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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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Hypermut 3: identifying specific mutational patterns in a defined nucleotide context that allows multistate characters

Abstract Motivation The detection of APOBEC3F- and APOBEC3G-induced mutations in virus sequences is useful for identifying hypermutated sequences. These sequences are not representative of viral evolution and can therefore alter the results of downstream sequence analyses if included. We previously published the software Hypermut, which detects hypermutation events in sequences relative to a reference. Two versions of this method are available as a webtool. Neither of these methods consider multistate characters or gaps in the sequence alignment. Results Here, we present an updated, user-friendly web and command-line version of Hypermut with functionality to handle multistate characters and gaps in the sequence alignment. This tool allows for straightforward integration of hypermutation detection into sequence analysis pipelines. As with the previous tool, while the main purpose is to identify G to A hypermutation events, any mutational pattern and context can be specified. Availability and implementation Hypermut 3 is written in Python 3. It is available as a command-line tool at https://github.com/MolEvolEpid/hypermut3 and as a webtool at https://www.hiv.lanl.gov/content/sequence/HYPERMUT/hypermutv3.html.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Accessible, uniform protein property prediction with a scikit-learn based toolset AIDE

Summary Protein property prediction via machine learning with and without labeled data is becoming increasingly powerful, yet methods are disparate and capabilities vary widely over applications. The software presented here, “Artificial Intelligence Driven protein Estimation (AIDE)”, enables instantiating, optimizing, and testing many zero-shot and supervised property prediction methods for variants and variable length homologs in a single, reproducible notebook or script by defining a modular, standardized application programming interface (API), i.e. drop-in compatible with scikit-learn transformers and pipelines. Availability and implementation AIDE is an installable, importable python package inheriting from scikit-learn classes and API and is installable on Windows, Mac, and Linux. Many of the wrapped models internal to AIDE will be effectively inaccessible without a GPU, and some assume CUDA. The newest stable, tested version can be found at https://github.com/beckham-lab/aide_predict and a full user guide and API reference can be found at https://beckham-lab.github.io/aide_predict/. Static versions of both at the time of writing can be found on Zenodo.

36 MATERIALS SCIENCE↗
DOE OSTI2024

The Ecosystem as Super-Organ/ism, Revisited: Scaling Hydraulics to Forests under Climate Change

Synopsis Classic debates in community ecology focused on the complexities of considering an ecosystem as a super-organ or organism. New consideration of such perspectives could clarify mechanisms underlying the dynamics of forest carbon dioxide (CO2) uptake and water vapor loss, important for predicting and managing the future of Earth’s ecosystems and climate system. Here, we provide a rubric for considering ecosystem traits as aggregated, systemic, or emergent, i.e., representing the ecosystem as an aggregate of its individuals or as a metaphorical or literal super-organ or organism. We review recent approaches to scaling-up plant water relations (hydraulics) concepts developed for organs and organisms to enable and interpret measurements at ecosystem-level. We focus on three community-scale versions of water relations traits that have potential to provide mechanistic insight into climate change responses of forest CO2 and H2O gas exchange and productivity: leaf water potential (Ψcanopy), pressure volume curves (eco-PV), and hydraulic conductance (Keco). These analyses can reveal additional ecosystem-scale parameters analogous to those typically quantified for leaves or plants (e.g., wilting point and hydraulic vulnerability) that may act as thresholds in forest responses to drought, including growth cessation, mortality, and flammability. We unite these concepts in a novel framework to predict Ψcanopy and its approaching of critical thresholds during drought, using measurements of Keco and eco-PV curves. We thus delineate how the extension of water relations concepts from organ- and organism-scales can reveal the hydraulic constraints on the interaction of vegetation and climate and provide new mechanistic understanding and prediction of forest water use and productivity.

Zoology↗
DOE OSTI2020

Joint galaxy–galaxy lensing and clustering constraints on galaxy formation

ABSTRACT We compare predictions for galaxy–galaxy lensing profiles and clustering from the Henriques et al. public version of the Munich semi-analytical model (SAM) of galaxy formation and the IllustrisTNG suite, primarily TNG300, with observations from KiDS + GAMA and SDSS-DR7 using four different selection functions for the lenses (stellar mass, stellar mass and group membership, stellar mass and isolation criteria, and stellar mass and colour). We find that this version of the SAM does not agree well with the current data for stellar mass-only lenses with $M_\ast \gt 10^{11}\, \mathrm{ M}_\odot$. By decreasing the merger time for satellite galaxies as well as reducing the radio-mode active galactic nucleus accretion efficiency in the SAM, we obtain better agreement, both for the lensing and the clustering, at the high-mass end. We show that the new model is consistent with the signals for central galaxies presented in Velliscig et al. Turning to the hydrodynamical simulation, TNG300 produces good lensing predictions, both for stellar mass-only (χ2 = 1.81 compared to χ2 = 7.79 for the SAM) and locally brightest galaxy samples (χ2 = 3.80 compared to χ2 = 5.01). With added dust corrections to the colours it matches the SDSS clustering signal well for red low-mass galaxies. We find that both the SAMs and TNG300 predict $\sim 50\, {{\ \rm per\ cent}}$ excessive lensing signals for intermediate-mass red galaxies with 10.2 < log10M*[M⊙] < 11.2 at $r \approx 0.6\, h^{-1}\, \text{Mpc}$, which require further theoretical development.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

