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At least 1,387 records · Page 77
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

A North Atlantic synthetic tropical cyclone tracks, intensity, and rainfall dataset

Tropical Cyclones (TCs) cause significant socio-economic damages to the US and Caribbean coastal regions annually, making it important to understand TC risk at the local-to-regional scales where their impacts are most prominent. However, the short length of the observed record and the substantial computational expense associated with high-resolution climate models make it difficult to assess TC risk using either approach. To overcome these challenges, we developed a database of synthetic TCs using the Risk Analysis Framework for Tropical Cyclones (RAFT). The database includes 50,000 synthetic TC tracks, along-track intensities and storm-induced precipitation. TC tracks generated in RAFT are in reasonable agreement with observations for spatial distribution of TC tracks and basin-scale distributions of TC translation speeds, lifetime maximum intensities and intensification rates. Also, spatial variations in coastal frequency and precipitation for landfalling TCs are well-reproduced in RAFT. In summary, the synthetic TC database based on RAFT provides a reasonable pathway for robust assessment of TC wind and rainfall risk for the US coastal regions and other areas affected by Atlantic TCs.

Xu, Wenwei↗
DOE OSTI2024

Dataset for: Price Controls for Scarcity Events in Real-Time and Transactive Energy Systems

Real time pricing (RTP) is often promoted as a mechanism to improve the economic efficiency of the electricity system. However, many regulators have been hesitant to adopt RTP due to concerns about exposing customers to extreme price swings. To balance these concerns, this paper proposes a methodology for establishing price controls, based on the supply of demand-side flexibility in the system. As an illustrative example, we measure price responsiveness using an agent-based simulation model that is representative of the ERCOT market. The model is composed of a distribution feeder that has 250 customers with active agents controlling their HVAC systems in response to the historical ERCOT RTP with an artificially added high-price event. These agents are subjected to increasing electricity prices during the event, which we then use to create a supply curve for demand-side resources in our modeled scarcity event. We set potential price caps at points on the supply curve where customers’ have exhausted their flexible capacity. Using historical prices, we examine the systemic costs of these price caps, and present regulatory options for recouping them. Utilities and regulators interested in limiting consumer risk from dynamic pricing can utilize these methods to develop rate structures and encourage conservation. The attached data upload allows for the duplication or modification of the analysis performed in this study.

Kerby, Jessica R↗
DOE OSTI2024

Dataset for "Enrichment of phosphates, lead, and mixed soil-organic particles in INPs at the Southern Great Plains site"

Ice nucleating particles (INPs) are rare particles that initiate primary ice formation, a critical step required for subsequent important cloud microphysical processes that ultimately govern cloud phase and cloud radiative properties. Laboratory studies have found that organic-rich dusts, such as those found in soils, are more efficient INPs compared to mineral dust. However, the atmospheric relevance of these organic-rich dusts are not well understood, particularly in regions with significant agricultural activity. The Agricultural Ice nuclei at the Southern Great Plains field campaign (AGINSGP) was conducted in rural Oklahoma to investigate how soil dusts contribute to INP populations in the Great Plains. We present chemical characterization of ambient and ice crystal residual particles from a single day of sampling using single particle mass spectrometry (SPMS) and scanning microscopy. Ambient particle concentrations were primarily carbonaceous or secondary aerosol, while dust particles were enhanced in the residual particles. Dust particles measured during residual sampling contained elevated signals for phosphate ($^{63}$PO$_2^-$ and $^{79}$PO$_3^-$) and lead ($^{208}$Pb$_2^+$). Nitrate was slightly depleted relative to ambient dust, and strong sulfate signals were not seen in the residual particles measured by the miniSPLAT. The residual and ambient particles measured by the miniSPLAT were approximately the same size, though this may be a reflection of the SPMS size-dependent transmission efficiency and not that of physical truth. This study shows that organic-rich soils may be important contributors to the ambient INP population in agricultural regions.

