 and ξ{sub e} = -2.165 ± 0.171. This closes the dynamic mass estimates of matter in the universe, obtained from large scale velocity dispersion in galaxy clusters, by baryons alone. Useful byproducts are the threshold X(CNO) abundances required to trigger the CNO cycle in the observed low metallicity stars in the universe.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1987

Petrographic evidence for nonlinear cooling rates and a volcanic origin for Apollo 15 KREEP basalts

The results of petrographic studies of Apollo 15 KREEP basalt fragments are discussed. The Apollo 15 KREEP basalts display a wide range of grain size and texture, with some samples showing evidence for a two-stage (slow early, fast late) cooling in the form of phenocrysts, glomerocrysts, and large proportions of residual quenched glass. Two-stage cooling is common in volcanic, dynamic environments. The inference that these and other Apollo 15 KREEP basalts are volcanic requires a reexamination of the chemical and isotopic constraints on the genesis and regenesis of KREEP and early lunar evolution.

Ryder, Graham↗
NASA NTRS2000

Automatic Data Traffic Control on DSM Architecture

We study data traffic on distributed shared memory machines and conclude that data placement and grouping improve performance of scientific codes. We present several methods which user can employ to improve data traffic in his code. We report on implementation of a tool which detects the code fragments causing data congestions and advises user on improvements of data routing in these fragments. The capabilities of the tool include deduction of data alignment and affinity from the source code; detection of the code constructs having abnormally high cache or TLB misses; generation of data placement constructs. We demonstrate the capabilities of the tool on experiments with NAS parallel benchmarks and with a simple computational fluid dynamics application ARC3D.

Frumkin, Michael↗