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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,567 records · Page 87
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

METACLUSTER—an R package for context-specific expression analysis of metabolic gene clusters

Abstract Summary Plants and microbes produce numerous compounds to cope with their environments but the biosynthetic pathways for most of these compounds have yet to be elucidated. Some biosynthetic pathways are encoded by enzymes collocated in the chromosome. To facilitate a more comprehensive condition and tissue-specific expression analysis of metabolic gene clusters, we developed METACLUSTER, a probabilistic framework for characterizing metabolic gene clusters using context-specific gene expression information. Availability and implementation METACLUSTER is freely available at https://github.com/mbanf/METACLUSTER. Supplementary information Supplementary data are available at Bioinformatics online.

Biochemistry & Molecular Biology↗
DOE OSTI2024

MISIP: a data standard for the reuse and reproducibility of any stable isotope probing-derived nucleic acid sequence and experiment

DNA/RNA-stable isotope probing (SIP) is a powerful tool to link in situ microbial activity to sequencing data. Every SIP dataset captures distinct information about microbial community metabolism, process rates, and population dynamics, offering valuable insights for a wide range of research questions. Data reuse maximizes the information derived from the labor and resource-intensive SIP approaches. Yet, a review of publicly available SIP sequencing metadata showed that critical information necessary for reproducibility and reuse was often missing. Here, we outline the Minimum Information for any Stable Isotope Probing Sequence (MISIP) according to the Minimum Information for any (x) Sequence (MIxS) framework and include examples of MISIP reporting for common SIP experiments. Our objectives are to expand the capacity of MIxS to accommodate SIP-specific metadata and guide SIP users in metadata collection when planning and reporting an experiment. The MISIP standard requires 5 metadata fields—isotope, isotopolog, isotopolog label, labeling approach, and gradient position—and recommends several fields that represent best practices in acquiring and reporting SIP sequencing data (e.g., gradient density and nucleic acid amount). The standard is intended to be used in concert with other MIxS checklists to comprehensively describe the origin of sequence data, such as for marker genes (MISIP-MIMARKS) or metagenomes (MISIP-MIMS), in combination with metadata required by an environmental extension (e.g., soil). The adoption of the proposed data standard will improve the reuse of any sequence derived from a SIP experiment and, by extension, deepen understanding of in situ biogeochemical processes and microbial ecology.

Simpson, Abigayle↗
DOE OSTI2024

Understanding Formation of Irradiation-Induced Defects through 4D-STEM, Electron Tomography, and WBDF-STEM

A major challenge in advancing nuclear materials for next-generation fission and proposed fusion reactors is to comprehensively understand the formation of irradiation-induced defects. Here it is essential to correlate the evolution of irradiation-induced defects and the degradation of mechanical properties, as they collectively dictate the material's lifespan and ensure nuclear safety. Scanning transmission electron microscopy (STEM) based techniques have emerged as indispensable tools for irradiation-induced defect characterization, offering high spatial resolution imaging and chemical analysis, such as electron energy loss spectroscopy (EELS) and energy dispersive X-ray spectroscopy (EDXS). These techniques have been effectively used to obtain an atomic-scale view of the defect structure. Recent advances in electron microscopy, particularly in 4D-STEM, offer detailed insight into microstructural evolution by capturing full 2D diffraction patterns at every pixel position. Using high-speed direct electron detectors, this technology generates a four-dimensional dataset, overcoming the limitations of traditional STEM imaging.

