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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 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Bus repeater and bit injector for MIL-STD-1553/1760 communications bus

A fault insertion device (FID) comprises a transceiver and an FPGA. The transceiver receives signals from a MIL-STD-1553/1760 communications bus. The FPGA evaluates the signals received from the communications bus against a set of rules stored by the FPGA. Based upon the set of rules, the FPGA can selectively modify messages received from the communications bus prior to transmission to a remote terminal or a bus controller that is configured to communicate on the communications bus.

Krein, Jason P.↗
DOE OSTI2021

Establishment of FXS-A9 panel with a single human X chromosome from fragile X syndrome-associated individual

Highlights: • We established mouse A9 cells with human X chromosome from FXS carrier and patient. • FXS-associated CGG repeats were stably maintained in established rodent cells. • Epigenetic status of CGG repeat region were maintained in established rodent cells. • Human FMR1 expression in these cells was according to each CGG repeat length. Fragile X syndrome (FXS) is the most common inheritable form of intellectual disability. FMR1, the gene responsible for FXS, is located on human chromosome Xq27.3 and contains a stretch of CGG trinucleotide repeats in its 5′ untranslated region. FXS is caused by CGG repeats that expand beyond 200, resulting in FMR1 silencing via promoter hypermethylation. The molecular mechanism underlying CGG repeat expansion, a fundamental cause of FXS, remains poorly understood, partly due to a lack of experimental systems. Accumulated evidence indicates that the large chromosomal region flanking a CGG repeat is critical for repeat dynamics. In the present study, we isolated and introduced whole human X chromosomes from healthy, FXS premutation carriers, or FXS patients who carried disease condition-associated CGG repeat lengths, into mouse A9 cells via microcell-mediated chromosome transfer. The CGG repeat length-associated methylation status and human FMR1 expression in these monochromosomal hybrid cells mimicked those in humans. Thus, this set of A9 cells containing CGG repeats from three different origins (FXS-A9 panel) may provide a valuable resource for investigating a series of genetic and epigenetic CGG repeat dynamics during FXS pathogenesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Structured light scanning artifact-based performance study

Structured light scanning is used to create a digital twin of a manufactured part, where features are extracted to determine if the part meets the designer’s intent and required tolerances. This paper describes repeatability and reproducibility analyses for a commercially-available structured light scanning system and measurement artifact. The repeatability study used five repeated scans at 15 measurement positions. Repeatability was assessed by randomly selecting one of the five scans at each of the 15 positions and creating a part mesh. This process was performed 50 times and the statistics for the dimension variations were calculated to isolate the scanning effects only. The same sequence was then performed for 10 of the 15 positions and five of the 15 positions to evaluate the repeatability sensitivity to the number of measurement positions. Reproducibility was assessed by selecting 15 positions to create a mesh and repeating the 15-position measurement sequence 10 times using different positions for each mesh construction. The statistics for the dimension variations were then calculated. This incorporated the effects of both scanning and the position and orientation of the part relative to the scanner. This sequence was repeated for 10-position and five-position scans to evaluate the corresponding sensitivity. Finally, the artifact dimensions from structured light scanning were compared to coordinate measuring machine measurements of the same features.

42 ENGINEERING↗
DOE OSTI2024

SpacerExtractor v0.9

The SpacerExtractor tool is meant to robustly identify and extract CRISPR spacers from metagenome short reads. Working from a database of known CRISPR repeats, SpacerExtractor quickly scans short reads for the corresponding repeat sequences, extract the potential spacer between two repeats, apply several quality control, denoising, and clustering steps, and provides a full non-redundant complement of spacers for each detected repeat. Because of the high variability observed at CRISPR loci, this read mining approach typically recovers a much larger diversity of spacers than can be found in assembled contigs. SpacerExtractor also includes commands to run CRISPR-Cas Typer on a new set of genomes or MAGs, and add newly predicted repeats to the repeat database.

