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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 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

MAGNETIC ACTIVITY ANALYSIS FOR A SAMPLE OF G-TYPE MAIN SEQUENCE KEPLER TARGETS

The variation of a stellar light curve owing to rotational modulation by magnetic features (starspots and faculae) on the star’s surface can be used to investigate the magnetic properties of the host star. In this paper, we use the periodicity and magnitude of the light-curve variation as two proxies to study the stellar magnetic properties for a large sample of G-type main sequence Kepler targets, for which the rotation periods were recently determined. By analyzing the correlation between the two magnetic proxies, it is found that: (1) the two proxies are positively correlated for most of the stars in our sample, and the percentages of negative, zero, and positive correlations are 4.27%, 6.81%, and 88.91%, respectively; (2) negative correlation stars cannot have a large magnitude of light-curve variation; and (3) with the increase of rotation period, the relative number of positive correlation stars decreases and the negative correlation one increases. These results indicate that stars with shorter rotation period tend to have positive correlation between the two proxies, and a good portion of the positive correlation stars have a larger magnitude of light-curve variation (and hence more intense magnetic activities) than negative correlation stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2024

Simultaneous enhancement of multiple functional properties using evolution-informed protein design

Abstract A major challenge in protein design is to augment existing functional proteins with multiple property enhancements. Altering several properties likely necessitates numerous primary sequence changes, and novel methods are needed to accurately predict combinations of mutations that maintain or enhance function. Models of sequence co-variation (e.g., EVcouplings), which leverage extensive information about various protein properties and activities from homologous protein sequences, have proven effective for many applications including structure determination and mutation effect prediction. We apply EVcouplings to computationally design variants of the model protein TEM-1 β -lactamase. Nearly all the 14 experimentally characterized designs were functional, including one with 84 mutations from the nearest natural homolog. The designs also had large increases in thermostability, increased activity on multiple substrates, and nearly identical structure to the wild type enzyme. This study highlights the efficacy of evolutionary models in guiding large sequence alterations to generate functional diversity for protein design applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Enrichment of root-associated Streptomyces strains in response to drought is driven by diverse functional traits and does not predict beneficial effects on plant growth

The genus Streptomyces has consistently been found enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment (DE) of Streptomyces in field-grown sorghum roots and identified five closely related but distinct amplicon sequence variants (ASVs) belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that DE scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified orthogroups involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces DE is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, DE in the root microbiome was shown not to predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.

Fonseca-Garcia, Citlali↗
DOE OSTI2014

Energies, fine structure, and radiative transitions of the high-lying core-excited states {sup 6}S{sup e,o}(n) and {sup 6}P{sup e,o}(n) (n=1–5) for the boron isoelectronic sequence

The Rayleigh–Ritz variation method using a multiconfiguration interaction wavefunction is carried out on the high-lying core-excited states {sup 6}S{sup e,o}(n) and {sup 6}P{sup e,o}(n) (n=1–5) for the boron isoelectronic sequence (Z=6–10), including mass polarization and relativistic corrections. Energy levels, fine structure, transition rates, and transition wavelengths for this system are calculated. Some energy levels of the high-n states are reported for the first time. Wavelengths of the electric-dipole transitions from these core-excited sextet states with quantum electro-dynamical effects and higher-order relativistic corrections are included. The lifetimes of the 1s2s2p{sup 2}3p{sup 6}S{sup o},1s2p{sup 3}3s{sup 6}S{sup o},1s2s2p{sup 2}3s{sup 6}P, 1s2s2p{sup 2}3d{sup 6}P, and 1s2p{sup 3}3p{sup 6}P states for the boron isoelectronic sequence are also reported. Our calculated results agree well in most cases with available theoretical and experimental data in the literature. -- Highlights: •The core-excited states {sup 6}S{sup e,o}(n) and {sup 6}P{sup e,o}(n) of B-like ions are studied. •Some energy levels for the high-n sextet series are reported for the first time. •Configuration structures of these states are checked by fine structure splittings. •Transition rates, wavelengths for these core-excited sextet states are reported.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

Structural and magnetic properties of Y-doped La{sub 0.5}Sr{sub 0.5}MnO{sub 3} manganite system: Evidence of step-like magnetization

