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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 271 records · Page 15
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Transcriptomic Analysis of Arachidonic Acid Pathway Genes Provides Mechanistic Insight into Multi-Organ Inflammatory and Vascular Diseases

Arachidonic acid (AA) metabolites have been associated with several diseases across various organ systems, including the cardiovascular, pulmonary, and renal systems. Lipid mediators generated from AA oxidation have been studied to control macrophages, T-cells, cytokines, and fibroblasts, and regulate inflammatory mediators that induce vascular remodeling and dysfunction. AA is metabolized by cyclooxygenase (COX), lipoxygenase (LOX), and cytochrome P450 (CYP) to generate anti-inflammatory, pro-inflammatory, and pro-resolutory oxidized lipids. As comorbid states such as diabetes, hypertension, and obesity become more prevalent in cardiovascular disease, studying the expression of AA pathway genes and their association with these diseases can provide unique pathophysiological insights. In addition, the AA pathway of oxidized lipids exhibits diverse functions across different organ systems, where a lipid can be both anti-inflammatory and pro-inflammatory depending on the location of metabolic activity. Therefore, we aimed to characterize the gene expression of these lipid enzymes and receptors throughout multi-organ diseases via a transcriptomic meta-analysis using the Gene Expression Omnibus (GEO) Database. In our study, we found that distinct AA pathways were expressed in various comorbid conditions, especially those with prominent inflammatory risk factors. Comorbidities, such as hypertension, diabetes, and obesity appeared to contribute to elevated expression of pro-inflammatory lipid mediator genes. Our results demonstrate that expression of inflammatory AA pathway genes may potentiate and attenuate disease; therefore, we suggest further exploration of these pathways as therapeutic targets to improve outcomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fracture Network Influence on Rock Damage and Gas Transport following an Underground Explosion

Simulations of rock damage and gas transport following underground explosions that omit preexisting fracture networks in the subsurface cannot fully characterize the influence of geo-structural variability on gas transport. Previous studies do not consider the impact that fracture network structure and variability have on gas seepage. In this study, we develop a sequentially coupled, axi-symmetric model to look at the damage pattern and resulting gas breakthrough curves following an underground explosion given different fracture network realizations. We simulate 0.327 and 0.164 kT chemical explosives with burial depths of 100 m for 90 stochastically generated fracture networks. Gases quickly reach the surface in 30% of the higher yield simulations and 5% of the lower yield simulations. The fast breakthrough can be attributed to the formation of connected pathways between fractures to the surface. The formation of a connected damage pathway to the surface is not clearly correlated with the fracture intensity (P32) in our simulations. Breakthrough curves with slower transport are highly variable depending on the fracture network sample. The variability in the breakthrough behavior indicates that ignoring the influence of fracture networks on rock damage, which strongly influences the hydraulic properties following an underground explosion, will likely lead to a large underestimation of the uncertainty in the gas transport to the surface. This work highlights the need for incorporation of fracture networks into models for accurately predicting gas seepage following underground explosions.

58 GEOSCIENCES↗
DOE OSTI2020

A Vector Sensor-Based Acoustic Characterization System for Marine Renewable Energy

NoiseSpotter is a passive acoustic monitoring system that characterizes, classifies, and geo-locates anthropogenic and natural sounds in near real time. It was developed with the primary goal of supporting the evaluation of potential acoustic effects of offshore renewable energy projects. The system consists of a compact array of three acoustic vector sensors, which measures acoustic pressure and the three-dimensional particle velocity vector associated with the propagation of an acoustic wave, thereby inherently providing bearing information to an underwater source of sound. By utilizing an array of three vector sensors, the application of beamforming techniques can provide sound source localization, allowing for characterization of the acoustic signature of specific underwater acoustic sources. Here, performance characteristics of the system are presented, using data from controlled acoustic transmissions in a quiet environment and ambient noise measurements in an energetic tidal channel in the presence of non-acoustic flow noise. Data quality is demonstrated by the ability to reduce non-acoustic flow noise contamination, while system utility is shown by the ability to characterize and localize sources of sound in the underwater environment.

