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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

VirJenDB: a FAIR (meta)data and bioinformatics platform for all viruses

High-throughput sequencing has generated an unprecedented volume of data. However, researcher-submitted data in repositories requires extensive curation and quality control for reuse. These tasks are hindered by the multiplicity of repositories, the sheer volume of the data, and the complexity of virus (meta)data curation. To address these challenges, VirJenDB offers a user-friendly platform to facilitate versioned, community-driven curation, and ontology development. Virus sequences were ingested from 16 sources, including ~200 fields of metadata or standards, covering taxonomy, sample, and host information. Up to 85 metadata fields have undergone at least one round of curation, and are linked to 15.4 million virus sequences, with 88 % from those infecting eukaryotes and the remaining infecting prokaryotes. Subsets were created, including a novel collection of 0.91 million viral operational taxonomic unit (vOTU) sequences across all viruses, while keeping the original sequences from each vOTU to facilitate downstream analyses, e.g. sequence variation. The VirJenDB web portal (https://www.virjendb.org) provides HTTPS and Application Programming Interface (API) access to the sequence datasets and metadata, offering a search engine, filtering, download, visualizations, and documentation. VirJenDB aims to connect the phage and eukaryotic virus research communities by supporting webtool integration, meta-analyses, and metadata schema extensions.

Saghaei, Shahram↗
DOE OSTI2019

Sequenceserver: A Modern Graphical User Interface for Custom BLAST Databases

Comparing newly obtained and previously known nucleotide and amino-acid sequences underpins modern biological research. BLAST is a well-established tool for such comparisons but is challenging to use on new data sets. We combined a user-centric design philosophy with sustainable software development approaches to create Sequenceserver, a tool for running BLAST and visually inspecting BLAST results for biological interpretation. Sequenceserver uses simple algorithms to prevent potential analysis errors and provides flexible text-based and visual outputs to support researcher productivity. Our software can be rapidly installed for use by individuals or on shared servers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Control of Large-Amplitude Combustion Oscillations Using Nanosecond Repetitively Pulsed Plasmas

This paper details the use of nanosecond repetitively pulsed discharges to attenuate combustion instabilities in a 14 kW swirl-stabilized methane/air combustor. The combustor exhibits large-amplitude pressure oscillations ranging from 1 to 4% of the mean pressure during which the flame exhibits bulk motion in each instability cycle, upstream and downstream, as revealed by high-speed chemiluminescence. Control is accomplished with an electrode comprising a pin anode at the centerline of the combustor, allowing a nanosecond spark to be generated in a region spanning close to the flame base, through the shear layers of the swirling flow and ending at the metallic combustor wall. The discharges are generated using 20 kV, 9 kHz pulses; and they correspond to about 120 W of mean power. This results in a suppression of the peak amplitude of the pressure oscillations by a factor of two to four, and 5 dB in the rms value. Using phase-averaged visualizations of the flame with and without plasma, we detail the sequence of flame motion in the course of the instability. With the plasma active, this reveals significant interactions between the flame and the plasma during the suppression. Finally, we present a state-space model of the thermoacoustic system, and we demonstrate open-loop control of the instabilities.

Engineering↗
DOE OSTI2019

Diffusion-weighted imaging as a part of PET/MR for small lesion detection in patients with primary abdominal and pelvic cancer, with or without TOF reconstruction technique