Cornwell, Gavin C↗
DOE OSTI2025

Dataset for the Danczak et al., 2025 manuscript about bacterial-fungal interactions

We generated genome-resolved multiomics data from a series of metagenomic and metatranscriptomic sequencing. Specifically, we acquired, functionally annotated, and taxonomically classified both bacterial and eukaryotic metagenome assembled genomes (MAGs). For bacterial MAGs, we assembled eukaryotic float metagenomic sequencing data from JGI using MEGAHIT, binned and refined MAGs using MetaWRAP and dRep, functionally annotated MAGs using eggNOG mapper, and assigned taxonomy using GTDB-tk. For eukaryotic MAGs, we first identified potentially eukaryotic contigs from a coassembly of eukaryotic float metagenomic sequencing data from JGI using EukRep and Whokaryote, binned MAGs using MetaBAT2, functionally annotated MAGs using eggNOG mapper, and assigned taxonomy using Eukulele. Bulk metatranscriptomic reads were mapped to bacterial MAGs and polyA-metatranscriptomic read were mapped to eukaryotic MAGs using bbmap.

Danczak, Robert E. [Pacific Northwest National Lab↗
DOE OSTI2025

DataSet for Elucidating molecular level interfacial interactions between a de novo protein and nucleated calcite with solid-state NMR

Biomineralization is the process by which organisms use biomolecules to produce hierarchically structured organic-inorganic composites. Using biology as inspiration, a protein construct (FD31) was previously designed to accelerate formation of nano-calcite with an unconventional {110} face. To understand the molecular interactions essential for protein aided calcite nucleation, solid-state nuclear magnetic resonance (ssNMR) spectroscopy was used in this work to characterize the FD31-calcite interface at the atomic level. Glutamic acid side chains designed to interact directly with calcium ions on the surface were found to have dynamics on the sub-millisecond timescale, indicating possible interactions between the protein and surface waters that were not included in the original model. Dipolar ssNMR recoupling techniques also showed that the protein backbone is ~2 Å closer to the surface than in the original docking model. Refined molecular simulations were done in the presence of explicit waters, which resulted in the protein backbone closer to the surface than in the original docking structure, providing better agreement with experiment and highlighting the important role played by water in FD31-calcite interactions. These studies provide the first experimental evidence to confirm that FD31 interactions with calcite are localized to the surface of the protein designed to serve as a template. However, these studies do indicate a more dynamic binding and closer binding mode between FD31 and the nucleated surface than originally proposed. In all, this enhanced molecular insight into the FD31-calcite interface has advanced our fundamental understanding of the atomic interactions at the organic-inorganic interface and will aid in the design of biological templates for the nucleation of inorganic crystals.

Saccuzzo Close, Emily Grace [Pacific Northwest Nat↗
DOE OSTI2020

Dataset for "FLEXPART-WRF simulations to assess dust transport in the convective boundary layer at the Southern Great Plains site"

Soil dusts are an important source of aerosol in agricultural regions and can affect the Earth’s radiation budget through the modification of cloud properties, and in particular, through their ability to act as ice nucleating particles. In order to impact cloud properties, agricultural soil dusts need to be transported from the point of emission to cloud-relevant altitudes. Vertical transport within the planetary boundary layer is strongly controlled by turbulence and is challenging to represent accurately in regional and global models. Large-eddy simulations (LES) are run at resolutions capable of resolving most of the turbulent energy directly and can thus better simulate vertical transport. In this study, we leverage the LES ARM Symbiotic Simulation and Observation (LASSO) large-eddy simulations to simulate vertical transport of agricultural dust within the turbulent boundary layer using a modified version of the stochastic dispersion model FLEXPART-WRF. We find that the modified model is better capable of simulating particle transport due to turbulence, and that particle size was the greatest factor in determining particle lifetime. Individual meteorology and particle density had intermediate effects upon particle transport, while release height had little effect upon simulation results. Finally, we utilize a quasi-single column model (QSCM) approach to determine how our results compare to a parameterized treatment of turbulence. The QSCM simulations led to greater tracer transport out of the boundary layer, with ramifications for any studies utilizing a Lagrangian stochastic model to understand tracer dispersion. These results highlight the importance of accurately simulating turbulence for understanding particle transport.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Dataset for "Development of heterogeneous ice nucleation rate coefficient parameterizations from ambient measurements"