36 MATERIALS SCIENCE↗
DOE OSTI2025

End-to-End Automated Segmentation Framework for Four-Dimensional Scanning Transmission Electron Microscopy Data

Four-dimensional scanning transmission electron microscopy (4D-STEM) is powerful for rapidly characterizing arrays of nanoparticles produced via high-throughput synthesis. However, such 4D-STEM datasets typically contain thousands of nanoparticles, each characterized by thousands of diffraction patterns spatially distributed across the nanoparticle, necessitating efficient and comprehensive analysis. We propose an end-to-end segmentation framework to automatically segment each nanoparticle into regions with distinct composition/orientation of crystal grains, using only the 4D-STEM data. Bragg disk information is extracted in a physics-informed manner from the diffraction patterns at each spatial location and combined with the real space coordinates to form feature vectors. These feature vectors are then used as inputs to a Gaussian mixture model (GMM) to segment the nanoparticle into distinct regions. We also develop two visualization tools based on the GMM outputs to infer the interface transition and the degree of superposition. Our framework comprehensively integrates machine learning tools and physics knowledge, and provides a basis for substantially compressing enormous 4D-STEM datasets, e.g., by replacing the full 4D-STEM dataset for each nanoparticle with only a single set of Bragg disk features for each distinct crystal grain identified in the nanoparticle. In this article, we demonstrate the power of our framework by presenting results for real, complex datasets.

47 OTHER INSTRUMENTATION↗
DOE OSTI2022

BioTransformer 3.0 – A Web Server for Accurately Predicting Metabolic Transformation Products

BioTransformer 3.0 is a freely available web server that supports accurate, rapid and comprehensive in silico metabolism prediction. It combines machine learning approaches with a rule-based system to predict small-molecule metabolism in human tissues, the human gut as well as the external environment (soil and water microbiota). Simply stated, BioTransformer takes a molecular structure as input (SMILES or SDF) and outputs an interactively viewable/sortable table of the predicted metabolites or transformation products (SMILES, PNG images) along with the enzymes that are predicted to be responsible for those reactions and richly annotated downloadable files (CSV and JSON). The entire process typically takes a few seconds. Previous versions of BioTransformer focused exclusively on predicting the metabolism of xenobiotics (such as plant natural products, drugs, cosmetics and other synthetic compounds) using a limited number of pre-defined steps and somewhat limited rule-based methods. BioTransformer 3.0, uses much more sophisticated methods and incorporates new databases, new constraints and new prediction modules to not only more accurately predict the metabolic transformation products of exogenous xenobiotics but also the transformation products of endogenous metabolites, such as amino acids, peptides, carbohydrates, organic acids, and lipids. BioTransformer 3.0 can also support customized sequential combinations of these transformations along with multiple iterations to simulate multi-step human and/or environmental biotransformation events. Performance tests indicate that BioTransformer 3.0 is 40-50% more accurate, much less prone to combinatorial “explosions” and far more comprehensive in terms of metabolite coverage/capabilities than previous versions of BioTransformer.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Gene Ontology knowledgebase in 2026

Abstract The Gene Ontology (GO) knowledgebase (https://geneontology.org) is a comprehensive resource describing the functions of genes. The GO knowledgebase is regularly updated and improved. We describe here the major updates that have been made in the past 3 years. The ontology and annotations have been expanded and revised, particularly in several areas of biology: cellular metabolism, multi-organism interactions (e.g. host-pathogen), extracellular matrix proteins, chromatin remodeling (e.g. the “histone code”), and noncoding RNA functions. We have released version 2 of a comprehensive set of integrated, reviewed annotations for human genes, which we call the “functionome.” We have also dramatically increased the number of GO-CAM models, with over 1500 models of metabolic and signaling pathways, primarily in human, mouse, budding and fission yeast, and fruit fly. Finally, we discuss our current recommendations and future prospects of AI in the use and development of GO.

Aleksander, Suzi A (ORCID:0000000167872901)↗
DOE OSTI2024

Quantitative proteomics reveals extensive lysine ubiquitination and transcription factor stability states in Arabidopsis

Abstract Protein activity, abundance, and stability can be regulated by post-translational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function; yet, we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich ubiquitinated peptides coupled with isobaric labeling to enable quantification of up to 18-multiplexed samples. This approach identified 17,940 ubiquitinated lysine sites arising from 6,453 proteins from Arabidopsis (Arabidopsis thaliana) primary roots, seedlings, and rosette leaves. Gene ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. We determined ubiquitinated lysine residues that directly regulate the stability of three transcription factors, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) using in vivo degradation assays. Furthermore, codon mutation of CIB1 to create a K166R conversion to prevent ubiquitination, via CRISPR/Cas9-derived adenosine base editing, led to an early flowering phenotype and increased expression of FLOWERING LOCUS T (FT). These comprehensive site-level ubiquitinome profiles provide a wealth of data for future functional studies related to modulation of biological processes mediated by this post-translational modification in plants.