Objectives: To investigate the value of diffusion-weighted imaging (DWI) in detection of small lesions (≤ 10 mm) in patients with primary abdominal and pelvic cancer in hybrid PET/MR with or without time-of-flight (TOF) technique. Materials and methods: Twenty patients (11 females and 9 males, mean age 67.23 ± 12.90 years) with histologically confirmed primary abdominal and pelvic cancer underwent hybrid PET/MR examination. A total of 64 small lesions were included in this study, which were divided into two groups (≤ 10 mm and 10–30 mm). Visual scores of small lesion detection ability were rated by five-point ordinal scale. The visual scores and detectability of small lesions on TOF PET image, noTOF PET image, and DWI sequences of hybrid PET/MR examination with or without TOF technique were analyzed. Logistic regression model was established for analysis in the value of DWI in hybrid PET/MR examination with or without TOF technique in detection of the small lesions between two groups. Results: The visual evaluation revealed the small lesion (≤ 10 mm) visual scores of DWI (mean ± SD: 4.23 ± 1.41), TOF PET image (mean ± SD: 4.14 ± 0.89), and noTOF PET image (mean ± SD: 2.68 ± 1.13);.and the visual scores of small lesions (10–30 mm) on DWI (mean ± SD: 4.98 ± 0.15), TOF PET image (mean ± SD: 4.57 ± 0.59), and noTOF PET image (mean ± SD: 3.98 ± 1.05). The visual scores of all small lesions on DWI were higher than that on TOF PET data and noTOF PET data in both two groups (**P < 0.01). The missed diagnosis rates of small FDG avid lesions (≤ 10 mm) of DWI and noTOF PET image were 9.1% and 9.1%, respectively. However, the TOF PET-based clinical diagnosis detected all small lesions (≤ 30 mm). DWI was of great importance in detection of small lesions (≤ 10 mm) in the absence of TOF technique in PET/MR examination (**P < 0.01). DWI’s effect on detection of small lesions(10-30 mm) has shown no difference between PET/MR examinations with TOF and without TOF techniques (P > 0.05). Conclusion: DWI has significant value in the detection of small lesions (≤ 10 mm) in hybrid PET/MR examination without TOF technique for patients with primary abdominal and pelvic cancer. However, it had less detection benefits in the small lesions (≤ 10 mm) in hybrid PET/MR examination with TOF PET image.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes

Background: Exploring metagenomic contigs and “binning” them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure. Results: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena’s usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset. Conclusions: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena, together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Emergent layer stacking arrangements in c-axis confined MoTe 2

The layer stacking order in 2D materials strongly affects functional properties and holds promise for next-generation electronic devices. In bulk, octahedral MoTe 2 possesses two stacking arrangements, the ferroelectric Weyl semimetal T d phase and the higher-order topological insulator 1T' phase. However, in thin flakes of MoTe 2 , it is unclear if the layer stacking follows the T d , 1T', or an alternative stacking sequence. Here, we use atomic-resolution scanning transmission electron microscopy to directly visualize the MoTe 2 layer stacking. In thin flakes, we observe highly disordered stacking, with nanoscale 1T' and T d domains, as well as alternative stacking arrangements not found in the bulk. We attribute these findings to intrinsic confinement effects on the MoTe 2 stacking-dependent free energy. Our results are important for the understanding of exotic physics displayed in MoTe 2 flakes. More broadly, this work suggests c-axis confinement as a method to influence layer stacking in other 2D materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2024

Microbial DNA Database and Demonstration

2024 Annual Review meeting talk, "Microbial DNA Database and Demonstration." Description of the NETL's PW DNA Database that will be 1) curated to make it more useable, 20 include metadata linked to each sequencing set, such as qPCR and geochemistry, and 30 allow better filtering and visualization. The database is hosted on KBase so terabytes worth of data can be used directly on the program without having to download it to personal computers.

Schweitzer, Hannah↗
DOE OSTI2020

Registration station for assembling insulating glass windows

An insulating glass unit (IGU) assembly line comprising a registration station capable of interleaving double and triple pane IGUs in accordance with an IOU production schedule. Visual indicators or prompts instruct operators at the assembly line in configuring a sequence of IGUs. Triple pane IGUs are assembled with minimal contamination of a center glass lite. A non-contact Bernoulli pad is used to lift a glass lite off from a horizontal or vertical support that conveys it from a glass washer to the registration station. Each of multiple pads has a capacity to lift approximately seven to ten pounds. Use of multiple pads per glass sheet or lite allows lites having dimensions up to 70 by 100 inches (assuming glass thickness of one quarter inch) to be assembled.

42 ENGINEERING↗
DOE OSTI2021

Persistent, “Mysterious” Seismoacoustic Signals Reported in Oklahoma State during 2019

Here, we report on the source of seismoacoustic pulses that were observed across the state of Oklahoma (OK) during summer of 2019, and the subject of national media coverage and speculation. Seismic network data collected across four U.S. states and interviews with witnesses to the pulse’s effect on residential structures demonstrate that they were triggered by routine ammunition disposal operations conducted by McAlester Army Ammunition Plant (McAAP). During these operations, conventional explosives destroy obsolete munitions stored in pits through a controlled sequence of electronically timed shots that occur over tens of minutes. Despite noise-abatement efforts that reduce coupling of acoustic energy with air, some lower frequency, subaudible (infrasonic) sound radiates from these shots as discrete pulses. We use nine months of blast log documents, seismic network records, analyst picks, and physical modeling to demonstrate that seismic stations as far as 640 km from McAAP sample these pulses, which record seasonal patterns in stratospheric and tropospheric winds, as well as the dynamic formation of waveguides and shadow zones. Digital short-term average to long-term average detectors that we augment with dynamic thresholds and time-binning operations identify these pulses with a fair probability, when compared with visual observations. Our analyses thereby provide estimates of observation rates for both partial and full sequences of these pulses, as well as single shots. We suggest that disposal operations can exploit existing, composite seismic networks to predict where residents are likely to witness blasting. Crucially, our data also show that dense seismic networks can record multiscale atmospheric processes in the absence of infrasound arrays.

