Search NASA⌕ Search

SEARCH · Search NASA

Results for “Manuscript”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 523 records · Page 29
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Will high-entropy carbides and borides be enabling materials for extreme environments?

Abstract The concept of multi-principal component has created promising opportunities for the development of novel high-entropy ceramics for extreme environments encountered in advanced turbine engines, nuclear reactors, and hypersonic vehicles, as it expands the compositional space of ceramic materials with tailored properties within a single-phase solid solution. The unique physical properties of some high-entropy carbides and borides, such as higher hardness, high-temperature strength, lower thermal conductivity, and improved irradiation resistance than the constitute ceramics, have been observed. These promising properties may be attributed to the compositional complexity, atomic-level disorder, lattice distortion, and other fundamental processes related to defect formation and phonon scattering. This manuscript serves as a critical review of the recent progress in high-entropy carbides and borides, focusing on synthesis and evaluations of their performance in extreme high-temperature, irradiation, and gaseous environments.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Towards automating structural discovery in scanning transmission electron microscopy *

Abstract Scanning transmission electron microscopy is now the primary tool for exploring functional materials on the atomic level. Often, features of interest are highly localized in specific regions in the material, such as ferroelectric domain walls, extended defects, or second phase inclusions. Selecting regions to image for structural and chemical discovery via atomically resolved imaging has traditionally proceeded via human operators making semi-informed judgements on sampling locations and parameters. Recent efforts at automation for structural and physical discovery have pointed towards the use of ‘active learning’ methods that utilize Bayesian optimization with surrogate models to quickly find relevant regions of interest. Yet despite the potential importance of this direction, there is a general lack of certainty in selecting relevant control algorithms and how to balance a priori knowledge of the material system with knowledge derived during experimentation. Here we address this gap by developing the automated experiment workflows with several combinations to both illustrate the effects of these choices and demonstrate the tradeoffs associated with each in terms of accuracy, robustness, and susceptibility to hyperparameters for structural discovery. We discuss possible methods to build descriptors using the raw image data and deep learning based semantic segmentation, as well as the implementation of variational autoencoder based representation. Furthermore, each workflow is applied to a range of feature sizes including NiO pillars within a La:SrMnO 3 matrix, ferroelectric domains in BiFeO 3 , and topological defects in graphene. The code developed in this manuscript is open sourced and will be released at github.com/nccreang/AE_Workflows .

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

Magnetohydrodynamics with physics informed neural operators

Abstract The modeling of multi-scale and multi-physics complex systems typically involves the use of scientific software that can optimally leverage extreme scale computing. Despite major developments in recent years, these simulations continue to be computationally intensive and time consuming. Here we explore the use of AI to accelerate the modeling of complex systems at a fraction of the computational cost of classical methods, and present the first application of physics informed neural operators (NOs) (PINOs) to model 2D incompressible magnetohydrodynamics (MHD) simulations. Our AI models incorporate tensor Fourier NOs as their backbone, which we implemented with the TensorLY package. Our results indicate that PINOs can accurately capture the physics of MHD simulations that describe laminar flows with Reynolds numbers Re ⩽ 250 . We also explore the applicability of our AI surrogates for turbulent flows, and discuss a variety of methodologies that may be incorporated in future work to create AI models that provide a computationally efficient and high fidelity description of MHD simulations for a broad range of Reynolds numbers. The scientific software developed in this project is released with this manuscript.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Computational and Systems Biology Advances to Enable Bioagent Agnostic Signatures

Enumerated threat agent lists have long driven biodefense priorities. The global SARS-CoV-2 pandemic demonstrated the limitations of searching for known threat agents as compared to a more agnostic approach. Recent technological advances are enabling agent-agnostic biodefense, especially through the integration of multi-modal observations of host-pathogen interactions directed by a human immunological model. Although well-developed technical assays exist for many aspects of human-pathogen interaction, the analytic methods and pipelines to combine and holistically interpret the results of such assays are immature and require further investments to exploit new technologies. In this manuscript, we discuss potential immunologically based bioagent-agnostic approaches and the computational tool gaps the community should prioritize filling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