Bushnell, Brian↗
DOE OSTI2026

Phosphoserine Charge State Drives Ion Condensation and Spatial Polyamine Presentation in Multirepeat Silaffin

Diatom silaffins direct silica biomineralization through heavily post-translationally modified repeat domains, yet how these modifications reshape the multirepeat conformational ensemble remains unknown. We report all-atom MD simulations of a 195-residue construct spanning repeats R1–R7 of Sil1p from Cylindrotheca fusiformis, carrying the full complement of native PTMs: phosphoserine (pSer), long-chain polyamines (LCPA), dimethyllysine (MLY), and trimethylhydroxylysine phosphate (TPL). We simulated three variants (Native, P1/singly deprotonated phosphate, and P2/doubly deprotonated phosphate) at two NaCl concentrations in triplicate for 500 ns each. All systems disorder from the AlphaFold 3 starting structure. Phosphate charge state, not ionic strength, is the dominant control of ensemble compaction and ion organization. Doubly deprotonated phosphate organizes an extensive Na + condensation shell (∼100 ions, 20% of box Na + ) and a heterogeneous bridging network that integrates both pSer and TPL phosphate groups. The resulting ensemble is compact with LCPA side chains exhibiting above-median solvent accessibility in 84% of simulation frames in P2 at 300 mM. This is higher than any other condition we simulated and indicates that polyamine groups are preferentially surface-presented in the most compact, ion-organized state. A charge-neutralization control confirms that this compact state is a structured intermediate maintained by the bridging network, not a simple collapsed globule. Here, this repeat-scale spatial organization is not captured by single-repeat peptide studies. Understanding the dynamics, mechanism, and spatial organization of PTM-rich silaffin at the repeat scale is a step closer to hierarchical biomimetic materials beyond simple silica morphologies.

Amines↗
DOE OSTI2023

Spectra and characteristics of somatic mutations induced by ionizing radiation in hematopoietic stem cells

Spectra and frequencies of spontaneous and X-ray-induced somatic mutations were revealed with mouse long-term hematopoietic stem cells (LT-HSCs) by whole-genome sequencing of clonal cell populations propagated in vitro from single isolated LT-HSCs. SNVs and small indels were the most common types of somatic mutations, and increased up to twofold to threefold by whole-body X-irradiation. Base substitution patterns in the SNVs suggested a role of reactive oxygen species in radiation mutagenesis, and signature analysis of single base substitutions (SBS) revealed a dose-dependent increase of SBS40. Most of spontaneous small deletions were shrinkage of tandem repeats, and X-irradiation specifically induced small deletions out of tandem repeats (non-repeat deletions). Presence of microhomology sequences in non-repeat deletions suggested involvement of microhomology mediated end-joining repair mechanisms as well as nonhomologous end-joining in radiation-induced DNA damages. We also identified multisite mutations and structural variants (SV), i.e., large indels, inversions, reciprocal translocations, and complex variants. The radiation-specificity of each mutation type was evaluated from the spontaneous mutation rate and the per-Gy mutation rate estimated by linear regression, and was highest with non-repeat deletions without microhomology, followed by those with microhomology, SV except retroelement insertions, and multisite mutations; these types were thus revealed as mutational signatures of ionizing radiation. Further analysis of somatic mutations in multiple LT-HSCs indicated that large fractions of postirradiation LT-HSCs originated from single LT-HSCs that survived the irradiation and then expanded in vivo to confer marked clonality to the entire hematopoietic system, with varying clonal expansion and dynamics depending on radiation dose and fractionation.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2023

Molecular and functional properties of human Plasmodium falciparum CSP C-terminus antibodies

Human monoclonal antibodies (mAbs) against the central repeat and junction domain of Plasmodium falciparum circumsporozoite protein (PfCSP) have been studied extensively to guide malaria vaccine design compared to antibodies against the PfCSP C terminus. Here, we describe the molecular characteristics and protective potential of 73 germline and mutated human mAbs against the highly immunogenic PfCSP C-terminal domain. Two mAbs recognized linear epitopes in the C-terminal linker with sequence similarity to repeat and junction motifs, whereas all others targeted conformational epitopes in the α-thrombospondin repeat (α-TSR) domain. Specificity for the polymorphic Th2R/Th3R but not the conserved RII+/CS.T3 region in the α-TSR was associated with IGHV3-21/IGVL3-21 or IGLV3-1 gene usage. Although the C terminus specific mAbs showed signs of more efficient affinity maturation and class-switching compared to anti-repeat mAbs, live sporozoite binding and inhibitory activity was limited to a single C-linker reactive mAb with cross-reactivity to the central repeat and junction. The data provide novel insights in the human anti-C-linker and anti-α-TSR antibody response that support exclusion of the PfCSP C terminus from malaria vaccine designs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

The Demographics, Stellar Populations, and Star Formation Histories of Fast Radio Burst Host Galaxies: Implications for the Progenitors