58 GEOSCIENCES↗
DOE OSTI2024

IsoForma: An R Package for Quantifying and Visualizing Positional Isomers in Top-Down LC-MS/MS Data

Proteoforms, the different forms of a protein with sequence variations including post-translational modifications (PTMs), execute vital functions in biological systems such as cell signaling and epigenetic regulation. Precisely defining the stoichiometry of PTMs has been challenging because, in the widely used bottom-up proteomics methods, the detection occurs at the peptide level and thus the link between peptides and their specific modification site is lost, resulting in proteoform ambiguity. Advances in top-down mass spectrometry (MS) technology have permitted the direct characterization of intact proteoforms and their exact number of modification sites, allowing for the relative quantification of positional isomers (PI). Proteins with positional isomers refers to proteoforms with identical total mass and set of modifications but varying PTM site combinations. The relative abundance of PI can be estimated by matching proteoform-specific fragment ions to top-down tandem MS (MS2) data to localize and quantify modifications. However, current approaches heavily rely on manual annotation. Here, we present IsoForma, an open-source R package for relative quantification of PI within a single tool. We benchmarked IsoForma’s performance against two existing workflows and highlight the similarity of the results and improvements in speed. Overall, IsoForma provides a streamlined process, reduces the time of conducting isoform-based analyses, and offers an essential framework for developing customized proteoform analysis workflows. Finally, the software is open source and available at https://github.com/EMSL-Computing/isoforma-lib.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A Methodology to Evaluate the Grid Reliability Impact of Oscillations Induced by Large Loads

The rapid growth of hyperscale AI data centers is bringing renewed attention to the reliability risk that sustained forced oscillations pose to bulk power systems, with cyclic computational workloads emerging as a new forcing source. Unlike the broadband, stochastic disturbances from traditional industrial loads such as arc furnaces, AI training and inference facilities can inject large active power swings concentrated at specific frequencies over extended durations - characteristics that existing grid planning practices do not account for. While the North American Electric Reliability Corporation (NERC) has recognized this gap and called for system-level studies of large load interconnections, no standardized methodology exists to screen, simulate, and quantify these risks at the planning stage. This report presents the Risk Assessment Tool for Large Load-induced Events (RATLLE), a Python-based, publicly available script suite developed at the Pacific Northwest National Laboratory to evaluate bulk power system reliability risks from data center-induced oscillations. RATLLE implements a three-module workflow: a screening module that identifies vulnerable interconnection locations and excitable system modes; a simulation module that models cyclic data center load behavior using a commercial positive sequence simulation platform; and an analysis module that computes risk metrics and generates interactive visualization dashboards. The risk metrics, formulated around simulation observables, map oscillation impacts to a three-stage severity scale spanning latent equipment fatigue through imminent cascading failure. The methodology is demonstrated on two Western Electricity Coordinating Council (WECC) system models: a publicly available 240-bus reduced representation and a detailed 2031 Heavy Winter planning case. Case studies illustrate that even modest 50 MW forced oscillations at resonant frequencies can produce wide-area power swings, N-1 security constraint violations, and cascading generator trips through protection actions - outcomes that would not occur under normal operating conditions without oscillations present. The results underscore the need for standardized oscillation impact assessment in large load interconnection studies and provide a reproducible, extensible framework for utilities to adopt or customize within their existing planning workflows.