SCONCE : a cosmic web finder for spherical and conic geometries

The latticework structure known as the cosmic web provides a valuable insight into the assembly history of large-scale structures. Despite the variety of methods to identify the cosmic web structures, they mostly rely on the assumption that galaxies are embedded in a Euclidean geometric space. Here, we present a novel cosmic web identifier called SCONCE (Spherical and CONic Cosmic wEb finder) that inherently considers the 2D (RA, DEC) spherical or the 3D (RA, DEC, z) conic geometry. The proposed algorithms in sconce generalize the well-known subspace constrained mean shift (SCMS) method and primarily address the predominant filament detection problem. They are intrinsic to the spherical/conic geometry and invariant to data rotations. We further test the efficacy of our method with an artificial cross-shaped filament example and apply it to the SDSS galaxy catalogue, revealing that the 2D spherical version of our algorithms is robust even in regions of high declination. Finally, using N-body simulations from Illustris, we show that the 3D conic version of our algorithms is more robust in detecting filaments than the standard SCMS method under the redshift distortions caused by the peculiar velocities of haloes. Our cosmic web finder is packaged in python as SCONCE-SCMS and has been made publicly available.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata

Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, for this work, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.

59 BASIC BIOLOGICAL SCIENCES↗
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 OSTI2022

CFM-ID 4.0 – a web server for accurate MS-based metabolite identification

The CFM-ID 4.0 web server (https://cfmid.wishartlab.com) is an online tool for predicting, annotating and interpreting tandem mass (MS/MS) spectra of small molecules. It is specifically designed to assist researchers pursuing studies in metabolomics, exposomics and analytical chemistry. More specifically, CFM-ID 4.0 supports the: 1) prediction of electrospray ionization quadrupole time-of-flight tandem mass spectra (ESI-QTOF-MS/MS) for small molecules over multiple collision energies (10 eV, 20 eV, and 40 eV); 2) annotation of ESI-QTOF-MS/MS spectra given the structure of the compound; and 3) identification of a small molecule that generated a given ESI-QTOF-MS/MS spectrum at one or more collision energies. The CFM-ID 4.0 web server makes use of a substantially improved MS fragmentation algorithm, a much larger database of experimental and in silico predicted MS/MS spectra and improved scoring methods to offer more accurate MS/MS spectral prediction and MS/MS-based compound identification. Compared to earlier versions of CFM-ID, this new version has an MS/MS spectral prediction performance that is ~22% better and a compound identification accuracy that is ~35% better on a standard (CASMI 2016) testing dataset. CFM-ID 4.0 also features a neutral loss function that allows users to identify similar or substituent compounds where no match can be found using CFM-ID’s regular MS/MS-to-compound identification utility. Finally, the CFM-ID 4.0 web server now offers a much more refined user interface that is easier to use, supports molecular formula identification (from MS/MS data), provides more interactively viewable data (including proposed fragment ion structures) and displays MS mirror plots for comparing predicted with observed MS/MS spectra. These improvements should make CFM-ID 4.0 much more useful to the community and should make small molecule identification much easier, faster, and more accurate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Correction to ‘Twenty-five years of Genomes OnLine Database (GOLD): data updates and new features in v.9’

In the originally published online version of this manuscript, there were two co-authors missing from the author list: Tanja Woyke (https://orcid.org/0000-0002-9485-5637) and Emiley Eloe-Fadrosh (https://orcid.org/0000-0002-8162-1276). The author list should read: ‘Supratim Mukherjee, Dimitri Stamatis, Cindy Tianqing Li, Galina Ovchinnikova, Jon Bertsch, Jagadish Chandrabose Sundaramurthi, Mahathi Kandimalla, Paul A. Nicolopoulos, Alessandro Favognano, Tanja Woyke, Emiley A. Eloe-Fardosh, I-Min A. Chen, Nikos C. Kyrpides and T.B.K. Reddy’. This emendation is outlined only in this correction notice to preserve the version of record.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2024

Correction to ‘Genomes OnLine Database (GOLD) v.8: overview and updates’

