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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 865 records · Page 48
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Sequence-directed dynamic covalent assembly of base-4-encoded oligomers

As an information-bearing biomacromolecule, DNA is encoded in base-4, where each residue site can be occupied by any one of four nucleobases. Mimicking the information dense, sequence-selective hybridization of DNA, we demonstrate two orthogonal dynamic covalent interactions to effect the selective assembly of molecular ladders and grids from base-4-encoded oligo(peptoid)s.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

An investigation of the star-forming main sequence considering the nebular continuum emission at low- z

Galaxy evolution has been studied by interpreting the spectral energy distribution of galaxies using spectral synthesis codes. This method has been crucial in discovering different pillars of modern galaxy evolution theories. However, this analysis was mostly carried out using spectral synthesis codes that are purely stellar, that is, they assume that the nebular contribution to the total continuum is negligible. The code FADO is the first publicly available population spectral synthesis tool that treats the contribution from ionised gas to the observed emission self-consistently. This is expected to have a particularly strong effect in star-forming (SF) galaxies. We study the impact of the nebular contribution on the determination of the star formation rate (SFR), stellar mass, and consequent effect on the star-forming main sequence (SFMS) at low redshift. We applied FADO to the spectral database of the SDSS to derive the physical properties of galaxies. As a comparison, we used the data in the MPA-JHU catalogue, which contains the properties of SDSS galaxies derived without the nebular contribution. We selected a sample of SF galaxies with Hα and Hβ flux measurements, and we corrected the fluxes for the nebular extinction through the Balmer decrement. We then calculated the Hα luminosity to estimate the SFR. Then, by combining the stellar mass and SFR estimates from FADO and MPA-JHU, the SFMS was obtained. The Hα flux estimates are similar between FADO and MPA-JHU. Because the Hα flux was used as tracer of the SFR, FADO and MPA-JHU agree in their SFR. The stellar mass estimates are slightly higher for FADO than for MPA-JHU on average. However, considering the uncertainties, the differences are negligible. With similar SFR and stellar mass estimates, the derived SFMS is also similar between FADO and MPA-JHU. Our results show that for SDSS normal SF galaxies, the additional modelling of the nebular contribution does not affect the retrieved fluxes and consequentially also does not influence SFR estimators based on the extinction-corrected Hα luminosity. For the stellar masses, the results point to the same conclusion. These results are a consequence of the fact that the vast majority of normal SF galaxies in the SDSS have a low nebular contribution. However, the obtained agreement might only hold for local SF galaxies, but higher-redshift galaxies might show different physical properties when FADO is used. This would then be an effect of the expected increased nebular contribution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S 1 , S 2 , S 3 , and S 0 , showing that a water molecule is inserted during the S 2 → S 3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O 2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S 2 → S 3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, Q A and Q B , are observed. At the donor site, tyrosine Y Z and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of O X (H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a “water wheel”-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S 2 → S 3 transition mirrors the appearance of O X electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus

Significance Microorganisms have evolved transcriptional networks to prioritize utilization of available nutrient sources. For filamentous fungi, such as Neurospora crassa , this entails distinguishing between a variety of organic and inorganic nitrogen sources. Here, we transcriptionally profiled the response of N. crassa to a variety of nitrogen sources and used DNA affinity purification sequencing to characterize the role of regulatory genes and their direct downstream targets. We identified a transcription factor responsible for regulating genes involved in amino acid and mannose metabolism. By comparing the genes regulated by transcription factors that regulate specific nitrogen utilization pathways and transcription factors that regulate utilization of all nitrogen sources that require metabolic processing before utilization, we revealed aspects of the nitrogen regulatory network.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction

Controlling the selectivity of a reaction is critical for target-oriented synthesis. Accessing complementary selectivity profiles enables divergent synthetic strategies, but is challenging to achieve in biocatalytic reactions given enzymes’ innate preferences of a single selectivity. Thus, it is critical to understand the structural features that control selectivity in biocatalytic reactions to achieve tunable selectivity. Here, we investigate the structural features that control the stereoselectivity in an oxidative dearomatization reaction that is key to making azaphilone natural products. Crystal structures of enantiocomplementary biocatalysts guided the development of multiple hypotheses centered on the structural features that control the stereochemical outcome of the reaction; however, in many cases, direct substitutions of active site residues in natural proteins led to inactive enzymes. Ancestral sequence reconstruction (ASR) and resurrection were employed as an alternative strategy to probe the impact of each residue on the stereochemical outcome of the dearomatization reaction. These studies suggest that two mechanisms are active in controlling the stereochemical outcome of the oxidative dearomatization reaction: one involving multiple active site residues in AzaH and the other dominated by a single Phe to Tyr switch in TropB and AfoD. Moreover, this study suggests that the flavin-dependent monooxygenases (FDMOs) adopt simple and flexible strategies to control stereoselectivity, which has led to stereocomplementary azaphilone natural products produced by fungi. This paradigm of combining ASR and resurrection with mutational and computational studies showcases sets of tools for understanding enzyme mechanisms and provides a solid foundation for future protein engineering efforts.

Science & Technology - Other Topics↗
DOE OSTI2024

Dissecting neurofilament tail sequence-phosphorylation-structure relationships with multicomponent reconstituted protein brushes

Neurofilaments (NFs) are multisubunit, bottlebrush-shaped intermediate filaments abundant in the axonal cytoskeleton. Each NF subunit contains a long intrinsically disordered tail domain, which protrudes from the NF core to form a “brush” surrounding each NF. Precisely how the tails’ variable charge patterns and repetitive phosphorylation sites mediate their conformation within the brush remains an open question in axonal biology. We address this problem by grafting recombinant NF tail protein constructs NF-Light, -Medium, and -Heavy (NFL, NFM, and NFH) to surfaces, yielding protein brushes of defined stoichiometry that can be phosphorylated in vitro. Atomic force microscopy measurements reveal that brush height depends on composition monotonically but not always linearly for binary NFL:NFM or NFL:NFH systems, and that NFM-based brushes are highly extended, while brushes incorporating the much larger NFH are surprisingly compact even after multisite phosphorylation. Complementary self-consistent field theory (SCFT) predicts multilayer brush morphologies for NFM and phosphorylated NFH brushes. Further experiments and SCFT analysis with designed mutants reveal that N-terminal negative charges in the NFH tail repel phosphorylated residues to generate the multilayer morphology, while the C-terminal charge-neutral region contributes to multilayer brush morphology but not total brush height. Charge-shuffled NFM variants show that charge segregation promotes brush collapse near physiological ionic strengths. Collectively, this study supports a role for NFM in establishing a dynamic range for NF brush conformation, lending insight into previous in vitro and in vivo findings. More broadly, this work establishes a platform for dissecting contributions of disordered protein sequence to conformation at interfaces.

Science & Technology - Other Topics↗
DOE OSTI2025

Sequence modeling of higher-order wave modes of quasi-circular, spinning, non-precessing binary black hole mergers

Higher-order gravitational wave modes from quasi-circular, spinning, non-precessing binary-black-hole (BBH) mergers encode rich information about the nonlinear dynamics of strong-field gravity. We present a transformer-based sequence-completion surrogate that, given an early-inspiral segment, forecasts the subsequent late inspiral, merger, and ringdown. The intended applications are (i) patching or completing expensive or interrupted numerical-relativity (NR) simulations and (ii) providing late-time cross-checks and rapid hybridization studies. The training set is built from the NRHybSur3dq8 surrogate, which provides spherical-harmonic modes up to $\ell$ ≤ 4 (excluding (4, 0) and (4,±1), and including (5, 5)) for mass ratios q ≤ 8, dimensionless spin components s$^{z}_{1,2}$ ϵ[–0.8, 0.8], and inclination angles θ ϵ [0, π]. Waveforms are supplied on the interval t ϵ [–5000M, –100 M) and the model autoregressively generates the plus and cross polarizations (h + , h x ) on t ϵ [–100 M, 130M]. Training on the Delta supercomputer with 16 NVIDIA A100 GPUs required ~15 h on more than 14 million hybrid waveforms. Evaluation on a held-out test set of 840,000 samples yields mean and median overlaps of 0.996 and 0.997, respectively, with respect to the surrogate ground truth.

black-hole merger↗
DOE OSTI2020

Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences

In recent years, ‘multi-omic’ sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. Furthermore, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Microbiome Comparison and Pathogen Identification for Three Migrating Passerines Captured During Spring Season in Jordan Using 16S rRNA Sequencing