Biswas, Shuchismita↗
DOE OSTI2019

Development and validation of a quantitative PCR assay method of assessing relative resistance of oat ( Avena sativa ) to crown rust ( Puccinia coronata f. sp. avenae )

Evaluation of oat crown rust resistance is usually based on visual assessment of disease severity or infection types. Visual assessment is subjective, prone to rater bias and requires expert knowledge. PCR‐based quantitative assays can overcome challenges associated with visual assessment. New TaqMan primers and probes were designed from Puccinia coronata f. sp. avenae (Pca) sequences. The primer–probe sets were specific to Pca, amplified using as little as 0.5 pg fungal DNA (fDNA) and allowed for scaling to variation in sample total DNA quantity. The quantitative PCR (qPCR) assay was validated using oat recombinant inbred lines (RILs) from the Provena × 94197A1‐9‐2‐2‐2‐5 cross evaluated under a controlled environment. For comparison with fDNA load, inoculation with the Pca race LCBB provided segregation data on the hypersensitive response, while Pca race LSLG provided data on segregation for reduced pustule number. fDNA content was positively correlated with both pustule number and infection type (IT). Composite interval mapping identified two quantitative trait loci (QTLs) on oat linkage groups Mrg12 and Mrg20 using visual and qPCR assessments (pustule number, IT and fDNA). In this study a qPCR assay method that can be used to assess the relative resistance of oat to crown rust was refined and validated, and single nucleotide polymorphisms (SNPs) closely linked with two QTLs derived from the crown rust resistant line 94197A1‐9‐2‐2‐2‐5 were identified.

Admassu‐Yimer, B.↗
DOE OSTI2022

Time Sequence Machine Learning-Based Data Intrusion Detection for Smart Voltage Source Converter-Enabled Power Grid

Smart inverters of distributed energy resources can enable cloud computing, condition monitoring, result visualization, remote control, and peer-to-peer energy trading in advanced power systems. However, the advent of data injection attacks in the communication architecture can alter measurement characteristics of power grids and have devastating consequences. In this article, we propose a time sequence machine learning-based anomaly detection methodology for detecting cyber intrusion into control signal setpoints and dc voltage signal measurement bias of the voltage source converter (VSC) in wind generators. We first investigated the effects of four types of denial of service, tampering signal, and stealthy-type data intrusion attacks on smart VSCs and overall wind farms. We then proposed a novel time sequence machine learning-based intrusion detection framework that can be implemented to detect different cyberattacks in the VSCs. The performance of the proposed framework has been compared with that of autoencoder and clustering-based intrusion detection framework. The proposed framework was validated by using the IEEE 39 bus power system in the presence of four wind farms in different locations. Using several metrics for intrusion detection performance, we validated the effectiveness of the proposed framework.

42 ENGINEERING↗
DOE OSTI2021

On the Use of Field RR Lyrae As Galactic Probes: IV. New Insights Into and Around the Oosterhoff Dichotomy

We discuss the largest and most homogeneous spectroscopic data set of field RR Lyrae variables (RRLs) available to date. We estimated abundances using both high-resolution and low-resolution ($Δ$S method) spectra for fundamental (RRab) and first overtone (RRc) RRLs. The iron abundances for 7941 RRLs were supplemented with similar estimates that are available in the literature, ending up with 9015 RRLs (6150 RRab, 2865 RRc). The metallicity distribution shows a mean value of $\langle$[Fe/H]$\rangle$ = -1.51 ± 0.01, and $σ$(standard deviation) = 0.41 dex with a long metal-poor tail approaching [Fe/H] ≃ - 3 and a sharp metal-rich tail approaching solar iron abundance. The RRab variables are more metal-rich ( $\langle$[Fe/H]$\rangle$ ab = -1.48 ± 0.01, $σ$ = 0.41 dex) than RRc variables ($\langle$[Fe/H]$\rangle$ c = -1.58 ± 0.01, $σ$ = 0.40 dex). The relative fraction of RRab variables in the Bailey diagram (visual amplitude versus period) located along the short-period (more metal-rich) and the long-period (more metalpoor) sequences are 80% and 20%, while RRc variables display an opposite trend, namely 30% and 70%, respectively. We found that the pulsation period of both RRab and RRc variables steadily decreases when moving from the metal-poor to the metal-rich regime. Furthermore, the visual amplitude shows the same trend, but RRc amplitudes are almost two times more sensitive than RRab amplitudes to metallicity. We also investigated the dependence of the population ratio (N $c$ /N tot ) of field RRLs on the metallicity and we found that the distribution is more complex than in globular clusters. The population ratio steadily increases from ~0.25 to ~0.36 in the metal-poor regime, it decreases from ~0.36 to ~0.18 for -1.8 ≤ [Fe/H] ≤ -0.9 and it increases to a value of ~0.3 approaching solar iron abundance.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