CONSTAX2: improved taxonomic classification of environmental DNA markers

Abstract Summary CONSTAX—the CONSensus TAXonomy classifier—was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability and implementation CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Data and scripts associated with the manuscript are available at https://github.com/liberjul/CONSTAXv2_ms_code. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

NEAR: Neural Embeddings for Amino acid Relationships

Protein language models (PLMs) have recently demonstrated potential to supplant classical protein database search methods based on sequence alignment, but are slower than common alignment-based tools and appear to be prone to a high rate of false labeling. Here, we present NEAR, a method based on neural representation learning that is designed to improve both speed and accuracy of search for likely homologs in a large protein sequence database. NEAR’s ResNet embedding model is trained using contrastive learning guided by trusted sequence alignments. It computes per-residue embeddings for target and query protein sequences, and identifies alignment candidates with a pipeline consisting of residue-level k-NN search and a simple neighbor aggregation scheme. Tests on a benchmark consisting of trusted remote homologs and randomly shuffled decoy sequences reveal that NEAR substantially improves accuracy relative to state-of-the-art PLMs, with lower memory requirements and faster embedding and search speed. While these results suggest that the NEAR model may be useful for standalone homology detection with increased sensitivity over standard alignment-based methods, in this manuscript we focus on a more straightforward analysis of the model’s value as a high-speed pre-filter for sensitive annotation. In that context, NEAR is at least 5x faster than the pre-filter currently used in the widely-used profile hidden Markov model (pHMM) search tool HMMER3, and also outperforms the pre-filter used in our fast pHMM tool, nail.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Publishing Environmental Assessment and Management Science: Crossing the Hurdles

Benefits accrue to scientists, resource managers, companies, and policymakers when environmental scientists publish in peer-reviewed journals. However, environmental scientists and practitioners face challenges, including the sometimes low value placed on journal articles, institutional vested interests in outcomes, and the changing priorities of employers and project sponsors. Confidentiality agreements can also lead scientists to assume publication is not an option. Case studies may be viewed by potential authors as too routine for peer-reviewed journals. On the basis of 30 years of experience, we suggest that publishing hurdles can be overcome and that environmental scientists have a range of options. The topics of manuscripts can include not only results from case studies and perspectives based on them but also byproducts of assessments, including definitions, plans, monitoring methods and models, and decision frameworks. Environmental scientists have unique opportunities to move science forward with their practical knowledge if they can move across the institutional, logistical, data-related, and content-related hurdles.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Standardized naming of microbiome samples in Genomes OnLine Database

The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

A best-practice guide to predicting plant traits from leaf-level hyperspectral data using partial least squares regression

Partial least squares regression (PLSR) modelling is a statistical technique for correlating datasets, and involves the fitting of a linear regression between two matrices. One application of PLSR enables leaf traits to be estimated from hyperspectral optical reflectance data, facilitating rapid, high-throughput, non-destructive plant phenotyping. This technique is of interest and importance in a wide range of contexts including crop breeding and ecosystem monitoring. The lack of a consensus in the literature on how to perform PLSR means that interpreting model results can be challenging, applying existing models to novel datasets can be impossible, and unknown or undisclosed assumptions can lead to incorrect or spurious predictions. We address this lack of consensus by proposing best practices for using PLSR to predict plant traits from leaf-level hyperspectral data, including a discussion of when PLSR is applicable, and recommendations for data collection. Further, we provide a tutorial to demonstrate how to develop a PLSR model, in the form of an R script accompanying this manuscript. This practical guide will assist all those interpreting and using PLSR models to predict leaf traits from spectral data, and advocates for a unified approach to using PLSR for predicting traits from spectra in the plant sciences.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

A practicable estimation of opening angle of dust torus in Type-1.9 AGN with double-peaked broad Hα