Jordan is located on an important spot along the Mediterranean and Black Sea Flyway. Hundreds of migratory bird species have been identified stopping over in Jordan during spring and autumn migratory seasons. Compared to mammals and economically important birds, the microbiomes of wild bird species are severely understudied. Gut microbial composition is a valuable source of information that reflects food preferences, foraging behavior, and the risk of pathogen transmission to humans and other animals. In this study, we assessed the microbiome composition of three species of migrating passerines (willow warblers, lesser whitethroats, and common reed warblers) captured during the spring migration stopover in Jordan in 2023. A total of 59 fecal samples were selected evenly from the three species and subjected to 16S sequencing and microbiome analysis. Our objectives were to determine the diversity of bacteria in these three species, assess the amount of intra- and inter-specific variation, and detect pathogenic genera and species that could pose health risks to humans, domestic animals, and wildlife. Bacteria mainly belonged to the phyla Proteobacteria (62%), Actinobacteriota (18%), Firmicutes (13%), Cyanobacteria (5%), and Bacteroidota (1%). The results reveal that lesser whitethroats had the greatest variation in bacterial genus richness, Shannon diversity, and microbial composition compared to willow warblers and common reed warblers. The three bird species harbored several pathogenic genera and species, including Campylobacter, Enterococcus, Escherichia-Shigella, Mycoplasma, Rickettsia, Clostridium perfringens, and Vibrio cholerae. We suggest further investigation to understand the relationship between migratory behavior and their gut microbiome. We advocate for the use of advanced molecular techniques to characterize the pathogens found in migratory birds that might have public and environmental health impacts in addition to economic loss.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

PLATO hare-and-hounds exercise: asteroseismic model fitting of main-sequence solar-like pulsators

ABSTRACT Asteroseismology is a powerful tool to infer fundamental stellar properties. The use of these asteroseismic-inferred properties in a growing number of astrophysical contexts makes it vital to understand their accuracy. Consequently, we performed a hare-and-hounds exercise where the hares simulated data for six artificial main-sequence stars and the hounds inferred their properties based on different inference procedures. To mimic a pipeline such as that planned for the PLATO mission, all hounds used the same model grid. Some stars were simulated using the physics adopted in the grid, others a different one. The maximum relative differences found (in absolute value) between the inferred and true values of the mass, radius, and age were 4.32, 1.33, and 11.25 per cent, respectively. The largest systematic differences in radius and age were found for a star simulated assuming gravitational settling, not accounted for in the model grid, with biases of −0.88 per cent (radius) and 8.66 per cent (age). For the mass, the most significant bias (−3.16 per cent) was found for a star with a helium enrichment ratio outside the grid range. Moreover, an ∼7 per cent dispersion in age was found when adopting different prescriptions for the surface corrections or shifting the classical observations by ±1σ. The choice of the relative weight given to the classical and seismic constraints also impacted significantly the accuracy and precision of the results. Interestingly, only a few frequencies were required to achieve accurate results on the mass and radius. For the age the same was true when at least one l = 2 mode was considered.

Cunha, M. S. (ORCID:0000000182377343)↗
DOE OSTI2021

Stars in the local galactic thick disc and halo in Gaia EDR3: a catalogue of half a million local main-sequence stars with photometric metallicities

We present a catalogue of 551 214 main-sequence stars in the local (d < 2 kpc) Galactic thick disc and halo, based on a search of stars with large proper motions ($\mu _{\rm tot} \gt 40.0~\rm mas\, yr^{-1}$) in the Gaia Early Data Release 3. We derive photometric metallicity calibrated from the colour–luminosity–metallicity distribution of 20 047 stars with spectroscopic metallicities, collected from various spectroscopic surveys, including SDSS SEGUE/APOGEE, GALAH DR3, and LAMOST DR6. We combine these results to construct an empirical colour–magnitude–metallicity grid, which can be used to estimate photometric metallicities for low-mass metal-poor stars of K and M subtypes from their absolute G magnitude and colour values. We find that low-mass, high-velocity stars in our catalogue share similar kinematics as reported in recent studies of more luminous Galactic halo stars. The pseudo-kinematic analysis of our sample recovers the main local halo structures, including the Gaia–Enceladus Stream and the Helmi stream; aside from these, the local halo stars appear to show a remarkably smooth distribution in velocity space. Since the future Gaia data release will provide radial velocity measurements for only a small number of our sample, our catalogue provides targets of high interest for the future spectroscopic observation programs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Jets from main sequence and white dwarf companions during common envelope evolution