16 TIDAL AND WAVE POWER↗
DOE OSTI2020

Revisiting MOA 2013-BLG-220L: A Solar-type Star with a Cold Super-Jupiter Companion

We present the analysis of high-resolution images of MOA-2013-BLG-220, taken with the Keck adaptive optics system six years after the initial observation, identifying the lens as a solar-type star hosting a super-Jupiter-mass planet. The masses of planets and host stars discovered by microlensing are often not determined from light-curve data, while the star–planet mass ratio and projected separation in units of Einstein ring radius are well measured. High-resolution follow-up observations after the lensing event is complete can resolve the source and lens. This allows direct measurements of flux, and the amplitude and direction of proper motion, giving strong constraints on the system parameters. Due to the high relative proper motion, μ{sub rel,Geo}=12.62±0.11 mas yr{sup −1}, the source and lens were resolved in 2019, with a separation of 77.1 ± 0.5 mas. Thus, we constrain the lens flux to K{sub Keck,lens}=17.92±0.02. By combining constraints from the model and Keck flux, we find the lens mass to be M{sub L}=0.88±0.05 M{sub ⊙} at D{sub L}=6.72±0.59 kpc. With a mass ratio of q=(3.00±0.03)×10{sup −3} the planet’s mass is determined to be M{sub P}=2.74±0.17 M{sub J} at a separation of r{sub ⊥}=3.03±0.27 au. The lens mass is much higher than the prediction made by Bayesian analysis that assumes all stars have an equal probability to host a planet of the measured mass ratio, and suggests that planets with mass ratios of a few times 10{sup −3} are more common orbiting massive stars. This demonstrates the importance of high-resolution follow-up observations for testing theories like these.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Model bias in simulating major chemical components of PM 2.5 in China

High concentrations of PM 2.5 (particulate matter with an aerodynamic diameter less than 2.5 µm) in China have caused severe visibility degradation. Accurate simulations of PM 2.5 and its chemical components are essential for evaluating the effectiveness of pollution control strategies and the health and climate impacts of air pollution. In this study, we compared the GEOS-Chem model simulations with comprehensive datasets for organic aerosol (OA), sulfate, nitrate, and ammonium in China. Model results are evaluated spatially and temporally against observations. The new OA scheme with a simplified secondary organic aerosol (SOA) parameterization significantly improves the OA simulations in polluted urban areas, highlighting the important contributions of anthropogenic SOA from semivolatile and intermediate-volatility organic compounds. The model underestimates sulfate and overestimates nitrate for most of the sites throughout the year. More significant underestimation of sulfate occurs in winter, while the overestimation of nitrate is extremely large in summer. The model is unable to capture some of the main features in the diurnal pattern of the PM 2.5 chemical components, suggesting inaccuracies in the presented processes. Potential model adjustments that may lead to a better representation of the boundary layer height, the precursor emissions, hydroxyl radical concentrations, the heterogeneous formation of sulfate and nitrate, and the wet deposition of nitric acid and nitrate have been tested in the sensitivity analysis. The results show that uncertainties in chemistry perhaps dominate the model biases. The proper implementation of heterogeneous sulfate formation and the good estimates of the concentrations of sulfur dioxide, hydroxyl radical, and aerosol liquid water are essential for the improvement of the sulfate simulation. The update of the heterogeneous uptake coefficient of nitrogen dioxide significantly reduces the modeled concentrations of nitrate. However, the large overestimation of nitrate concentrations remains in summer for all tested cases. The possible bias in the chemical production and the wet deposition of nitrate cannot fully explain the model overestimation of nitrate, suggesting issues related to the atmospheric removal of nitric acid and nitrate. A better understanding of the atmospheric nitrogen budget, in particular, the role of the photolysis of particulate nitrate, is needed for future model developments. Moreover, the results suggest that the remaining underestimation of OA in the model is associated with the underrepresented production of SOA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Aerosol responses to precipitation along North American air trajectories arriving at Bermuda