Biochemistry & Molecular Biology↗
DOE OSTI2013

Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells

Both diffusible factors acting in trans and chromatin components acting in cis are implicated in gene regulation, but the extent to which either process causally determines a cell’s transcriptional identity is unclear. We recently used cell fusion to define a class of silent genes termed ‘‘cis-silenced’’ (or ‘‘occluded’’) genes, which remain silent even in the presence of transacting transcriptional activators. We further showed that occlusion of lineage-inappropriate genes plays a critical role in maintaining the transcriptional identities of somatic cells. Here, we present, for the first time, a comprehensive map of occluded genes in somatic cells. Specifically, we mapped occluded genes in mouse fibroblasts via fusion to a dozen different rat cell types followed by whole-transcriptome profiling. We found that occluded genes are highly prevalent and stable in somatic cells, representing a sizeable fraction of silent genes. Occluded genes are also highly enriched for important developmental regulators of alternative lineages, consistent with the role of occlusion in safeguarding cell identities. Alongside this map, we also present whole-genome maps of DNA methylation and eight other chromatin marks. These maps uncover a complex relationship between chromatin state and occlusion. Furthermore, we found that DNA methylation functions as the memory of occlusion in a subset of occluded genes, while histone deacetylation contributes to the implementation but not memory of occlusion. Our data suggest that the identities of individual cell types are defined largely by the occlusion status of their genomes. The comprehensive reference maps reported here provide the foundation for future studies aimed at understanding the role of occlusion in development and disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Transposon insertional mutagenesis in Saccharomyces uvarum reveals trans-acting effects influencing species-dependent essential genes

To understand how complex genetic networks perform and regulate diverse cellular processes, the function of each individual component must be defined. Comprehensive phenotypic studies of mutant alleles have been successful in model organisms in determining what processes depend on the normal function of a gene. These results are often ported to newly sequenced genomes by using sequence homology. However, sequence similarity does not always mean identical function or phenotype, suggesting that new methods are required to functionally annotate newly sequenced species. We have implemented here comparative analysis by high-throughput experimental testing of gene dispensability in Saccharomyces uvarum, a sister species of Saccharomyces cerevisiae. We created haploid and heterozygous diploid Tn7 insertional mutagenesis libraries in S. uvarum to identify species-dependent essential genes, with the goal of detecting genes with divergent functions and/or different genetic interactions. Comprehensive gene dispensability comparisons with S. cerevisiae predicted diverged dispensability at 12% of conserved orthologs, and validation experiments confirmed 22 differentially essential genes. Despite their differences in essentiality, these genes were capable of cross-species complementation, demonstrating that trans-acting factors that are background-dependent contribute to differential gene essentiality. This study shows that direct experimental testing of gene disruption phenotypes across species can inform comparative genomic analyses and improve gene annotations. Our method can be widely applied in microorganisms to further our understanding of genome evolution.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Block orbital-selective Mott insulators: A spin excitation analysis