The magnetic and transport properties of bulk doped manganite, La{sub 0.5−y}Y{sub y}Sr{sub 0.5}MnO{sub 3} have been studied as a function of yttrium doping, y, for 0 ≤ y ≤ 0.25. In the absence of the yttrium this is a well studied half-doped manganite which is a metallic ferromagnet. The end members of this system (with y = 0 and 0.25) are found to be structurally different (rhombohedral and orthorhombic, respectively) due to the large distortions caused by the yttrium. These distortions make this series of compounds particularly interesting. The magnetization obtained in zero field cooled (ZFC) and field cooled (FC) studies show dramatic changes as the value of y is raised above 0.05. The magnetic behavior is further investigated by a study of the hysteresis loops, frequency dependent susceptibility and studies of the magnetic relaxation. The results are understood in terms of the average size of the cation on the A site, , and the variance, σ{sup 2} (= ∑y{sub i}{sup 2}r{sub i}{sup 2} - {sup 2}). The value of the variance, σ{sup 2}, increases rapidly with doping, y, induces melting of the long range ferromagnetic ordering, exhibiting a stepwise variation of magnetization (metamagnetic like). Based on the present results a magnetic phase diagram has been drawn demonstrating different magnetic phase sequences with the variation of σ{sup 2}.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2014

TU-C-12A-07: Characterization of Longitudinal Reproducibility of Quantitative Diffusion Imaging Data Acquired with Four Different Protocols Using a Phantom

Purpose: To characterize and compare the longitudinal reproducibility of diffusion imaging data acquired with four different protocols using a phantom. Methods: The Diffusive Quantitative Imaging Phantom (DQIP) was constructed using fifteen cylindrical compartments within a larger compartment, filled with deionized water doped with CuSO4 and NaCl. The smaller compartments contained arrays of hexagonal or cylindrical glass capillaries of varying inner diameters, for differing restraint of water diffusion. The sensitivity of diffusion imaging metrics to signal-to-noise ratio (SNR) was probed by doping compartments with differing ratios of deuterium oxide to H2O. A cork phantom enclosure was constructed to increase thermal stability during scanning and a cork holder was made to reproduce scanner positioning. Four different protocols of DWI (diffusion weighted imaging) and DTI (Diffusion tensor imaging) imaging were assembled on a GE Excite HDx 3.0T MRI scanner to collect imaging data over 9-10 days. Data was processed with in-house software created in Matlab to obtain fractional anisotropy (FA) and apparent diffusion coefficient (ADC) values. Results: All DTI and DWI sequences showed good longitudinal stability of mean FA and ADC values per compartment, exhibiting low standard deviation ∼9%. A t-test was performed to compare mean FA values from the DTI clinical protocol to those of the DTI special protocol, indicating significantly different values in the majority of compartments. ANOVA performed on ADC values for all DTI and DWI sequences also showed significantly different values in a majority of compartments. Conclusion: This work has the potential for quantifying systemic variations between diffusion imaging sequences from different platforms. Characterization of DWI and DTI performance were done over four sequences with predictable results. This data suggests that the DQIP phantom may be a reliable method of monitoring day-to-day and scan-to-scan variation in diffusion imaging sequences from different platforms. Schott Glass North America and The Phantom Laboratory have donated materials and personnel time to this project.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

maslov-group/FUN-PROSE

mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.

Liu, Simon↗
DOE OSTI2023

FUN-PROSE: A deep learning approach to predict condition-specific gene expression in fungi

mRNA levels of all genes in a genome is a critical piece of information defining the overall state of the cell in a given environmental condition. Being able to reconstruct such condition-specific expression in fungal genomes is particularly important to metabolically engineer these organisms to produce desired chemicals in industrially scalable conditions. Most previous deep learning approaches focused on predicting the average expression levels of a gene based on its promoter sequence, ignoring its variation across different conditions. Here we present FUN-PROSE—a deep learning model trained to predict differential expression of individual genes across various conditions using their promoter sequences and expression levels of all transcription factors. We train and test our model on three fungal species and get the correlation between predicted and observed condition-specific gene expression as high as 0.85. We then interpret our model to extract promoter sequence motifs responsible for variable expression of individual genes. We also carried out input feature importance analysis to connect individual transcription factors to their gene targets. A sizeable fraction of both sequence motifs and TF-gene interactions learned by our model agree with previously known biological information, while the rest corresponds to either novel biological facts or indirect correlations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Optimizing Cell-based Antimicrobials through Pooled Genomic Libraries

