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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 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

General Applications for Hamilton Vantage (GenApps for Vantage) v0.6.1

General applications for Hamilton Vantage is a flexible liquid handling method used to automate the most widely applicable types of automated liquid transfers. General applications can also be used as a tool to onboard new fully-automated workflows by breaking them down step by step into single transfers. The goal of General Applications is to make using the Hamilton Vantage liquid handler as easy & practical as using a handheld pipette for the end user. The software supports plate-to-plate transfers for a variety of method types including: Stamp: One-to-One, Stamp: One-To-Many, Split, Combine, Hitpick, and Qtray plating. General Applications eliminates the need for automation engineers to customize individual methods for each new workflow that gets onboarded. Steps can be customized within GenApps according to the needs of the researcher. The software utilizes a GUI to prompt the users to input variables – Allowing for flexible control over plate types, transfer volumes, number of replicates, tip types, liquid classes, mixing steps, aspiration/dispense heights and more. General Applications also generates a deck image and setup instructions to guide the researcher on how to load the deck and start the instrument.

Yoder, Sam↗
DOE OSTI2026

Detector Interface for Streaming, Control, and Open-source integration (DISCO) v1.0.0

This suite consists of a multi-package ecosystem featuring detector emulators, EPICS areaDetector drivers, and remote server frameworks designed for the Advanced Light Source (ALS). Engineered for high-bandwidth devices—including VFCCD, Timepix3, Timepix4, and related pixel detectors—the software simulates hardware, wraps vendor SDKs into remote-callable servers, and integrates with open-source control systems. Key Capabilities: Distributed SDK Architecture: Server packages wrap hardware-specific SDKs, allowing areaDetector drivers to execute remote framework calls. This isolates proprietary libraries from the EPICS IOC, enhancing stability and enabling distributed computing across beamline networks. Device Support: Custom drivers for VFCCD, the Timepix family, and similar sensors optimize the data path from hardware control to high-speed transport. Full-Stack Emulation: Sophisticated emulator packages allow end-to-end pipeline testing and software development without requiring physical hardware or beam time. Integrated Workflows: Supports high-bandwidth streaming for real-time analysis and robust, metadata-rich file-based workflows (e.g., HDF5/NeXus). By standardizing interfaces across heterogeneous hardware, this suite reduces technical debt. It provides the ALS with a scalable, open-source solution to manage massive data rates within a unified control environment.

Mahl, Johannes [Lawrence Berkeley National Laborat↗
DOE OSTI2026

ClusterWeave

ClusterWeave is a workflow for biosynthetic target discovery and prioritization. It assembles annotation, BGC detection, BiG-SCAPE family context, shortlist generation, and clinker-ready panel staging into one reproducible workflow.

Martin, StantonL↗
DOE OSTI2020

Nested active learning for efficient model contextualization and parameterization: pathway to generating simulated populations using multi-scale computational models

There is increasing interest in the use of mechanism-based multi-scale computational models (such as agent-based models (ABMs)) to generate simulated clinical populations in order to discover and evaluate potential diagnostic and therapeutic modalities. The description of the environment in which a biomedical simulation operates (model context) and parameterization of internal model rules (model content) requires the optimization of a large number of free parameters. In this work, we utilize a nested active learning (AL) workflow to efficiently parameterize and contextualize an ABM of systemic inflammation used to examine sepsis. Contextual parameter space was examined using four parameters external to the model’s rule set. The model’s internal parameterization, which represents gene expression and associated cellular behaviors, was explored through the augmentation or inhibition of signaling pathways for 12 signaling mediators associated with inflammation and wound healing. We have implemented a nested AL approach in which the clinically relevant (CR) model environment space for a given internal model parameterization is mapped using a small Artificial Neural Network (ANN). The outer AL level workflow is a larger ANN that uses AL to efficiently regress the volume and centroid location of the CR space given by a single internal parameterization. We have reduced the number of simulations required to efficiently map the CR parameter space of this model by approximately 99%. In addition, we have shown that more complex models with a larger number of variables may expect further improvements in efficiency.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Simulation process and data flow for a large system dynamics model

This paper documents the workflow and supporting technologies that a large system dynamics model, the biomass scenario model, employs to streamline the data preparation, simulation, quality control, and analysis process at the National Renewable Energy Laboratory. The workflow centers on automation of routine aspects of the flow of data between data stores, simulations, and visualizations. It enforces quality checks on data, reproducibility of computations, and traceability of results, while maintaining complete archives of modeling and analysis artifacts. The resulting frictionless simulation/analysis environment supports large-scale sensitivity analysis, interactive creation of ensembles of simulations, and rapid visualization-based exploration of simulation results.