Ice nucleating particles (INPs) are a rare subset of particles that can have an outsized impact relative to their prevalence. To simulate INP variability, models require parameterizations for the most important sources of INPs. Most parameterizations in the literature were developed from laboratory experiments that used proxies for ambient particles. Whether these laboratory models effectively represent ambient aerosol is still not well understood and parameterizations developed from field measurements may be more atmospherically relevant. Expanding on previous work in which we used an ice chamber and an single particle mass spectrometer (SPMS) to characterize INP composition, we use the combined measurements to calculate heterogeneous ice nucleation rate coefficients for ambient particles. We find good agreement between our results for dust and sea spray aerosol with previous results. We also determine the relative contribution of each measurement to the total measurement uncertainty using a Monte Carlo approach and find that the biggest source of uncertainty is the sampling efficiency of the SPMS.

Cornwell, Gavin C↗
DOE OSTI2020

DATASET: Rapid growth of anthropogenic organic nanoparticles greatly alters cloud lifecycle in the Amazon rainforest

Atmospheric nanoparticles can significantly influence Earth’s climate if they grow to sizes large enough to nucleate cloud droplets. While the contribution of extremely low volatility vapors to nanoparticle growth has been discussed extensively, the role of semivolatile organics has been largely overlooked. Here we examine the growth and impacts of air pollution nanoparticles from an isolated metropolis amidst the Amazon rainforest. Although extremely low volatility organics are necessary for the initial growth of nanoparticles, model analysis suggests that dynamic gas-particle partitioning of semivolatile oxidation products of anthropogenic and natural hydrocarbons is predominantly responsible for the observed rapid growth to 50 nm. Furthermore, cloud-resolving simulations demonstrate that the grown particles appreciably modify shallow cloud droplet size distribution, suppress precipitation, and enhance the transition to deep clouds. With condensable semivolatile organics typically formed in greater proportion, similar nanoparticle growth and impacts on clouds could likely occur in heavily urbanized forested regions globally.

Zaveri, Rahul A↗
DOE OSTI2023

Dataset for SIAM MPI23 Project "Model inversion for complex physical systems using low-dimensional surrogates"

Training and testing data for the SIAM MPI23 workshop "Model inversion for complex physical systems using low-dimensional surrogates". The data consists of ensembles of input and output pairs corresponding to queries of a 2D saturated groundwater flow model. The inputs consist of random vectors which map to discretized model parameter fields via a Kosambi-Karhunen-Loève expansion. Output corresponds to discretized pressure fields.

basis adaptation, conditional Karhunen-Loève expan↗
DOE OSTI2025

Next-generation sequencing dataset of genome-scale CRISPRi in Synechococcus sp. PCC 7002 across seven conditions

A 33,298-member sgRNA library developed for Synechococus sp. PCC 7002 was screened with two replicates across seven growth conditions and sequenced with Illumina NextSeq (paired end, 2x150 bp) for a total of ~700M reads. The original plasmid library and the library after transformation into a dCas9-containing and dCas9-absent strain were also sequenced as a reference for initial sgRNA abundance.

genome- wide screens environmental acclimation spe↗
DOE OSTI2014

Wind Integration National Dataset (WIND) Toolkit

Wind resource data for North America was produced using the Weather Research and Forecasting Model (WRF). The WRF model was initialized with the European Centre for Medium Range Weather Forecasts Interim Reanalysis (ERA-Interm) data set with an initial grid spacing of 54 km. Three internal nested domains were used to refine the spatial resolution to 18, 6, and finally 2 km. The WRF model was run for years 2007 to 2014. While outputs were extracted from WRF at 5 minute time-steps, due to storage limitations instantaneous hourly time-step are provided for all variables while full 5 min resolution data is provided for wind speed and wind direction only. The following variables were extracted from the WRF model data: - Wind Speed at 10, 40, 60, 80, 100, 120, 140, 160, 200 m - Wind Direction at 10, 40, 60, 80, 100, 120, 140, 160, 200 m - Temperature at 2, 10, 40, 60, 80, 100, 120, 140, 160, 200 m - Pressure at 0, 100, 200 m - Surface Precipitation Rate - Surface Relative Humidity - Inverse Monin Obukhov Length