DNA synthesis and assembly technologies ushered in through synthetic biology have great promise for biomanufacturing, bioremediation, and the development of living therapeutics. Unfortunately, predicting sequence to function relationships, including for biosynthetic pathways expressed in a new host organism, is difficult and often requires many iterative cycles of design, construction, and testing. We are working to develop data-driven approaches to identify the genetic determinants of growth defects and productivity for the expression of a cell-based antimicrobial. We assayed the growth, pigment production, and antimicrobial activity of a collection of over 10,000 genetic mutants of the violacein biosynthetic pathway and sequenced the genetic variation of these mutants. Through this project, we have developed an innovative codebase to automate the determination of pigmentation and antimicrobial clearing diameter for tens of thousands of genetic mutants cultivated on agar dishes. Further, we have written DNA sequence analysis code to demultiplex & provide consensus sequences from high-throughput PacBio long-read circular consensus sequencing (CCS) datasets. From this foundation, we plan to map DNA sequence to function to predict an optimal genetic design to maximize antimicrobial activity while minimizing deleterious growth effects. The workflows and algorithms developed through this project can be broadly applied to other engineered functions in microbes, uncovering sequence to function relationships for complex phenotypes where function impacts fitness.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Sexual reproduction, sporophyte development and molecular variation in the model moss Physcomitrella patens : introducing the ecotype Reute

Summary Rich ecotype collections are used for several plant models to unravel the molecular causes of phenotypic differences, and to investigate the effects of environmental adaption and acclimation. For the model moss Physcomitrella patens collections of accessions are available, and have been used for phylogenetic and taxonomic studies, for example, but few have been investigated further for phenotypic differences. Here, we focus on the Reute accession and provide expression profiling and comparative developmental data for several stages of sporophyte development, as well as information on genetic variation via genomic sequencing. We analysed cross‐technology and cross‐laboratory data to define a confident set of 15 mature sporophyte‐specific genes. We find that the standard laboratory strain Gransden produces fewer sporophytes than Reute or Villersexel, although gametangia develop with the same time course and do not show evident morphological differences. Reute exhibits less genetic variation relative to Gransden than Villersexel, yet we found variation between Gransden and Reute in the expression profiles of several genes, as well as variation hot spots and genes that appear to evolve under positive Darwinian selection. We analyzed expression differences between the ecotypes for selected candidate genes in the GRAS transcription factor family, the chalcone synthase family and in genes involved in cell wall modification that are potentially related to phenotypic differences. We confirm that Reute is a P. patens ecotype, and suggest its use for reverse‐genetics studies that involve progression through the life cycle and multiple generations.

Hiss, Manuel↗
DOE OSTI2022

Peptoid-Directed Formation of Five-Fold Twinned Au Nanostars through Particle Attachment and Facet Stabilization

While bio-inspired synthesis offers great potential for controlling nucleation and growth of inorganic particles, precisely tuning biomolecule-particle interactions is a long-standing challenge. Herein, we used variations in peptoid sequence to manipulate peptoid-Au interaction, leading to synthesis of concave five-fold twinned, five-pointed Au nanostars via a process of repeated particle attachment and facet stabilization. Ex situ and liquid-phase TEM observations show that a balance between particle attachment biased to occur near the star points, preferential growth along the [100] direction, and stabilization of (111) facets is critical to forming star-shaped particles. Molecular simulations predict that interaction strengths between peptoids and distinct Au facets differ significantly and thus can alter attachment kinetics and surface energies to form the stars. This work provides new insights into how sequence-defined ligands affect particle growth to regulate crystal morphology.

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

On the distribution of stacking faults at dissociated medium-angle grain boundaries: Crystallographic geometry and metastability