09 BIOMASS FUELS↗
DOE OSTI2022

Real-Time Highly Resolved Spatial-Temporal Vehicle Energy Consumption Estimation Using Machine Learning and Probe Data

Real-time highly resolved spatial-temporal vehicle energy consumption is a key missing dimension in transportation data. Most roadway link-level vehicle energy consumption data are estimated using average annual daily traffic measures derived from the Highway Performance Monitoring System; however, this method does not reflect day-to-day energy consumption fluctuations. As transportation planners and operators are becoming more environmentally attentive, they need accurate real-time link-level vehicle energy consumption data to assess energy and emissions; to incentivize energy-efficient routing; and to estimate energy impact caused by congestion, major events, and severe weather. This paper presents a computational workflow to automate the estimation of time-resolved vehicle energy consumption for each link in a road network of interest using vehicle probe speed and count data in conjunction with machine learning methods in real time. The real-time pipeline can deliver energy estimates within a couple seconds on query to its interface. The proposed method was evaluated on the transportation network of the metropolitan area of Chattanooga, Tennessee. The volume estimation results were validated with ground truth traffic volume data collected in the field. To demonstrate the effectiveness of the proposed method, the energy consumption pipeline was applied to real-world data to quantify road transportation-related energy reduction because of mitigation policies to slow the spread of COVID-19 and to measure energy loss resulting from congestion.

Severino, Joseph↗
DOE OSTI2022

Non-target RNA depletion strategy to improve sensitivity of next-generation sequencing for the detection of RNA viruses in poultry

PCR-based assays have become the benchmark for detecting pathogens of poultry and other livestock; however, these techniques are limited in their ability to detect multiple infecting agents, provide limited genetic information on the pathogen, and, for RNA viruses, must be reviewed frequently to assure high sensitivity and specificity. In contrast, untargeted, high-throughput sequencing can rapidly detect all infecting agents in a sample while providing genomic sequence information to allow more in-depth characterization of viruses. Although next-generation sequencing (NGS) offers many advantages, one of its primary limitations is low sensitivity to pathogens given the abundance of host and other non-target sequences in sequencing libraries. We explored methods for improving the sensitivity of NGS to detect respiratory and enteric viruses in poultry from RNA extracts of swab samples. We employed commercial and custom-designed negative enrichment strategies to selectively deplete the most abundant rRNA reads from the host and non-target bacteria; host RNA was diminished from up to 40% of total reads to as low as 3%, and the total number of reads assigned to abundant bacterial classes were reduced greatly. Our treatment resulted in up to a 700-fold increase in the number of viral reads, detection of a greater number of viral agents, and higher average genome coverage for pathogens. Depletion assays added only 2 h to the NGS library preparation workflow. Custom depletion probe design offered significant cost savings (US$7–12 per sample) compared to commercial kits (US$30–50 per sample).

Parris, D. Joshua↗
DOE OSTI2025

HDF5 in the exascale era: Delivering efficient and scalable parallel I/O for exascale applications