In this manuscript, an independent method is proposed to estimate opening angle of dust torus in AGN, through unique properties of Type-1.9 AGN with double-peaked broad Hα (Type-1.9 DPAGN) coming from central accretion disc. Type-1.9 AGN without broad Hβ can be expected by the commonly accepted unified model of AGN, considering central BLRs seriously obscured by dust torus with its upper boundary in the line of sight. For the unique Type-1.9 DPAGN, accretion disc originations of double-peaked broad Hα can be applied to determine the inclination angle of the central accretion disc, which is well accepted as substitute of the half opening angle of the central dust torus. Then, among low redshift Type-1.9 DPAGN in SDSS, SDSS J1607+3319 at redshift 0.063 is collected, and the half opening angle of the central dust torus is determined to be around 46 ± 4°, after considering the disfavoured BBH system to explain the double-peaked broad Hα through long-term none variabilities and disfavoured local physical conditions to explain the disappearance of broad Hβ through virial BH mass properties. The results indicate that more detailed studying on dust torus of AGN can be appropriately done through Type-1.9 DPAGN in the near future.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Genomes OnLine Database (GOLD) v.8: overview and updates

The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) is a manually curated, daily updated collection of genome projects and their metadata accumulated from around the world. The current version of the database includes over 1.17 million entries organized broadly into Studies (45 770), Organisms (387 382) or Biosamples (101 207), Sequencing Projects (355 364) and Analysis Projects (283 481). These four levels contain over 600 metadata fields, which includes 76 controlled vocabulary (CV) tables containing 3873 terms. GOLD provides an interactive web user interface for browsing and searching by a wide range of project and metadata fields. Users can enter details about their own projects in GOLD, which acts as a gatekeeper to ensure that metadata is accurately documented before submitting sequence information to the Integrated Microbial Genomes (IMG) system for analysis. In order to maintain a reference dataset for use by members of the scientific community, GOLD also imports projects from public repositories such as GenBank and SRA. Here, the current status of the database, along with recent updates and improvements are described in this manuscript.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

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

We report the Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute (DOE-JGI) continues to maintain its role as one of the flagship genomic metadata repositories of the world. The ever-increasing number of projects and metadata are freely available to the user community world-wide. GOLD’s metadata is consumed by scientists and remains an important source for large-scale comparative genomics analysis initiatives. Encouraged by this active user engagement and growth, GOLD has continued to add new components and capabilities. The new features such as a public Application Programming Interface (API) and Ecosystem landing page as well as the growth of different entities in this current GOLD v.9 edition are described in detail in this manuscript.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genomes OnLine Database (GOLD) v.10: new features and updates

The Genomes OnLine Database (GOLD; https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute is a comprehensive online metadata repository designed to catalog and manage information related to (meta)genomic sequence projects. GOLD provides a centralized platform where researchers can access a wide array of metadata from its four organization levels namely Study, Organism/Biosample, Sequencing Project and Analysis Project. GOLD continues to serve as a valuable resource and has seen significant growth and expansion since its inception in 1997. With its expanded role as a collaborative platform, it not only actively imports data from other primary repositories like National Center for Biotechnology Information but also supports contributions from researchers worldwide. This collaborative approach has enriched the database with diverse datasets, creating a more integrated resource to enhance scientific insights. As genomic research becomes increasingly integral to various scientific disciplines, more researchers and institutions are turning to GOLD for their metadata needs. To meet this growing demand, GOLD has expanded by adding diverse metadata fields, intuitive features, advanced search capabilities and enhanced data visualization tools, making it easier for users to find and interpret relevant information. This manuscript provides an update and highlights the new features introduced over the last 2 years.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