In the originally published online version of this manuscript, there were two co-authors missing from the author list: Tanja Woyke (https://orcid.org/0000-0002-9485-5637) and Emiley Eloe-Fadrosh (https://orcid.org/0000-0002-8162-1276). The list should now read: ‘Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Jagadish Chandrabose Sundaramurthi, Janey Lee, Mahathi Kandimalla, Tanja Woyke, Emiley A. Eloe-Fardosh, I-Min A. Chen, Nikos C. Kyrpides and T.B.K. Reddy’. The emendation is outlined only in this correction notice to preserve the version of record.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2023

Phycobilisome protein ApcG interacts with PSII and regulates energy transfer in Synechocystis

Photosynthetic organisms harvest light using pigment–protein complexes. In cyanobacteria, these are water-soluble antennae known as phycobilisomes (PBSs). The light absorbed by PBS is transferred to the photosystems in the thylakoid membrane to drive photosynthesis. The energy transfer between these complexes implies that protein–protein interactions allow the association of PBS with the photosystems. However, the specific proteins involved in the interaction of PBS with the photosystems are not fully characterized. Here, we show in Synechocystis sp. PCC 6803 that the recently discovered PBS linker protein ApcG (sll1873) interacts specifically with PSII through its N-terminal region. Growth of cyanobacteria is impaired in apcG deletion strains under light-limiting conditions. Furthermore, complementation of these strains using a phospho-mimicking version of ApcG causes reduced growth under normal growth conditions. Interestingly, the interaction of ApcG with PSII is affected when a phospho-mimicking version of ApcG is used, targeting the positively charged residues interacting with the thylakoid membrane, suggesting a regulatory role mediated by phosphorylation of ApcG. Low-temperature fluorescence measurements showed decreased PSI fluorescence in apcG deletion and complementation strains. The PSI fluorescence was the lowest in the phospho-mimicking complementation strain, while the pull-down experiment showed no interaction of ApcG with PSI under any tested condition. In conclusion, our results highlight the importance of ApcG for selectively directing energy harvested by the PBS and imply that the phosphorylation status of ApcG plays a role in regulating energy transfer from PSII to PSI.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Implementation of Stochastic Gradient Descent in an Automated Glow Peak Identification Software for Multiple Thermoluminescent Dosimeter Types

A glow-curve analysis code was previously developed in C++ to analyze thermoluminescent dosimeter glow curves using automated peak detection while applying a first-order kinetics model. A newer version of this code was implemented to improve the automated peak detection and curve fitting models. The Stochastic Gradient Descent Algorithm was introduced to replace the prior approach of taking first and second-order derivatives for peak detection. Additionally, early stopping mechanisms were invoked to improve the previously used Levenberg-Marquardt Algorithm employed for curve fitting. The two software versions were compared through glow curve analysis of different thermoluminescent dosimeter materials and calculation of the corresponding figures of merit. Altogether improvements were shown, namely an increase in the number of peaks detected and a reduction of the mean figure of merit by approximately 46%.

137Cs↗
DOE OSTI2026

Nonadiabatic strong-field photoionization revisited: Detailed analysis

We develop a theoretical framework to interpret “bump-like” enhancements in the energy distribution of electrons emitted from cesium atoms subjected to intense infrared laser fields, as observed in a recent experiment. These emissions, detected at energies approaching twice the ponderomotive energy (2⁢𝑈 p ), indicate a mechanism where electrons are nonadiabatically ejected with substantial inward velocity following ionization. The bump-like features arise from returning trajectories that scatter off the residual ion. We interpret these experimental results classically using a periodically driven version of the Bohr model and quantum mechanically through Keldysh's adiabaticity parameter (𝛾 K ) and Reiss's continuum-state intensity parameter 𝒵 in a Coulomb-corrected version of the strong-field approximation (SFA) that incorporates “complex” electronic trajectories. Notably, our theoretical analysis shows that these emissions are independent of the specific short-range form of the atomic potential.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2023

Inverse modeling of circular lattices via orbit response measurements in the presence of degeneracy

The number and location of beam position monitors (BPMs) and steerers with respect to the quadrupoles in a circular lattice can lead to degeneracy in the context of fitting linear optics and extracting lattice information from measured closed orbits. Furthermore, the measurement uncertainties due to the imperfection of BPMs and steerers can be propagated by the fitting process in ways that prohibit the successful extraction of discrepancies between lattice elements in the real machine and their description in the corresponding model. We systematically studied the influence of the placement of BPMs and steerers on the reconstruction of linear optics and corresponding lattice information. The derivative of orbit response coefficients with respect to the quadrupole strengths, the Jacobian, is derived as an analytical formula. This analytical version of the Jacobian is used to further derive the theoretical limitations of fitting linear optics from closed orbits in terms of the placement of BPMs and steerers. It is further demonstrated that when evaluating the Jacobian during the fitting procedure, the analytical version can be used in place of the conventional finite-difference computation. This allows for greatly improved efficiency when computing the Jacobian during each iteration of the fitting procedure. The approach is tested with large-scale simulations and the findings are verified by measurement data taken on SIS18 synchrotron at GSI Helmholtz Centre for Heavy Ion Research. The presented methods are of general nature and can be applied to other accelerator lattices as well. The fitting procedure by using the analytical Jacobian is tested in conjunction with various methods for mitigating quasidegeneracy and the results agree with those obtained by using the conventional Jacobian via finite-difference approximation.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Exploring self-consistency of the equations of axion electrodynamics in Weyl semimetals