Grain boundaries in FCC metals with low stacking-fault energy can form in dissociated configurations of stacking faults. Perhaps the most studied example is 9R stacking at boundaries near Σ3{112}, where the distribution of stacking faults is related to the emission of Shockley partial dislocations. Here, we combine atomic-resolution electron microscopy, atomistic simulations, and dislocation theory to demonstrate that boundaries vicinal to Σ33a support the stabilization of dissociated 9R stacking within a narrow range of inclinations. This boundary is interesting since its misorientation (20.05°) lies in the medium-angle regime, just past the upper misorientation limit for low-angle boundaries, motivating questions for how best to describe it in terms of dislocations. Our HAADF-STEM observations of thin film bicrystals, supported by atomistic modeling, reveal that this inclination dependence arises from specific geometric constraints on the arrangement of Shockley partial dislocations at the interface. Quantification of stacking-fault distributions across multiple boundaries indicates that the density and spacing of faults closely follow the ideal 9R motif, with subtle variations reflecting the complex energy landscape of these boundaries. Through energetic analysis, we establish the presence of competing metastable states enabled by variations in stacking sequences, emphasizing the significant role of crystallographic geometry. We generalize our analysis as a function of misorientation, showing how 9R at the Σ33a boundary is related to previous observations and calculations of HCP at a 29.7° boundary. This study provides a crystallographically grounded framework connecting dislocation structures, stacking-fault distributions, and metastability at grain boundaries in FCC metals.

Atomistic modeling↗
DOE OSTI2024

Genome resources for three modern cotton lines guide future breeding efforts

Cotton ( Gossypium hirsutum L.) is the key renewable fibre crop worldwide, yet its yield and fibre quality show high variability due to genotype-specific traits and complex interactions among cultivars, management practices and environmental factors. Modern breeding practices may limit future yield gains due to a narrow founding gene pool. Precision breeding and biotechnological approaches offer potential solutions, contingent on accurate cultivar-specific data. Here we address this need by generating high-quality reference genomes for three modern cotton cultivars (‘UGA230’, ‘UA48’ and ‘CSX8308’) and updating the ‘TM-1’ cotton genetic standard reference. Despite hypothesized genetic uniformity, considerable sequence and structural variation was observed among the four genomes, which overlap with ancient and ongoing genomic introgressions from ‘Pima’ cotton, gene regulatory mechanisms and phenotypic trait divergence. Differentially expressed genes across fibre development correlate with fibre production, potentially contributing to the distinctive fibre quality traits observed in modern cotton cultivars. These genomes and comparative analyses provide a valuable foundation for future genetic endeavours to enhance global cotton yield and sustainability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Molecular and biochemical characterization of rice developed through conventional integration of nDart1-0 transposon gene

Mutations, the genetic variations in genomic sequences, play an important role in molecular biology and biotechnology. During DNA replication or meiosis, one of the mutations is transposons or jumping genes. An indigenous transposon nDart1-0 was successfully introduced into local indica cultivar Basmati-370 from transposon-tagged line viz., GR-7895 (japonica genotype) through conventional breeding technique, successive backcrossing. Plants from segregating populationsshowed variegated phenotypes were tagged as BM-37 mutants. Blast analysis of the sequence data revealed that the GTP-binding protein, located on the BAC clone OJ1781_H11 of chromosome 5, contained an insertion of DNA transposon nDart1-0. The nDart1-0 has “A” at position 254 bp, whereas nDart1 homologs have “G”, which efficiently distinguishes nDart1-0 from its homologs. The histological analysis revealed that the chloroplast of mesophyll cells in BM-37 was disrupted with reduction in size of starch granules and higher number of osmophillic plastoglobuli, which resulted in decreased chlorophyll contents and carotenoids, gas exchange parameters (Pn, g, E, Ci), and reduced expression level of genes associated with chlorophyll biosynthesis, photosynthesis and chloroplast development. Along with the rise of GTP protein, the salicylic acid (SA) and gibberellic acid (GA) and antioxidant contents(SOD) and MDA levels significantly enhanced, while, the cytokinins (CK), ascorbate peroxidase (APX), catalase (CAT), total flavanoid contents (TFC) and total phenolic contents (TPC) significantly reduced in BM-37 mutant plants as compared with WT plants. These results support the notion that GTP-binding proteins influence the process underlying chloroplast formation. Therefore, it is anticipated that to combat biotic or abiotic stress conditions, the nDart1-0 tagged mutant (BM-37) of Basmati-370 would be beneficial.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

Binary interactions as a possible scenario for the formation of multiple stellar populations in globular clusters