FastProNGS: fast preprocessing of next-generation sequencing reads

Background Next-generation sequencing technology is developing rapidly and the vast amount of data that is generated needs to be preprocessed for downstream analyses. Yet, until now, software that can efficiently make all the quality assessments and filtration of raw data is still lacking. Results We developed FastProNGS to integrate the quality control process with automatic adapter removal. Parallel processing was implemented to speed up the process by allocating multiple threads. Compared with similar up-to-date preprocessing tools, FastProNGS is by far the fastest. Read information before and after filtration can be output in plain-text, JSON, or HTML formats with user-friendly visualization. Conclusions FastProNGS is a rapid, standardized, and user-friendly tool for preprocessing next-generation sequencing data within minutes. It is an all-in-one software that is convenient for bulk data analysis. It is additionally very flexible and can implement different functions using different user-set parameter combinations.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Combined Imaging and RNA-Seq on a Microfluidic Platform for Viral Infection Studies

The goal of this work was to pioneer a novel, low-overhead protocol for simultaneously assaying cell-surface markers and intracellular gene expression in a single mammalian cell. The purpose of developing such a method is to be able to understand the mechanisms by which pathogens engage with individual mammalian cells, depending on their cell surface proteins, and how both host and pathogen gene expression changes are reflective of these mechanisms. The knowledge gained from such analyses of single cells will ultimately lead to more robust pathogen detection and countermeasures. Our method was aimed at streamlining both the upstream cell sample preparation using microfluidic methods, as well as the actual library making protocol. Specifically, we wanted to implement a random hexamer-based reverse transcription of all RNA within a single cell (as opposed to oligo dT-based which would only capture polyadenylated transcripts), and then use a CRISPR-based method called scDash to deplete ribosomal DNAs (since ribosomal RNAs make up the majority of the RNA in a mammalian cell). After significant troubleshooting, we demonstrate that we are able to prepare cDNA from RNA using the random hexamer primer, and perform the rDNA depletion. We also show that we can visualize individually stained cells, setting up the pipeline for connecting surface markers to RNA-sequencing profiles. Finally, we test a number of devices for various parts of the pipeline, including bead generation, optical barcoding and cell dispensing, and demonstrate that while some of these have potential, more work is needed to optimize this part of the pipeline.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Shock tube experiments on the three-layer Richtmyer–Meshkov instability

Here, a vertical shock tube is used for experiments on the three-layer Richtmyer–Meshkov instability. Two closely spaced membrane-less interfaces are formed by the flow of two different sects of three gases: one with air above CO 2 above SF 6 and the other with helium above air above SF 6 . The lightest of the three gases enters the shock tube at the top of the driven section and flows downward. Conversely, the heaviest gas enters at the bottom of the shock tube and flows upward while the intermediate density gas enters at the middle through porous plates. All three gases are allowed to escape through holes at the layer location, leaving an approximately 30-mm layer of intermediate-density gas suspended between the lightest gas from above and the heaviest gas from below. A single-mode, two-dimensional initial perturbation is then imposed on the lower interface by oscillating the shock tube in the horizontal direction. The flow is visualized by seeding the intermediate gas with particles and illuminating it with a pulsed laser. Image sequences are then captured using high-speed video cameras. Perturbation amplitude measurements are made from the three-layer system and compared with measurements from 2, two-layer systems. It is observed that the presence of the upper, initially flat interface produces a decrease in growth of instability amplitude in the nonlinear phase over an equivalent single-interface configuration.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

NEAMS Workbench MOOSE Integration Update

The Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench is a graphical user interface (GUI) that provides a common analysis environment for the accelerated use of the NEAMS toolkit. To improve design and analysis of current and future nuclear energy systems, the NEAMS Workbench provides an integrated development environment for model creation, review, execution, output review, and visualization for integrated tools. In addition to a GUI, the NEAMS Workbench provides the Workbench Analysis Sequence Processor, an open-source tool set that facilitates input-content assistance for supported domain-specific input languages and user-friendly syntaxes. These supported syntaxes enable accelerated development and deployment of enhanced user inputs and workflows. The Multiphysics Object-Oriented Simulation Environment (MOOSE) has been supported in the NEAMS Workbench since 2016 and receives continuous updates. Efforts to improve MOOSE-based tool integration in the NEAMS Workbench are ongoing. This document details the current and planned enhancements of the NEAMS Workbench and the MOOSE framework to improve integration and usability of MOOSE-based applications within the NEAMS Workbench.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