North American pollution outflow is ubiquitous over the western North Atlantic Ocean, especially in winter, making this location a suitable natural laboratory for investigating the impact of precipitation on aerosol particles along air mass trajectories. We take advantage of observational data collected at Bermuda to seasonally assess the sensitivity of aerosol mass concentrations and volume size distributions to accumulated precipitation along trajectories (APT). The mass concentration of particulate matter with aerodynamic diameter less than 2.5 µm normalized by the enhancement of carbon monoxide above background (PM 2.5 /ΔCO) at Bermuda was used to estimate the degree of aerosol loss during transport to Bermuda. Results for December–February (DJF) show that most trajectories come from North America and have the highest APTs, resulting in a significant reduction (by 53 %) in PM 2.5 /ΔCO under high-APT conditions (> 13.5 mm) relative to low-APT conditions (< 0.9 mm). Moreover, PM 2.5 /ΔCO was most sensitive to increases in APT up to 5 mm (–0.044 µg m –3 ppbv –1 mm –1 ) and less sensitive to increases in APT over 5 mm. While anthropogenic PM 2.5 constituents (e.g., black carbon, sulfate, organic carbon) decrease with high APT, sea salt, in contrast, was comparable between high- and low-APT conditions owing to enhanced local wind and sea salt emissions in high-APT conditions. The greater sensitivity of the fine-mode volume concentrations (versus coarse mode) to wet scavenging is evident from AErosol RObotic NETwork (AERONET) volume size distribution data. A combination of GEOS-Chem model simulations of the 210 Pb submicron aerosol tracer and its gaseous precursor 222 Rn reveals that (i) surface aerosol particles at Bermuda are most impacted by wet scavenging in winter and spring (due to large-scale precipitation) with a maximum in March, whereas convective scavenging plays a substantial role in summer; and (ii) North American 222 Rn tracer emissions contribute most to surface 210 Pb concentrations at Bermuda in winter (~75 %–80 %), indicating that air masses arriving at Bermuda experience large-scale precipitation scavenging while traveling from North America. A case study flight from the ACTIVATE field campaign on 22 February 2020 reveals a significant reduction in aerosol number and volume concentrations during air mass transport off the US East Coast associated with increased cloud fraction and precipitation. These results highlight the sensitivity of remote marine boundary layer aerosol characteristics to precipitation along trajectories, especially when the air mass source is continental outflow from polluted regions like the US East Coast.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Process-based and observation-constrained SOA simulations in China: the role of semivolatile and intermediate-volatility organic compounds and OH levels

Organic aerosol (OA) is a major component of tropospheric submicron aerosol that contributes to air pollution and causes adverse effects on human health. Chemical transport models have difficulties in reproducing the variability in OA concentrations in polluted areas, hindering understanding of the OA budget and sources. Herein, we apply both process-based and observation-constrained schemes to simulate OA in GEOS-Chem. Comprehensive data sets of surface OA, OA components, secondary organic aerosol (SOA) precursors, and oxidants were used for model–observation comparisons. The base models generally underestimate the SOA concentrations in China. In the revised schemes, updates were made on the emissions, volatility distributions, and SOA yields of semivolatile and intermediate-volatility organic compounds (SVOCs and IVOCs) and additional nitrous acid sources. With all the model improvements, both the process-based and observation-constrained SOA schemes can reproduce the observed mass concentrations of SOA and show spatial and seasonal consistency with each other. Our best model simulations suggest that anthropogenic SVOCs and IVOCs are the dominant source of SOA, with a contribution of over 50% in most of China, which should be considered for pollution mitigation in the future. The residential sector may be the predominant source of SVOCs and IVOCs in winter, despite large uncertainty remaining in the emissions of IVOCs from the residential sector in northern China. The industry sector is also an important source of IVOCs, especially in summer. More SVOC and IVOC measurements are needed to constrain their emissions. Besides, the results highlight the sensitivity of SOA to hydroxyl radical (OH) levels in winter in polluted environments. The addition of nitrous acid sources can lead to over 30% greater SOA mass concentrations in winter in northern China. It is important to have good OH simulations in air quality models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Impacts of long-range-transported mineral dust on summertime convective cloud and precipitation: a case study over the Taiwan region

As one of the most abundant atmospheric aerosols and effective ice nuclei, mineral dust affects clouds and precipitation in the Earth system. Here numerical experiments are carried out to investigate the impacts of dust aerosols on summertime convective clouds and precipitation over the mountainous region of Taiwan by acting as ice-nucleating particles. We run the Weather Research and Forecasting model (WRF) with the Morrison two-moment and spectral-bin microphysics (SBM) schemes at 3 km resolution, using dust number concentrations from a global chemical transport model (GEOS-Chem-APM). The case study indicates that the long-range-transported mineral dust, with relatively low number concentrations, can notably affect the properties of convective clouds (ice and liquid water contents, cloud top height, and cloud coverage) and precipitation (spatial pattern and intensity). The effects of dust are evident during strong convective periods, with significantly increased ice water contents in the mixed-phase regime via the enhanced heterogeneous freezing. With both the Morrison and SBM schemes, we see the invigoration effects of dust aerosols on the convective intensity through enhanced condensation and deposition latent heating. The low-altitude dust particles are uplifted to the freezing level by updrafts, which, in turn, enhance the convective cloud development through immersion freezing and convective invigoration. Compared to the Morrison scheme, the SBM scheme predicts more realistic precipitation and different invigoration effects of dust. The differences are partially attributed to the saturation adjustment approach utilized in the bulk scheme, which leads to a stronger enhancement of condensation at midlatitudes to low altitudes and a weaker deposition increase at the upper level.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Factors controlling marine aerosol size distributions and their climate effects over the northwest Atlantic Ocean region