We present a comprehensive study of the spin excitations—as measured by the dynamical spin structure factor S(q,ω)—of the so-called block-magnetic state of low-dimensional orbital-selective Mott insulators. We realize this state via both a multi-orbital Hubbard model and a generalized Kondo-Heisenberg Hamiltonian. Due to various competing energy scales present in the models, the system develops periodic ferromagnetic islands of various shapes and sizes, which are antiferromagnetically coupled. The 2×2 particular case was already found experimentally in the ladder material BaFe2Se3 that becomes superconducting under pressure. Here we discuss the electronic density as well as Hubbard and Hund coupling dependence of S(q,ω) using density matrix renormalization group method. Several interesting features were identified: (1) An acoustic (dispersive spin-wave) mode develops. (2) The spin-wave bandwidth establishes a new energy scale that is strongly dependent on the size of the magnetic island and becomes abnormally small for large clusters. (3) Optical (dispersionless spin excitation) modes are present for all block states studied here. In addition, a variety of phenomenological spin Hamiltonians have been investigated but none matches entirely our results that were obtained primarily at intermediate Hubbard U strengths. Our comprehensive analysis provides theoretical guidance and motivation to crystal growers to search for appropriate candidate materials to realize the block states, and to neutron scattering experimentalists to confirm the exotic dynamical magnetic properties unveiled here, with a rich mixture of acoustic and optical features.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Electronic structure and lattice dynamics of 1⁢𝑇−VSe 2 : Origin of the three-dimensional charge density wave

To characterize in detail the charge density wave (CDW) transition of 1⁢𝑇−VSe 2 , its electronic structure and lattice dynamics are comprehensively studied by means of x-ray diffraction, muon spectroscopy, angle resolved photoemission (ARPES), diffuse and inelastic x-ray scattering, and state-of-the-art first-principles density functional theory calculations. Resonant elastic x-ray scattering does not show any resonant enhancement at either V or Se, indicating that the CDW peak at the 𝐾 edges describes a purely structural modulation of the electronic ordering. ARPES experiments identify (i) a pseudogap at 𝑇 > 𝑇⁢ CDW , which leads to a depletion of the density of states in the ML-M'L' plane at 𝑇 < 𝑇⁢ CDW , and (ii) anomalies in the electronic dispersion reflecting a sizable impact of phonons on it. A diffuse scattering precursor, characteristic of soft phonons, is observed at room temperature (RT) and leads to the full collapse of the low-energy phonon (𝜔 1 ) with propagation vector (0.25 0 −0.3) r.l.u. Here, we show that the frequency and linewidth of this mode are anisotropic in momentum space, reflecting the momentum dependence of the electron-phonon interaction (EPI), hence demonstrating that the origin of the CDW is, to a much larger extent, due to the momentum dependent EPI with a small contribution from nesting. The pressure dependence of the 𝜔 1 soft mode remains nearly constant up to 13 GPa at RT, with only a modest softening before the transition to the high-pressure monoclinic C2/m phase. The wide set of experimental data is well captured by our state-of-the art first-principles anharmonic calculations with the inclusion of van der Waals corrections in the exchange-correlation functional. The comprehensive description of the electronic and dynamical properties of VSe 2 reported here adds important pieces of information to the understanding of the electronic modulations in the family of transition-metal dichalcogenides.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2015

Fermi surface interconnectivity and topology in Weyl fermion semimetals TaAs, TaP, NbAs, and NbP

The family of binary compounds including TaAs, TaP, NbAs, and NbP was recently discovered as the first realization of Weyl semimetals. In order to develop a comprehensive description of the charge carriers in these Weyl semimetals, we performed detailed and systematic electronic band structure calculations which reveal the nature of Fermi surfaces and their complex interconnectivity in TaAs, TaP, NbAs, and NbP. In conclusion, our work reports a comparative and comprehensive study of Fermi surface topology and band structure details of all known members of the Weyl semimetal family and hence provides the fundamental knowledge for realizing the many predicted exotic topological quantum physics of Weyl semimetals based on the TaAs class of materials.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Magnetic field dependence of nonlinear magnetic response and tricritical point in the monoaxial chiral helimagnet Cr 1 / 3 Nb S 2