ABSTRACT It has long been speculated that jet feedback from accretion on to the companion during a common envelope (CE) event could affect the orbital evolution and envelope unbinding process. We present global 3D hydrodynamical simulations of CE evolution (CEE) that include a jet subgrid model and compare them with an otherwise identical model without a jet. Our binary consists of a 2-M⊙ red giant branch primary and a 1- or 0.5-M⊙ main sequence (MS) or white dwarf (WD) secondary companion modelled as a point particle. We run the simulations for 10 orbits (40 d). Our jet model adds mass at a constant rate $\dot{M}_\mathrm{j}$ of the order of the Eddington rate, with maximum velocity vj of the order of the escape speed, to two spherical sectors with the jet axis perpendicular to the orbital plane. We explore the influence of the jet on orbital evolution, envelope morphology and envelope unbinding, and assess the dependence of the results on the jet mass-loss rate, launch speed, companion mass, opening angle, and accretion rate. In line with our theoretical estimates, jets are choked around the time of first periastron passage and remain choked thereafter. Subsequent to choking, but not before, jets efficiently transfer energy to bound envelope material. This leads to increases in unbound mass of up to $\sim 10{{\ \rm per\ cent}}$, as compared to the simulations without jets. We also estimate the cumulative effects of jets over a full CE phase, finding that jets launched by MS and WD companions are unlikely to dominate envelope unbinding.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Clash of Titans: the impact of cluster mergers in the galaxy cluster red sequence

ABSTRACT Merging of galaxy clusters are some of the most energetic events in the Universe, and they provide a unique environment to study galaxy evolution. We use a sample of 84 merging and relaxed SPT galaxy clusters candidates, observed with the Dark Energy Camera in the 0.11 < z < 0.88 redshift range, to build colour–magnitude diagrams to characterize the impact of cluster mergers on the galaxy population. We divided the sample between relaxed and disturbed, and in two redshifts bin at z = 0.55. When comparing the high-z to low-z clusters we find the high-z sample is richer in blue galaxies, independently of the cluster dynamical state. In the high-z bin, we find that disturbed clusters exhibit a larger scatter in the red sequence, with wider distribution and an excess of bluer galaxies compared to relaxed clusters, while in the low-z bin we find a complete agreement between the relaxed and disturbed clusters. Our results support the scenario in which massive cluster halos at z < 0.55 galaxies are quenched as satellites of another structure, i.e. outside the cluster, while at z ≥ 0.55 the quenching is dominated by in situ processes.

Aldás, Franklin (ORCID:0000000290215114)↗
DOE OSTI2021

Deciphering enhancer sequence using thermodynamics-based models and convolutional neural networks

Abstract Deciphering the sequence-function relationship encoded in enhancers holds the key to interpreting non-coding variants and understanding mechanisms of transcriptomic variation. Several quantitative models exist for predicting enhancer function and underlying mechanisms; however, there has been no systematic comparison of these models characterizing their relative strengths and shortcomings. Here, we interrogated a rich data set of neuroectodermal enhancers in Drosophila, representing cis- and trans- sources of expression variation, with a suite of biophysical and machine learning models. We performed rigorous comparisons of thermodynamics-based models implementing different mechanisms of activation, repression and cooperativity. Moreover, we developed a convolutional neural network (CNN) model, called CoNSEPT, that learns enhancer ‘grammar’ in an unbiased manner. CoNSEPT is the first general-purpose CNN tool for predicting enhancer function in varying conditions, such as different cell types and experimental conditions, and we show that such complex models can suggest interpretable mechanisms. We found model-based evidence for mechanisms previously established for the studied system, including cooperative activation and short-range repression. The data also favored one hypothesized activation mechanism over another and suggested an intriguing role for a direct, distance-independent repression mechanism. Our modeling shows that while fundamentally different models can yield similar fits to data, they vary in their utility for mechanistic inference. CoNSEPT is freely available at: https://github.com/PayamDiba/CoNSEPT.

59 BASIC BIOLOGICAL SCIENCES↗