Abstract. Aerosols over Earth's remote and spatially extensive ocean surfaces have important influences on planetary climate. However, these aerosols and their effects remain poorly understood, in part due to the remoteness and limited observations over these regions. In this study, we seek to understand factors that shape marine aerosol size distributions and composition in the northwest Atlantic Ocean region. We use the GEOS-Chem model with the TwO-Moment Aerosol Sectional (TOMAS) microphysics algorithm model to interpret measurements collected from ship and aircraft during the four seasonal campaigns of the North Atlantic Aerosols and Marine Ecosystems Study (NAAMES) conducted between 2015 and 2018. Observations from the NAAMES campaigns show enhancements in the campaign-median number of aerosols with diameters larger than 3 nm in the lower troposphere (below 6 km), most pronounced during the phytoplankton bloom maxima (May/June) below 2 km in the free troposphere. Our simulations, combined with NAAMES ship and aircraft measurements, suggest several key factors that contribute to aerosol number and size in the northwest Atlantic lower troposphere, with significant regional-mean (40–60∘ N and 20–50∘ W) cloud-albedo aerosol indirect effect (AIE) and direct radiative effect (DRE) processes during the phytoplankton bloom. These key factors and their associated simulated radiative effects in the region include the following: (1) particle formation near and above the marine boundary layer (MBL) top (AIE: −3.37 W m−2, DRE: −0.62 W m−2); (2) particle growth due to marine secondary organic aerosol (MSOA) as the nascent particles subside into the MBL, enabling them to become cloud-condensation-nuclei-sized particles (AIE: −2.27 W m−2, DRE: −0.10 W m−2); (3) particle formation and growth due to the products of dimethyl sulfide, above and within the MBL (−1.29 W m−2, DRE: −0.06 W m−2); (4) ship emissions (AIE: −0.62 W m−2, DRE: −0.05 W m−2); and (5) primary sea spray emissions (AIE: +0.04 W m−2, DRE: −0.79 W m−2). Our results suggest that a synergy of particle formation in the lower troposphere (particularly near and above the MBL top) and growth by MSOA contributes strongly to cloud-condensation-nuclei-sized particles with significant regional radiative effects in the northwest Atlantic. To gain confidence in radiative effect magnitudes, future work is needed to understand (1) the sources and temperature dependence of condensable marine vapors forming MSOA, (2) primary sea spray emissions, and (3) the species that can form new particles in the lower troposphere and grow these particles as they descend into the marine boundary layer.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Summertime ozone pollution in China affected by stratospheric quasi-biennial oscillation

In recent years, the near-surface ozone (O 3 ) level has been rising fast in China, with increasing damage to human health and ecosystems. In this study, the impact of stratospheric quasi-biennial oscillation (QBO) on interannual variations in summertime tropospheric O 3 over China is investigated based on GEOS-Chem model simulations and satellite retrievals. QBO has a significant positive correlation with near-surface O 3 concentrations over central China (92.5–112.5° E, 26–38° N) when the sea surface temperature (SST) over the eastern tropical Pacific is warmer than normal, with a correlation coefficient of 0.53, but QBO has no significant effect on O 3 under the cold SST anomaly. Compared to the easterly phase of QBO, the near-surface O 3 concentrations have an increase of up to 3 ppb (5% relative to the average) over central China during its westerly phase under the warm SST anomaly. O 3 also increases above the surface and up to the upper troposphere, with a maximum increase of 2–3 ppb (3%–5%) in 850–500 hPa over central China when comparing westerly phase to easterly phase. Process-based analysis and sensitivity simulations suggest that the O 3 increase over central China is mainly attributed to the anomalous downward transport of O 3 during the westerly phase of QBO when a warm SST anomaly occurs in the eastern tropical Pacific, while the local chemical reactions and horizontal transport processes partly offset the O 3 increase. This work suggests a potentially important role of QBO and the related vertical transport process in affecting near-surface O 3 air quality, with an indication for O 3 pollution prediction and prevention.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Quantifying the impacts of marine aerosols over the southeast Atlantic Ocean using a chemical transport model: implications for aerosol–cloud interactions