We present a comprehensive study of the magnetization dynamics and phase evolution in the chiral helimagnet Cr 1/3 NbS 2 , which realizes a chiral soliton lattice (CSL). The magnetic field dependence of the ac magnetic response is analyzed for the first five harmonic components, M nω (H ) (n = 1–5), using a phase sensitive measurement over a frequency range, f = 11–10 000 Hz. At a critical field, the modulated CSL continuously evolves from a helicity-rich to a ferromagnetic domain-rich structure, where the crossover is revealed by the onset of an anomalous nonlinear magnetic response that coincides with extremely slow dynamics. The behavior is indicative of the formation of a spatially coherent array of large ferromagnetic domains, which relax on macroscopic time scales. The frequency dependence of the ac magnetic loss displays an asymmetric distribution of relaxation times across the highly nonlinear CSL regime, which shift to shorter time scales with increasing temperature. We experimentally resolve the tricritical point at T TCP in a temperature regime above the ferromagnetic Curie temperature which separates the linear and nonlinear magnetic regimes of the CSL at the phase transition. A comprehensive phase diagram is constructed which summarizes the features of the field and temperature dependence of the magnetic crossovers and phase transitions in Cr 1/3 NbS 2 .

36 MATERIALS SCIENCE↗
DOE OSTI2020

Gamow-shell-model description of Li isotopes and their mirror partners

Background: Weakly bound and unbound nuclei close to particle drip lines are laboratories of new nuclear structure physics at the extremes of neutron/proton excess. The comprehensive description of these systems requires an open quantum system framework that is capable of treating resonant and nonresonant many-body states on equal footing. Purpose: In this work, we develop the complex-energy configuration interaction approach to describe binding energies and spectra of selected 5 ≤ $\textit{A}$ ≤ 11 nuclei. Method: We employ the complex-energy Gamow shell model (GSM) assuming a rigid 4 He core. The effective Hamiltonian, consisting of a core-nucleon Woods-Saxon potential and a simplified version of the Furutani-Horiuchi-Tamagaki interaction with the mass-dependent scaling, is optimized in the $\textit{sp}$ space. To diagonalize the Hamiltonian matrix, we employ the Davidson method and the Density Matrix Renormalization Group technique. Results: We report our optimized GSM Hamiltonian offers a good reproduction of binding energies and spectra with the root-mean-square (rms) deviation from experiment of 160 keV. Since the model performs well when used to predict known excitations that have not been included in the fit, it can serve as a reliable tool to describe poorly known states. A case in point is our prediction for the pair of unbound mirror nuclei 10 Li – 10 N in which a huge Thomas-Ehrman shift dramatically alters the pattern of low-energy excitations. Conclusion: The new model will enable comprehensive studies of structure and reactions aspects of light drip-line nuclei.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2017

Quantified Gamow shell model interaction for p s d -shell nuclei

Background: The structure of weakly bound and unbound nuclei close to particle drip lines is one of the major science drivers of nuclear physics. A comprehensive understanding of these systems goes beyond the traditional configuration interaction approach formulated in the Hilbert space of localized states (nuclear shell model) and requires an open quantum system description. The complex-energy Gamow shell model (GSM) provides such a framework as it is capable of describing resonant and nonresonant many-body states on equal footing. Purpose: To make reliable predictions, quality input is needed that allows for the full uncertainty quantification of theoretical results. In this study, we carry out the optimization of an effective GSM (one-body and two-body) interaction in the psdf-shell-model space. The resulting interaction is expected to describe nuclei with 5 ≤ A ≲ 12 at the p-sd-shell interface. Method: The one-body potential of the 4 He core is modeled by a Woods-Saxon + spin-orbit + Coulomb potential, and the finite-range nucleon-nucleon interaction between the valence nucleons consists of central, spin-orbit, tensor, and Coulomb terms. The GSM is used to compute key fit observables. The χ 2 optimization is performed using the Gauss-Newton algorithm augmented by the singular value decomposition technique. The resulting covariance matrix enables quantification of statistical errors within the linear regression approach. Results: The optimized one-body potential reproduces nucleon- 4 He scattering phase shifts up to an excitation energy of 20 MeV. The two-body interaction built on top of the optimized one-body field is adjusted to the bound and unbound ground-state binding energies and selected excited states of the helium, lithium, and beryllium isotopes up to A = 9 . A very good agreement with experimental results was obtained for binding energies. First applications of the optimized interaction include predictions for two-nucleon correlation densities and excitation spectra of light nuclei with quantified uncertainties. In conclusion: The new interaction will enable comprehensive and fully quantified studies of structure and reactions aspects of nuclei from the psd region of the nuclear chart.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2018