The Natural Products Magnetic Resonance Database (NP-MRD) for 2025

The Natural Products Magnetic Resonance Database or NP-MRD (https://np-mrd.org) is a comprehensive, freely accessible, web-based resource for the deposition, distribution, extraction and retrieval of nuclear magnetic resonance (NMR) data on natural products. The NP-MRD was initially established to support compound de-replication and data dissemination for the natural products community. However, that community has now grown to include many users from the metabolomics, microbiomics, foodomics and nutrition science fields. Indeed, since its launch in 2021, the NP-MRD has expanded enormously in size, scope and popularity. The current version of NP-MRD now contains nearly 7X more compounds (281,859 vs. 40,908) and 7X more NMR spectra (5.1 million vs. 817,000) than the first release. More specifically, an additional 4.6 million predicted spectra and another 11,000 spectra simulated from experimental chemical shifts were deposited into the database. Likewise, the number of NMR raw spectral data depositions has grown from a 165 spectra per year to more than 10,000 per year. As a result of this expansion, the number of monthly webpage views has grown from 55 to 20,000 and the number of monthly visitors has increased from 7 to 2500. To address this growth and to better support the expanding needs of its diverse community of users, many additional improvements to the NP-MRD have been made. These include significant enhancements to the data submission process, important improvements to the visualization and display of NMR spectra, notable updates to the database’s spectral search utilities and useful additions to support better NMR spectral analysis/prediction. Significant efforts have also been undertaken to remediate and update many of NP-MRD’s database entries. This manuscript describes these database improvements and expansion efforts, along with how they have been implemented and what future upgrades to the NP-MRD are planned.

Artifical Intelligence↗
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 OSTI2024

A Review of the Resuspension of Radioactively Contaminated Particles by Vehicle and Pedestrian Traffic—Current Theory, Practice, Gaps, and Needs

Here, the resuspension of radioactively contaminated particles in a built environment, such as from urban surfaces like foliage, building exteriors, and roadways, is described empirically by current plume and dosimetry models used for hazard assessment and long-term risk purposes. When applying these models to radiological contamination emergencies affecting urban areas, the accuracy of the results for recent contamination deposition is impacted in two main ways. First, the data supporting the underlying resuspension equations was acquired for open, quiescent conditions with no vehicle traffic or human activities, so it is not necessarily representative of the urban environment. Second, mechanical disturbance by winds in urban canyons and during emergency operations caused by vehicle traffic and human activities are not directly considered by the equations. Accordingly, plume and dosimetry models allow the user to input certain compensating values, but the models do not necessarily supply users instructions on what values to use. This manuscript reviews the available literature to comprehensively and consistently pool data for resuspension due to mechanically induced resuspension applicable to urban contamination. Because there are few studies that directly measured radioactive resuspension due to vehicles and pedestrians, this review novelly draws on a range of other studies involving non-radioactive particles, ranging from outdoor air pollution emissions to indoor allergen transport. The results lead to tabulated, recommended values for specific conditions in the emergency phase to help users of plume and dosimetry models maintain the conservativeness needed to properly capture the potential radiation dose posed by mechanically induced resuspension. These values are of benefit to model users until better data are available. The results also suggest the types of data that may result in improved plume and dose modeling.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2025

Duality defect in a deformed transverse-field Ising model

Physical quantities with long lifetimes have both theoretical significance in the study of quantum many-body systems and practical implications for quantum technologies. In this manuscript, we investigate the roles played by topological defects in the construction of quasiconserved quantities, using as a prototypical example the Kramers-Wannier duality defect in a deformed one-dimensional quantum transverse-field Ising model. We construct the duality defect Hamiltonian in three different ways: half-chain Kramers-Wannier transformation, utilization of techniques in the Ising fusion category, and defect-modified weak integrability breaking deformation. The third method is also applicable for the study of generic integrable defects under weak integrability breaking deformations. We also work out the deformation of defect-modified higher charges in the model and study their slower decay behavior. Furthermore, we consider the corresponding duality defect twisted deformed Floquet transverse-field Ising model and investigate the stability of the isolated zero mode associated with the duality defect in the integrable Floquet Ising model, under such weak integrability breaking deformation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