The southeast Atlantic region, characterized by persistent stratocumulus clouds, has one of the highest uncertainties in aerosol radiative forcing and significant variability across climate models. In this study, we analyze the seasonally varying role of marine aerosol sources and identify key uncertainties in aerosol composition at cloud-relevant altitudes over the southeast Atlantic using the GEOS-Chem chemical transport model. We evaluate simulated aerosol optical depth (AOD) and speciated aerosol concentrations against those collected from ground observations and aircraft campaigns such as LASIC, ORACLES, and CLARIFY, conducted during 2017. The model consistently underestimates AOD relative to AERONET, particularly at remote locations like Ascension Island. However, when compared with aerosol mass concentrations from aircraft campaigns during the biomass burning period, it performs adequately at cloud-relevant altitudes, with a normalized mean bias (NMB) between -3.5 % (CLARIFY) and -7.5 % (ORACLES). At these altitudes, in the model, organic aerosols (63 %) dominate during the biomass burning period, while sulfate (41 %) prevails during austral summer, when dimethylsulfide (DMS) emissions peak in the model. Our findings indicate that marine sulfate can account for up to 69 % of total sulfate during the high-DMS period. Sensitivity analyses indicate that refining DMS emissions and oxidation chemistry may increase sulfate aerosol produced from marine sources, highlighting that there remains large uncertainty as to the role of DMS emissions in the marine boundary layer. Additionally, we find marine primary organic aerosol emissions may substantially increase total organic aerosol concentrations, particularly during austral summer. This study underscores the imperative need to refine marine emissions and their chemical transformations, as aerosols from marine sources are a major component of total aerosols at cloud-relevant altitudes and may impact uncertainties in aerosol radiative forcing over the southeast Atlantic.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Observationally constrained analysis of sulfur cycle in the marine atmosphere with NASA ATom measurements and AeroCom model simulations

The atmospheric sulfur cycle plays a key role in air quality, climate, and ecosystems, such as pollution, radiative forcing, new particle formation, and acid rain. In this study, we compare the spatially and temporally resolved measurements from the NASA Atmospheric Tomography (ATom) mission with simulations from five AeroCom III models for four sulfur species (dimethyl sulfide (DMS), sulfur dioxide (SO 2 ), particulate methanesulfonate (MSA), and particulate sulfate (SO 4 )). We focus on remote regions over the Pacific, Atlantic, and Southern oceans from near the surface to ~12 km altitude range covering all four seasons. In general, the differences among model results can be greater than 1 order of magnitude. Comparing with observations, model-simulated SO 2 is generally low, whereas SO 4 is generally high. Simulated DMS concentrations near the sea surface exceed observed levels by a factor of 5 in most cases, suggesting potential overestimation of DMS emissions in all models. With GEOS model simulations of tagging emission from anthropogenic, biomass burning, volcanic, and oceanic sources, we find that anthropogenic emissions are the dominant source of sulfate aerosol (40 %–60 % of the total amount) in the ATom measurements at almost all altitudes, followed by volcanic emissions (18 %–32 %) and oceanic sources (16 %–32 %). Similar source contributions can also be derived at broad ocean basins and on monthly scales, indicating the representativeness of ATom measurements for global ocean. Our work presents the first assessment of AeroCom sulfur study using ATom measurements, providing directions for improving sulfate simulations, which remain the largest uncertainty in radiative forcing estimates in aerosol climate models.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Comparison of scattering ratio profiles retrieved from ALADIN/Aeolus and CALIOP/CALIPSO observations and preliminary estimates of cloud fraction profiles