We present a comprehensive catalog of observations and stellar population properties for 23 highly secure host galaxies of fast radio bursts (FRBs). Our sample comprises 6 repeating FRBs and 17 apparent nonrepeaters. We present 82 new photometric and 8 new spectroscopic observations of these hosts. Using stellar population synthesis modeling and employing nonparametric star formation histories (SFHs), we find that FRB hosts have a median stellar mass of ≈10 9.9 M ⊙ , mass-weighted age ≈5.1 Gyr, and ongoing star formation rate ≈1.3 M ⊙ yr -1 but span wide ranges in all properties. Classifying the hosts by degree of star formation, we find that 87% (20 of 23 hosts) are star-forming, two are transitioning, and one is quiescent. The majority trace the star-forming main sequence of galaxies, but at least three FRBs in our sample originate in less-active environments (two nonrepeaters and one repeater). Across all modeled properties, we find no statistically significant distinction between the hosts of repeaters and nonrepeaters. However, the hosts of repeating FRBs generally extend to lower stellar masses, and the hosts of nonrepeaters arise in more optically luminous galaxies. While four of the galaxies with the clearest and most prolonged rises in their SFHs all host repeating FRBs, demonstrating heightened star formation activity in the last ≲100 Myr, one nonrepeating host shows this SFH as well. Our results support progenitor models with short delay channels (i.e., magnetars formed via core-collapse supernova) for most FRBs, but the presence of some FRBs in less-active environments suggests a fraction form through more delayed channels.

79 ASTRONOMY AND ASTROPHYSICS↗
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 OSTI2025

A new probe of μ Hz gravitational waves with FRB timing

We propose Fast Radio Burst (FRB) timing, which uses the precision measurements of the arrival time differences of repeated FRB signals along multiple sightlines, as a new probe of gravitational waves (GWs) around nHz to μHz frequencies, with the highest frequency limited by FRB repeating period. The anticipated experiment requires a sightline separation of tens of AU, achieved by sending radio telescopes to space. We find the signal of arrival time difference induced by GWs depends only on the local GWs in the solar system and we can correlate the measurements from different FRB sources or the same source with different repeaters, which leads to a better sensitivity with a larger number of FRB repeaters detected. Here, the projected sensitivity shows this method is a competitive probe in the nHz to μ Hz frequency range. It can fill the 'μHz gap' between pulsar timing arrays and Laser Interferometer Space Antenna (LISA) and is complementary to other proposals of GW detection in this frequency band.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2026

Ancient co-option of LTR retrotransposons as yeast centromeres

Centromeres ensure accurate chromosome segregation, yet their DNA evolves rapidly across eukaryotes leaving the origins of new centromere architectures unclear. The brewer’s yeast Saccharomyces cerevisiae exemplifies this long-standing puzzle. Its centromeres shifted ancestrally from large, repeat-rich, epigenetically specified forms to the compact, genetically defined ‘point’ centromeres. How this transition occurred has remained unresolved6. Here we identify evolutionarily related ‘proto-point’ centromeres that provide a resolution to the evolutionary origins of point centromeres. Proto-point centromeres contain a single centromeric nucleosome positioned over an AT-rich core, accompanied by relaxed organization and sequence variability of flanking cis-elements. In two species, these proto-point centromeres lie within retrotransposon-derived repeat clusters, linking ancestral repeat-rich centromeres to genetically encoded ones. Comparative and phylogenetic analyses indicate that proto-point and point centromeres evolved in an ancestor with retrotransposon-rich centromeres. These results identify long-terminal-repeat retrotransposons, specifically Ty5 sequences, as the genetic substrate for point-centromere evolution and provide a mechanistic route by which an epigenetic centromere can become genetically specified. More broadly, they show how selfish elements can be co-opted to perform essential chromosomal functions.

Haase, Max A. B. [Max Planck Institute of Molecula↗
DOE OSTI2025

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Chang, Marina P. [Stanford Univ., CA (United State↗
DOE OSTI2021

Comparing Global Spray Combustion Characteristics and Local Shot-to-Shot Variations in a Reacting n -Heptane Spray