Accurately modeling real-world systems requires scientific applications at exascale to generate massive amounts of data and manage data storage efficiently. However, parallel input and output (I/O) faces challenges due to new application workflows and the state-of-the-art memory, interconnect, and storage architectures considered in exascale designs. The storage hierarchy has expanded with node-local persistent memory, solid-state storage, and traditional disk and tape-based storage, thus requiring efficiency at each layer and much more efficient data movement among these layers. This paper discusses how the ExaHDF5 project improved the I/O performance and data management for exascale architectures by enhancing HDF5, a widely used parallel I/O library. The team developed an Asynchronous I/O Virtual Object Layer (VOL) connector that allowed overlapping I/O with computation. They also created a Cache VOL to complement asynchronous I/O by incorporating fast storage layers, such as burst buffer and node-local storage, into the parallel I/O workflow through caching and staging data. Additionally, the team enabled data aggregation and I/O at the node level by using a Subfiling Virtual File Driver (VFD). To demonstrate superior I/O performance with HDF5 at exascale, the ExaHDF5 team collaborated with several exascale applications. In this paper, we show I/O performance improvements for three applications: Cabana (a particle-based simulation library), EQSIM (a regional earthquake simulation software), and E3SM (a climate system modeling library).

Asynchronous I/Ol↗
DOE OSTI2025

Spatial top-down proteomics for the functional characterization of human kidney

Background: The Human Proteome Project has credibly detected nearly 93% of the roughly 20,000 proteins which are predicted by the human genome. However, the proteome is enigmatic, where alterations in amino acid sequences from polymorphisms and alternative splicing, errors in translation, and post-translational modifications result in a proteome depth estimated at several million unique proteoforms. Recently mass spectrometry has been demonstrated in several landmark efforts mapping the human proteoform landscape in bulk analyses. Herein, we developed an integrated workflow for characterizing proteoforms from human tissue in a spatially resolved manner by coupling laser capture microdissection, nanoliter-scale sample preparation, and mass spectrometry imaging. Results: Using healthy human kidney sections as the case study, we focused our analyses on the major functional tissue units including glomeruli, tubules, and medullary rays. After laser capture microdissection, these isolated functional tissue units were processed with microPOTS (microdroplet processing in one-pot for trace samples) for sensitive top-down proteomics measurement. This provided a quantitative database of 616 proteoforms that was further leveraged as a library for mass spectrometry imaging with near-cellular spatial resolution over the entire section. Notably, several mitochondrial proteoforms were found to be differentially abundant between glomeruli and convoluted tubules, and further spatial contextualization was provided by mass spectrometry imaging confirming unique differences identified by microPOTS, and further expanding the field-of-view for unique distributions such as enhanced abundance of a truncated form (1-74) of ubiquitin within cortical regions. Conclusions: We developed an integrated workflow to directly identify proteoforms and reveal their spatial distributions. Where of the 20 differentially abundant proteoforms identified as discriminate between tubules and glomeruli by microPOTS, the vast majority of tubular proteoforms were of mitochondrial origin (8 of 10) where discriminate proteoforms in glomeruli were primarily hemoglobin subunits (9 of 10). These trends were also identified within ion images demonstrating spatially resolved characterization of proteoforms that has the potential to reshape discovery-based proteomics because the proteoforms are the ultimate effector of cellular functions. Applications of this technology have the potential to unravel etiology and pathophysiology of disease states, informing on biologically active proteoforms, which remodel the proteomic landscape in chronic and acute disorders.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Single-cell proteomics of Arabidopsis leaf mesophyll reveals dynamic protein responses to water-deficit stress

Background The application of single-cell omics tools to biological systems can provide unique insights into diverse cellular populations and their heterogeneous responses to internal and external perturbations. Thus far, most single-cell studies in plant systems have been limited to RNA-sequencing approaches, which only provide indirect readouts of cellular functions. Results Here, we present a single-cell proteomics workflow for plant cells that integrates tape-sandwich protoplasting, piezoelectric cell sorting, nanoPOTS sample preparation, and ion mobility-based MS data acquisition method for label-free single-cell proteomics analysis of Arabidopsis leaf mesophyll cells. From a single leaf protoplast, over 3,000 proteins were quantified with high precision. The workflow is demonstrated to identify stress associated changes in protein abundance by analyzing 117 protoplasts from well-watered and water-deficit stressed plants. Additionally, we describe a new approach for constructing covarying protein networks at the single-cell level and demonstrate how single-cell protein covariation analysis can reveal previously unrecognized protein functions while also capturing stress-induced changes in protein–protein dynamics. Conclusions The label-free scProteomic approach presented here represents a significant advance through the demonstration of a facile protoplast isolation method combined with deep and precise proteomic coverage of Arabidopsis leaf mesophyll cell types. We believe this study will serve as an informative reference to future plant scProteomic investigations.