The space-borne active sounders have been contributing invaluable vertically resolved information of atmospheric optical properties since the launch of Cloud-Aerosol Lidar and Infrared Pathfinder Satellite Observation (CALIPSO) in 2006. To build long-term records from space-borne lidars useful for climate studies, one has to understand the differences between successive space lidars operating at different wavelengths, flying on different orbits, and using different viewing geometries, receiving paths, and detectors. In this article, we compare the results of Atmospheric Laser Doppler INstrument (ALADIN) and Cloud-Aerosol Lidar with Orthogonal Polarization (CALIOP) lidars for the period from 28 June to 31 December 2019. First, we build a dataset of ALADIN–CALIOP collocated profiles (Δdist<1°; Δtime<6 h). Then we convert ALADIN's 355 nm particulate backscatter and extinction profiles into the scattering ratio vertical profiles SR(z) at 532 nm using molecular density profiles from Goddard Earth Observing System Data Assimilation System, version 5 (GEOS-5 DAS). And finally, we build the CALIOP and ALADIN globally gridded cloud fraction profiles CF(z) by applying the same cloud detection threshold to the SR(z) profiles of both lidars at the same spatial resolution. Before comparing the SR(z) and CF(z) profiles retrieved from the two analyzed lidar missions, we performed a numerical experiment to estimate the best achievable cloud detection agreement CDA norm (z) considering the differences between the instruments. We define CDA norm (z) in each latitude–altitude bin as the occurrence frequency of cloud layers detected by both lidars, divided by a cloud fraction value for the same latitude–altitude bin. We simulated the SR(z) and CF(z) profiles that would be observed by these two lidars if they were flying over the same atmosphere predicted by a global model. By analyzing these simulations, we show that the theoretical limit for CDA$_{norm}^{theor}$(z) for a combination of ALADIN and CALIOP instruments is equal to 0.81±0.07 at all altitudes. In other words, 19 % of the clouds cannot be detected simultaneously by two instruments due to said differences. The analyses of the actual observed CALIOP–ALADIN collocated dataset containing ~78 000 pairs of nighttime SR(z) profiles revealed the following points: (a) the values of SR(z) agree well up to ~3 km height. (b) The CF(z) profiles show agreement below ~3 km, where ~80 % of the clouds detected by CALIOP are detected by ALADIN as expected from the numerical experiment. (c) Above this height, the CDA$_{norm}^{obs}$(z) reduces to ~50 %. (d) On average, better sensitivity to lower clouds skews ALADIN's cloud peak height in pairs of ALADIN–CALIOP profiles by ~0.5±0.6 km downwards, but this effect does not alter the heights of polar stratospheric clouds and high tropical clouds thanks to their strong backscatter signals. (e) The temporal evolution of the observed CDA$_{norm}^{obs}$(z) does not reveal any statistically significant change during the considered period. This indicates that the instrument-related issues in ALADIN L0/L1 have been mitigated, at least down to the uncertainties of the following CDA$_{norm}^{obs}$(z) values: 68±12 %, 55±14 %, 34±14 %, 39±13 %, and 42±14 % estimated at 0.75, 2.25, 6.75, 8.75, and 10.25 km, respectively.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

CompLaB v1.0: a scalable pore-scale model for flow, biogeochemistry, microbial metabolism, and biofilm dynamics

Abstract. Microbial activity and chemical reactions in porous media depend on the local conditions at the pore scale and can involve complex feedback with fluid flow and mass transport. We present a modeling framework that quantitatively accounts for the interactions between the bio(geo)chemical and physical processes and that can integrate genome-scale microbial metabolic information into a dynamically changing, spatially explicit representation of environmental conditions. The model couples a lattice Boltzmann implementation of Navier–Stokes (flow) and advection–diffusion-reaction (mass conservation) equations. Reaction formulations can include both kinetic rate expressions and flux balance analysis, thereby integrating reactive transport modeling and systems biology. We also show that the use of surrogate models such as neural network representations of in silico cell models can speed up computations significantly, facilitating applications to complex environmental systems. Parallelization enables simulations that resolve heterogeneity at multiple scales, and a cellular automaton module provides additional capabilities to simulate biofilm dynamics. The code thus constitutes a platform suitable for a range of environmental, engineering and – potentially – medical applications, in particular ones that involve the simulation of microbial dynamics.