Detailed study of the decay Cl 31 ( β γ ) S 31

Background: 31 Cl is a neutron-deficient isotope with a half-life of T 1/2 = 190 (1) ms. The nuclear structure of its daughter, 31 S, is important for the determination of the thermonuclear 30 P(p,γ) 31 S reaction rate, which affects the final isotopic abundances of the ejecta from classical oxygen-neon novae. Purpose: Here, we aim to determine the β feedings, γ-decay branchings, and excitation energies of states populated in 31 S and create a comprehensive decay scheme for comparison with predictions based on the shell model. Methods: Using a 31 Cl rare istope beam implanted into a plastic scintillator and an array of high-purity Ge detectors, γ rays from the 31 Cl(βγ) 31 S decay sequence were measured. Shell-model calculations using the USDB and the recently-developed USDE interactions were performed for comparison. Results: A 31 Cl β-decay scheme was constructed from the experimental data and compared to the USDB and USDE shell-model calculations based on the β feeding and γ-decay branches of each observed state. 33 new γ-ray transitions and ten new β decay branches were observed. The β feeding and γ-decay branches of each observed state were compared to those from the USDB and USDE shell-model calculations. For every allowed transition predicted by the USD calculations up to an excitation energy of 6.4 MeV in 31 S, an analogous transition was found in the experimental data, enabling a one-to-one comparison with the shell model. Using these identifications, spin and parity arguments were made for observed states. Conclusions: The new 31 Cl γ-decay scheme presented in this work is the most complete and precise one for this nucleus constructed to date, incorporating statistics over an order of magnitude higher than previous work on 31 Cl β-delayed γ decay. Of particular interest is the discovery of a 6390-keV state that mixes with the isobaric analog state and affects the 30 P(p,γ) 31 S reaction rate. Other states observed in the decay are not expected to strongly affect the 30 P(p,γ) 31 S reaction rate, but the comprehensive comparison to the shell model helps to clarify spin and parity assignments of resonances that might affect the rate.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2019

Multiplicity dependence of light-flavor hadron production in p p collisions at s = 7 TeV

Comprehensive results on the production of unidentified charged particles, $π^±, K^±, K^0_S, K^*(892)^0, p,$ $\bar{p}$, $\phi$ (1020), Λ, $\bar{Λ}$, $\Xi^-$, $\bar{\Xi}^+$, $Ω^-$, and $\bar{Ω}^+$ hadrons in proton-proton ($pp$) collisions at $\sqrt{s}$ = 7 TeV at midrapidity ($|y|$ < 0.5) as a function of charged-particle multiplicity density are presented. In order to avoid autocorrelation biases, the actual transverse momentum ($p$ T ) spectra of the particles under study and the event activity are measured in different rapidity windows. In the highest multiplicity class, the charged-particle density reaches about 3.5 times the value measured in inelastic collisions. While the yield of protons normalized to pions remains approximately constant as a function of multiplicity, the corresponding ratios of strange hadrons to pions show a significant enhancement that increases with increasing strangeness content. Furthermore, all identified particle-to-pion ratios are shown to depend solely on charged-particle multiplicity density, regardless of system type and collision energy. The evolution of the spectral shapes with multiplicity and hadron mass shows patterns that are similar to those observed in $p$-Pb and Pb-Pb collisions at Large Hadron Collider energies. The obtained $p$ T distributions and yields are compared to expectations from QCD-based $pp$ event generators as well as to predictions from thermal and hydrodynamic models. These comparisons indicate that traces of a collective, equilibrated system are already present in high-multiplicity $pp$ collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