Arabidopsis↗
DOE OSTI2022

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks

Background Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent; however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and microbial contributions to biogeochemical cycling. Results We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry studies using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the microbiome, potential microbial metabolic handoffs and metabolite exchange, reconstruction of functional networks, and determination of microbial contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, community-scale microbial functional networks using a newly defined metric “MW-score” (metabolic weight score), and metabolic Sankey diagrams. METABOLIC takes ~ 3 h with 40 CPU threads to process ~ 100 genomes and corresponding metagenomic reads within which the most compute-demanding part of hmmsearch takes ~ 45 min, while it takes ~ 5 h to complete hmmsearch for ~ 3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut. Conclusion METABOLIC enables the consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available under GPLv3 at https://github.com/AnantharamanLab/METABOLIC.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Early arrival waveform inversion using data uncertainties and matching filters with application to near-surface seismic refraction data

We develop an early arrival waveform inversion (EAWI) technique for high-resolution near-surface velocity estimation by iteratively updating the P-wave velocity model to minimize the difference between the observed and calculated seismic refraction data. Traditional EAWI uses a least-squares penalty function and an acoustic forward-modeling engine. Conventional least-squares error is sensitive to data with low signal-to-noise ratio (S/N) and iterations of EAWI stop at a local-minimum data misfit or at the preassigned maximum number of iterations. These stopping criteria can result in overfitting the data. In addition, fitting the elastic field data with an acoustic modeling engine can introduce artifacts in velocity estimation, especially in land data with significant elastic effects. To overcome these challenges, we develop a robust EAWI (REAWI) method by (1) incorporating the data uncertainties into the penalty function and (2) mitigating the elastic effects using a matching filter workflow. The data uncertainties are estimated from waveform reciprocal errors. When full-waveform reciprocity is not available, trace interpolation is applied. The proposed method prevents closely fitting data with low S/N, avoids overall overfitting by stopping the iterations when a normalized chi-square ([Formula: see text]) waveform misfit of one is achieved, and is less affected by elastic effects. Numerical examples and application to near-surface refraction data at a groundwater contamination site suggest that the final REAWI models are more accurate than the corresponding EAWI models, at the same level of misfit. This is the first known application of a matching filter workflow to real land data. The final REAWI models satisfy an appropriate misfit between the real data and predicted elastic P-wave data, making this approach in this respect equivalent to elastic waveform inversion. We also develop a method to analyze model constraint by examining the energy of the wavefield Fréchet derivative thereby avoiding the influence of the data residuals in traditional Fréchet kernels.

Geochemistry & Geophysics↗
DOE OSTI2022

CSEM Fluid Monitoring Methodology Using Real Data Examples

Conference presentation at International Meeting for Applied Geoscience & Energy (IMAGE), Houston, Texas, August 28 – September 1, 2023. Using field data from hydrocarbon and CO 2 applications, we illustrate the importance of a workflow and adaption to the target on hand. Verifying the geophysical acquisition and processing steps with 3D modeling and checking them against a 3D anisotropic log-derived model maintains confidence in the workflow and minimizes the influence on the data. This allows us to predict data validity and to certify the data with respect to the borehole logs.

20 FOSSIL-FUELED POWER PLANTS↗
DOE OSTI2020

Data from Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity

Annotation of untargeted high-resolution full-scan LC-MS metabolomics data remains challenging due to individual metabolites generating multiple LC-MS peaks arising from isotopes, adducts, and fragments. Adduct annotation is a particular challenge, as the same mass difference between peaks can arise from adduct formation, fragmentation, or different biological species. To address this, here we describe a buffer modification workflow (BMW) in which the same sample is run by LC-MS in both liquid chromatography solvent with 14NH3–acetate buffer and in solvent with the buffer modified with 15NH3–formate. Buffer switching results in characteristic mass and signal intensity changes for adduct peaks, facilitating their annotation. This relatively simple and convenient chromatography modification annotated yeast metabolomics data with similar effectiveness to growing the yeast in isotope-labeled media. Application to mouse liver data annotated both known metabolite and known adduct peaks with 95% accuracy. Overall, it identified 26% of ∼27 000 liver LC-MS features as putative metabolites, of which ∼2600 showed HMDB or KEGG database formula match. This workflow is well suited to biological samples that cannot be readily isotope labeled, including plants, mammalian tissues, and tumors.