API↗
DOE OSTI2020

Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design

Solving environmental and social challenges such as climate change requires a shift from our current non-renewable manufacturing model to a sustainable bioeconomy. To lower carbon emissions in the production of fuels and chemicals, plant biomass feedstocks can replace petroleum using microorganisms as biocatalysts. The anaerobic thermophile Clostridium thermocellum is a promising bacterium for bioconversion due to its capability to efficiently degrade lignocellulosic biomass. However, the complex metabolism of C. thermocellum is not fully understood, hindering metabolic engineering to achieve high titers, rates, and yields of targeted molecules. In this study, we developed an updated genome-scale metabolic model of C. thermocellum that accounts for recent metabolic findings, has improved prediction accuracy, and is standard-conformant to ensure easy reproducibility. We illustrated two applications of the developed model. We first formulated a multi-omics integration protocol and used it to understand redox metabolism and potential bottlenecks in biofuel (e.g., ethanol) production in C. thermocellum. Second, we used the metabolic model to design modular cells for efficient production of alcohols and esters with broad applications as flavors, fragrances, solvents, and fuels. The proposed designs not only feature intuitive push-and-pull metabolic engineering strategies, but also present novel manipulations around important central metabolic branch-points. We anticipate the developed genome-scale metabolic model will provide a useful tool for system analysis of C. thermocellum metabolism to fundamentally understand its physiology and guide metabolic engineering strategies to rapidly generate modular production strains for effective biosynthesis of biofuels and biochemicals from lignocellulosic biomass.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Replicates, read numbers, and other important experimental design considerations for microbial RNA-seq identified using Bacillus thuringiensis datasets

RNA-seq is being used increasingly for gene expression studies and it is revolutionizing the fields of genomics and transcriptomics. However, the field of RNA-seq analysis is still evolving. Therefore, we specifically designed this study to contain large numbers of reads and four biological replicates per condition so we could alter these parameters and assess their impact on differential expression results. Bacillus thuringiensis strains ATCC10792 and CT43 were grown in two Luria broth medium lots on four dates and transcriptomics data were generated using one lane of sequence output from an Illumina HiSeq2000 instrument for each of the 32 samples, which were then analyzed using DESeq2. Genome coverages across samples ranged from 87 to 465X with medium lots and culture dates identified as major variation sources. Significantly differentially expressed genes (5% FDR, two-fold change) were detected for cultures grown using different medium lots and between different dates. The highly differentially expressed iron acquisition and metabolism genes, were a likely consequence of differing amounts of iron in the two media lots. Indeed, in this study RNA-seq was a tool for predictive biology since we hypothesized and confirmed the two LB medium lots had different iron contents (~two-fold difference). Furthermore, this study shows that the noise in data can be controlled and minimized with appropriate experimental design and by having the appropriate number of replicates and reads for the system being studied. We outline parameters for an efficient and cost effective microbial transcriptomics study.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Analysis of metabolomics datasets with high-performance computing and metabolite atlases

Even with the widespread use of liquid chromatography mass spectrometry (LC/MS) based metabolomics, there are still a number of challenges facing this promising technique. Many, diverse experimental workflows exist; yet there is a lack of infrastructure and systems for tracking and sharing of information. Here, we describe the Metabolite Atlas framework and interface that provides highly-efficient, web-based access to raw mass spectrometry data in concert with assertions about chemicals detected to help address some of these challenges. This integration, by design, enables experimentalists to explore their raw data, specify and refine features annotations such that they can be leveraged for future experiments. Fast queries of the data through the web using SciDB, a parallelized database for high performance computing, make this process operate quickly. Furthermore, by using scripting containers, such as IPython or Jupyter, to analyze the data, scientists can utilize a wide variety of freely available graphing, statistics, and information management resources. In addition, the interfaces facilitate integration with systems biology tools to ultimately link metabolomics data with biological models.

59 BASIC BIOLOGICAL SCIENCES↗