Recent works have provided evidence that an axial anomaly can arise in Weyl semimetals. If this is the case, then the electromagnetic response of Weyl semimetals should be governed by the equations of axion electrodynamics. These equations capture both the chiral magnetic and anomalous Hall effects in the limit of linear response, while at higher orders their solutions can provide detectable electromagnetic signatures of the anomaly. In this work, we consider three versions of axion electrodynamics that have been proposed in the Weyl semimetal literature. These versions differ in the form of the chiral magnetic term and in whether or not the axion is treated as a dynamical field. In each case, we look for solutions to these equations for simple sample geometries subject to applied external fields. We find that in the case of a linear chiral magnetic term generated by a nondynamical axion, self-consistent solutions can generally be obtained. In this case, the magnetic field inside of the Weyl semimetal can be magnified significantly, providing a testable signature for experiments. Self-consistent solutions can also be obtained for dynamical axions, but only in cases where the chiral magnetic term vanishes identically. Finally, for a nonlinear form of the chiral magnetic term frequently considered in the literature, we find that there are no self-consistent solutions aside from a few special cases.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Numerical relativity in spherical coordinates: A new dynamical spacetime and general relativistic MHD evolution framework for the Einstein Toolkit

We present SphericalNR, a new framework for the publicly available Einstein Toolkit that numerically solves the Einstein field equations coupled to the equations of general relativistic magnetohydrodynamic (GRMHD) in a 3+1 split of spacetime in spherical coordinates without symmetry assumptions. The spacetime evolution is performed using reference-metric versions of either the Baumgarte-Shapiro-Shibata-Nakamura equations or the fully covariant and conformal Z4 system with constraint damping. We have developed a reference-metric version of the Valencia formulation of GRMHD with a vector potential method, guaranteeing the absence of magnetic monopoles during the evolution. In our framework, every dynamical field (both spacetime and matter) is evolved using its components in an orthonormal basis with respect to the spherical reference metric. Furthermore, all geometric information about the spherical coordinate system is encoded in source terms appearing in the evolution equations. This allows for the straightforward extension of Cartesian high-resolution shock-capturing finite volume codes to use spherical coordinates with our framework. To this end, we have adapted GRHydro, a Cartesian finite volume GRMHD code already available in the Einstein Toolkit, to use spherical coordinates. We present the full evolution equations of the framework, as well as details of its implementation in the Einstein Toolkit. Finally, we validate SphericalNR by demonstrating it passes a variety of challenging code tests in static and dynamical spacetimes.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Hadronic interaction model sibyll 2.3d and extensive air showers

We present a new version of the hadron interaction event generator SIBYLL. While the core ideas of the model have been preserved, the new version handles the production of baryon pairs and leading particles in a new way. In addition, production of charmed hadrons is included. Updates to the model are informed by high-precision measurements of the total and inelastic cross sections with the forward detectors at the LHC that constrain the extrapolation to ultrahigh energy. Minimum-bias measurements of particle spectra and multiplicities support the tuning of fragmentation parameters. This paper demonstrates the impact of these changes on air-shower observables such as X max and N μ , drawing comparisons with other contemporary cosmic-ray interaction models.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Addition of tabulated equation of state and neutrino leakage support to illinoisgrmhd

Here we have added support for realistic, microphysical, finite-temperature equations of state (EOS) and neutrino physics via a leakage scheme to illinoisgrmhd, an open-source GRMHD code for dynamical spacetimes in the einstein toolkit. These new features are provided by two new, nrpy+-based codes: nrpyeos, which performs highly efficient EOS table lookups and interpolations, and nrpyleakage, which implements a new, adaptive mesh refinement (AMR)-capable neutrino leakage scheme in the einstein toolkit. We have performed a series of strenuous validation tests that demonstrate the robustness of these new codes, particularly on the Cartesian AMR grids provided by carpet. Furthermore, we show results from fully dynamical GRMHD simulations of single unmagnetized neutron stars, and magnetized binary neutron star mergers. This new version of illinoisgrmhd, as well as nrpyeos and nrpyleakage, is pedagogically documented in jupyter notebooks and fully open source. The codes will be proposed for inclusion in an upcoming version of the einstein toolkit.

79 ASTRONOMY AND ASTROPHYSICS↗