Conversion↗
DOE OSTI2025

Data for "Discovery, Characterization, and Application of Chromosomal Integration Sites in the Hyperthermophilic Archaeon Sulfolobus islandicus"

Sulfolobus islandicus , an emerging archaeal model organism, offers unique advantages for metabolic engineering and synthetic biology applications owing to its ability to thrive in extreme environments. Although several genetic tools have been established for this organism, the lack of well-characterized chromosomal integration sites has limited its potential as a cellular factory. Here, we systematically identified and characterized 13 artificial CRISPR RNAs targeting eight integration sites in S. islandicus using the CRISPR-COPIES pipeline and a multi-omics-informed computational workflow. We leveraged the endogenous CRISPR-Cas system to integrate the reporter gene lacS and validated heterologous expression through a β-galactosidase assay, revealing significant positional effects. As a proof of concept, we utilized these sites to genetically manipulate lipid ether composition by overexpressing glycerol dibiphytanyl glycerol tetraether (GDGT) ring synthase B (GrsB). This study expands the genetic toolbox for S. islandicus and advances its potential as a robust platform for archaeal synthetic biology and industrial biotechnology.

AI/ML↗
DOE OSTI2026

Frontier Job-Centric Telemetry Dataset

Comprehensive analysis of high-performance computing (HPC) systems requires linking workload execution to system behavior. This kind of analysis is vital for diagnosing performance issues, managing capacity, detecting anomalous workloads, and understanding how applications interact with system hardware. This job-centric telemetry dataset unifies scheduler job records with node-level measurements, enabling direct association between workloads and their corresponding power, thermal, and performance characteristics. It contains sanitized, scheduler related metadata for 152,400 individual jobs that ran on the Frontier supercomputer and ended on selected days throughout 2024 and 2025, a subpopulation of ~6.8% of the total number of allocated jobs with non-zero run time on the system over that same period. Each is linked with files that contain telemetry time series records of the power utilization and temperature behavior of its allocated nodes and their processors during the run time of the job. Where available, a portion of the job files also contain network performance time series. Jobs are sampled from select days that reflect normal levels of user activity and possess job size distributions with large numbers of leadership class jobs (>20% of Frontier nodes). Jobs in this dataset attempt to best represent successful user workflows.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2022

Tailored approach to study Legionella infection using a lattice light sheet microscope (LLSM)

Legionella is a genus of ubiquitous environmental pathogens found in freshwater systems, moist soil, and composted materials. More than four decades of Legionella research has provided important insights into Legionella pathogenesis. Although standard commercial microscopes have led to significant advances in understanding Legionella pathogenesis, great potential exists in the deployment of more advanced imaging techniques to provide additional insights. The lattice light sheet microscope (LLSM) is a recently developed microscope for 4D live cell imaging with high resolution and minimum photo-damage. We built a LLSM with an improved version for the optical layout with two path-stretching mirror sets and a novel reconfigurable galvanometer scanner ( RGS ) module to improve the reproducibility and reliability of the alignment and maintenance of the LLSM. We commissioned this LLSM to study Legionella pneumophila infection with a tailored workflow designed over instrumentation, experiments, and data processing methods. Our results indicate that Legionella pneumophila infection is correlated with a series of morphological signatures such as smoothness, migration pattern and polarity both statistically and dynamically. Our work demonstrates the benefits of using LLSM for studying long-term questions in bacterial infection. Our free-for-use modifications and workflow designs on the use of LLSM system contributes to the adoption and promotion of the state-of-the-art LLSM technology for both academic and commercial applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Bayesian Optical Heterodyne Tomography

We introduce a complete workflow for Bayesian quantum state tomography of generic continuous-variable states. We also summarize experimental results applying this workflow to the tomographic reconstruction of thermal and coherent states of light.

Chapman, Joseph↗