In support of efforts to develop improved models of turbulent spray behavior and combustion in diesel engines, experimental data and analysis must be obtained for guidance and validation. For Reynolds-averaged Navier–Stokes (RANS)-based Computational fluid dynamics (CFD) modeling approaches, representative ensemble average experimental results are important. For high-fidelity models such as large eddy simulations (LES)-based CFD, precise individual experimental results are desirable. However, making comparisons between a given experiment and LES is a challenge since local parameters cannot be directly compared. In this work, an optically accessible constant pressure flow rig (CPFR) is utilized to acquire diesel-like fuel injection and reaction behavior simultaneously with three optical diagnostic techniques: rainbow Schlieren deflectometry (RSD), OH* chemiluminescence (OH*), and two-color pyrometry (2CP). The CPFR allows a large number of repeated injection experiments to be performed for statistical analysis and convergence using ensemble-averaging techniques, while maintaining highly repeatable test conditions. Even for stable test conditions, variations in local turbulent fuel–air mixing introduce variability, which manifests as significant differences in OH* and 2CP results. Experimental measurements of characteristic parameters including liquid and vapor jet penetration, liftoff length, soot temperature and concentration, and turbulent flame speed, along with the shot-to-shot variability of each dataset, are presented and discussed. Finally, a statistical method is utilized to analyze the extent of this variability, and to identify superlative injections within the dataset for discussion and analysis of shot-to-shot variations.

42 ENGINEERING↗
DOE OSTI2026

Post-fire soil respiration in late growing season (2023 and 2024), Kougarok Fire Complex, Seward Peninsula, Alaska

Field soil respiration data collected in 2023 and 2024 from burned and unburned tussock tundra sites in the Kougarok Fire Complex, near Nome, on the Seward Peninsula of Alaska. Specifically, we measured soil properties and late-growing season CO2 fluxes in patches of unique plant functional types (forbs, shrubs, and graminoids) across two years in tundra recovering from repeated wildfires over the decade. The goal was to identify the main drivers of soil respiration in Arctic tundra underlain by discontinuous permafrost that is recovering from two recent, repeated wildfires that differed in fire age and number of times burned, thereby resulting in different levels of vegetation and subsurface property changes (i.e., successional trajectories). There are five files in *.csv format with one data file and four data description files including data, dictionary, methods, terminology, and file-level metadata. The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), is a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research. The NGEE Arctic Phase 3 project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska. Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).

Santos, Fernanda [ORNL] (ORCID:0000000191555623)↗
DOE OSTI2020

Measurement Uncertainty in One-of-a-kind Experiments

A golden standard in science is to repeat an experimental measurement multiple times and calculate the measured value with experimental uncertainty by following well developed statistical procedures. For various reasons – cost, technical difficulty, international treaties, ethics of dealing with human or animal subjects, ecology - many important experiments and observations can not be repeated. Astronomy, earthquakes, hurricanes produce data from one-of-a-kind events. When information is not available in any other way, it should not be dismissed as qualitative, anecdotal evidence only. Analyzed in a mathematically rigorous way, it produces quantitative experimental data. Analysis of data from one-of-a-kind event differs from analysis of repeated experiments’ data. For repeated experiments, the experimental error includes a range of true values generated by repetitions of the experiment, and measurement uncertainty caused by detectors. They are independent. Repetitions of any experiment, as similar as achievable, always have built-in differences resulting in a range of the true values rather than in a single value. Measurement uncertainty depends on the measurement system only. Digital measurements have very small uncertainty, frequently smaller than the range of true experimental values resulting from built-in differences in the experiment repetitions. When data from one–of–a kind experiment are analyzed, only the measurement uncertainty can be reported.

42 ENGINEERING↗
DOE OSTI2020

Uncertainty in Experimental Data Analysis [Slides]

The talk was presented virtually to the Institute of Fundamental Technological Research, Polish Academy of Sciences in Warsaw, Poland, December 21, 2020. Astronomical observations, unusual medical cases, physics experiments too costly to repeat, natural events like earthquakes, hurricanes – all of them are impossible to repeat yet produce important scientific information not achievable in other way. This data should not be treated as qualitative, anecdotal evidence only. It should be analyzed in a mathematically rigorous way to produce quantitative experimental data. Analysis method for one-of-a-kind event data differs from analysis of a repeated experiment data. For a repeated experiments the experimental error includes a range of true values generated by repetitions of the experiment, and measurement uncertainty caused by detectors. They are independent. Repetitions of any experiment, as similar as achievable, always have built-in differences resulting in a range of the true values rather than in a single true experimental value. Measurement uncertainty depends on the measurement system only. Modern digital measurements have very small uncertainty, frequently smaller than the range of true experimental values resulting from built-in differences in the experiment repetitions. When data from one-of-a-kind experiment are analyzed, only the measurement uncertainty can be reported.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