Observations have revealed the presence of multiple stellar populations in globular clusters (GCs) that exhibit wide abundance variations and multiple sequences in the Hertzsprung-Russell (HR) diagram. We present a scenario for the formation of multiple stellar populations in GCs. In this scenario, initial GCs are single-generation clusters, and our model predicts that the stars with anomalous abundances observed in GCs are merged stars and accretor stars produced by binary interactions—rapidly rotating stars at the moment of their formation—and that these stars are more massive than normal single stars in the same evolutionary stage. We find that, due to their own evolution, these rapidly rotating stars have surface abundances, effective temperatures, and luminosities that are different from normal single stars in the same evolutionary stage. This stellar population of binaries reproduces two important points of observational evidence of multiple stellar populations: a Na-O anticorrelation and multiple sequences in the HR diagram. This evidence suggests that binary interactions may be a possible scenario for the formation of multiple stellar populations in GCs.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Unpinning the skyrmion lattice in MnSi: Effect of substitutional disorder

By employing magnetization and small angle neutron scattering measurements, we have investigated the behavior of the skyrmion lattice (SKL) and the helical order in MnSi 0.992 Ga 0.008 . Our results indicate that the order of the SKL is sensitive to the orientation of an applied magnetic field with respect to the crystal lattice and to variations in the sequence of small temperature and applied magnetic field changes. The disorder caused by the substitution of the heavier element Ga for Si is sufficient to reduce the pinning of the SKL to the underlying crystalline lattice, reducing the propensity for the SKL to be aligned with the crystal lattice. This tendency is most evident when the applied field is not well oriented with respect to the high symmetry axes of the crystal resulting in disorder in the long range SKL while maintaining sharp short range (radial) order. We have also investigated the effect of substituting heavier elements into MnSi on the reorientation process of the helical domains with field cycling in MnSi 0.992 Ga 0.008 and Mn 0.985 Ir 0.015 Si A comparison of the reorientation process in these materials with field reduction indicates that the substitution of heavier elements on either Mn or Si sites creates a higher energy barrier for the reorientation of the helical order and for the formation of domains.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Technical Report: Algorithm and Implementation for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

This report describes the design and implementation of an algorithm for estimating relative microbial abundances, together with confidence limits, using data from metagenomic DNA sequencing. For the background behind this project and a detailed discussion of our modeling approach for metagenomic data, we refer the reader to our earlier technical report, dated March 4, 2014. Briefly, we described a fully Bayesian generative model for paired-end sequence read data, incorporating the effects of the relative abundances, the distribution of sequence fragment lengths, fragment position bias, sequencing errors and variations between the sampled genomes and the nearest reference genomes. A distinctive feature of our modeling approach is the use of a Chinese restaurant process (CRP) to describe the selection of genomes to be sampled, and thus the relative abundances. The CRP component is desirable for fitting abundances to reads that may map ambiguously to multiple targets, because it naturally leads to sparse solutions that select the best representative from each set of nearly equivalent genomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Variations of the ISM compactness across the main sequence of star forming galaxies: Observations and simulations

The majority of star-forming galaxies follow a simple empirical correlation in the star formation rate (SFR) versus stellar mass (M{sub *}) plane, of the form SFR∝M{sub ∗}{sup α}, usually referred to as the star formation main sequence (MS). The physics that sets the properties of the MS is currently a subject of debate, and no consensus has been reached regarding the fundamental difference between members of the sequence and its outliers. Here we combine a set of hydro-dynamical simulations of interacting galactic disks with state-of-the-art radiative transfer codes to analyze how the evolution of mergers is reflected upon the properties of the MS. We present Chiburst, a Markov Chain Monte Carlo spectral energy distribution (SED) code that fits the multi-wavelength, broad-band photometry of galaxies and derives stellar masses, SFRs, and geometrical properties of the dust distribution. We apply this tool to the SEDs of simulated mergers and compare the derived results with the reference output from the simulations. Our results indicate that changes in the SEDs of mergers as they approach coalescence and depart from the MS are related to an evolution of dust geometry in scales larger than a few hundred parsecs. This is reflected in a correlation between the specific star formation rate, and the compactness parameter C, that parametrizes this geometry and hence the evolution of dust temperature (T{sub dust}) with time. As mergers approach coalescence, they depart from the MS and increase their compactness, which implies that moderate outliers of the MS are consistent with late-type mergers. By further applying our method to real observations of luminous infrared galaxies (LIRGs), we show that the merger scenario is unable to explain these extreme outliers of the MS. Only by significantly increasing the gas fraction in the simulations are we able to reproduce the SEDs of LIRGs.

79 ASTRONOMY AND ASTROPHYSICS↗