58 GEOSCIENCES↗
DOE OSTI2024

Bacteroides expand the functional versatility of a universal transcription factor and transcribed DNA to program capsule diversity

This record contains a list of Snakemake rules (Snakefile) to process a raw *.fastq.gz (from GEO record: GSE281607) using Cutadapt, map a processed *.fastq file using Bowtie, convert mapped reads to *.bed files using Samtools and Bedtools, and count the occurance of each Bacteriodes fragilis str NCTC 9343 genome position anywhere in a mapped read and as the 3' end of a mapped read using Bedtools. It further contains *ebwt files to assist with Bowtie mapping, *genome file to be used with Bedtools, a *.fasta file (useful to regenerate *ebwt files), and the completely processed *bed and *txt read files (generated by Snakemake and R) as references. In addition, a *.pdb file is included and represents the predicted interaction between UpeY and UpaZ.

Landick, Robert↗
DOE OSTI2024

Parallax-corrected VISST-derived pixel-level products from satellite GOES-16

The NASA Langley group led by William Smith produced GOES-16 satellite cloud retrievals over an approximate 10 by 10 degree region over the CACTI field campaign location. These retrievals are described here: https://www.arm.gov/capabilities/vaps/visst and are available for download here . They use algorithms historically called VISST that are now referred to as SatCORPS. More information can be found in Trepte et al. (2019), Minnis et al. (2021), and Yost et al. (2021). If using this dataset, please cite these references, the CACTI VISST dataset DOI found at the download link above, and this dataset’s DOI. The CACTI VISST pixel-level retrievals are on a 2 km spatial grid and available every 15 minutes (every 10 minutes late in the campaign), producing 21,765 files for the entire field campaign between October 2018 and April 2019. They are not corrected for parallax error, which is an offset in the actual geographical location of a cloud above the surface due to the satellite viewing the cloud partly from the side off nadir. This dataset applies a correction for parallax using the location relative to the satellite and the retrieved cloud top height above the surface, which allows the dataset to be geo-located with surface-based observations. The parallax correction for each location depends on the longitude, latitude and cloud top height above ground level (AGL) for that longitude and latitude in the original VISST files. The cloud top height AGL requires first computing the surface elevation at each VISST grid point. Data from the Advanced Spaceborne Thermal Emission and Reflection (ASTER) Global Digital Elevation Map Version 3 at 30-m resolution is projected onto the VISST grid using conservative coarsening (conserving surface elevation) in the xESMF Python package. The surface elevation is then subtracted from the VISST-retrieved cloud top height above mean sea level. These cloud top heights AGL are then combined with longitude and latitude to estimate the latitude and longitude corrections. Due to variability in cloud top height, the parallax shifts produce an irregular grid of values since higher cloud tops are shifted further than lower cloud tops. A ball tree-based neighbor search with Haversine distance is performed using the Python-based scikit-learn library to find the nearest VISST grid point to each parallax correction-shifted point. The data value of the shifted point is then assigned to that VISST grid point. In this manner, the irregular geographical shifts to correct for parallax are projected back to the rectilinear VISST grid. Because relatively higher clouds should obscure lower clouds, the variable values for the highest cloud top are preferentially chosen if two or more values are assigned to a grid point. The parallax correction should be viewed as an improved but still imperfect estimation of the cloud top locations, largely because the cloud top height is an imperfect retrieval. Please see the attached README document for further information. Users are encouraged to contact the authors with any additional questions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

A multi-scale time-series dataset of anthropogenic heat from buildings in Los Angeles County

The dataset contains hourly Anthropogenic heat (AH) from buildings in Los Angeles County, based on weather data from 2018. The hourly AH is aggregated at three spatial resolutions: 450m x 450m grid, 12km x 12km grid, and census tract. The AH is broken down into three components: building envelope surface convection, heating, ventilation, and air conditioning (HVAC) system heat release, and zone exfiltration and exhaust air heat loss. The dataset is created with the physics-based EnergyPlus building energy models to calculate individual buildings' AH considering WRF-UCM simulated microclimate conditions. Please refer to the paper "A multi-scale time-series dataset of anthropogenic heat from buildings in Los Angeles County" for more information about the data generation workflow and the data validation procedure. The data set contains two folders: the "output_data" folder holds the simulation results (EP_output and EP_output_csv), building metadata (building_metadata.geojson and building_metadata.csv), aggregated heat emission and energy consumption time-series data (hourly_heat_energy), and geographical data (geo_data) associated with the GEOID referenced in heat and energy consumption data. The "input_data" folder contains the raw data used to generate files in the "output_data" folder as well as data sets used in the validation. The code repository (https://github.com/IMMM-SFA/xu_etal_2022_sdata) holds the processing scripts for data curation, validation, and visualization.

Energy↗