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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Baltimore Ecosystem Study: Soil atmosphere fluxes of carbon dioxide, nitrous oxide and methane, 1998 - ongoing

The Baltimore Ecosystem Study (BES) established a network of long-term permanent biogeochemical study plots in 1998. These plots provide long-term data on vegetation, soil and hydrologic processes in the key ecosystem types within the urban ecosystem. The network of study plots includes forest plots (upland and riparian), chosen to represent the range of forest conditions in the area and grass plots (to represent home lawns). Plots are instrumented with lysimeters (drainage and tension) to sample soil solution chemistry, time domain reflectometry probes to measure soil moisture, dataloggers to measure and record soil temperature, and trace gas flux chambers to measure the flux of carbon dioxide, nitrous oxide and methane from soil to the atmosphere. Measurements of in situ nitrogen mineralization, nitrification and denitrification were made at approximately monthly intervals from Fall 1998 - Fall 2000. Detailed vegetation characterization (all layers) was done in summer 1998 and 2015. Data from these plots has been published in Groffman et al. (2006, 2009), Groffman and Pouyat (2009), Savva et al. (2010), Costa and Groffman (2013), Duncan et al. (2013), Waters et al. (2014), Ni and Groffman (2018), Templeton et al. (2019). Literature Cited Costa, K.H. and P.M. Groffman. 2013. Factors regulating net methane flux in urban forests and grasslands. Soil Science Society of America Journal 77:850 - 855. Duncan, J. M., L. E. Band, and P. M. Groffman. 2013. Towards closing the watershed nitrogen budget: Spatial and temporal scaling of denitrification. Journal of Geophysical Research Biogeosciences 118:1-5; DOI: 10.1002/jgrg.20090 Groffman PM, Pouyat RV, Cadenasso ML, Zipperer WC, Szlavecz K, Yesilonis IC,. Band LE and Brush GS. 2006. Land use context and natural soil controls on plant community composition and soil nitrogen and carbon dynamics in urban and rural forests. Forest Ecology and Management 236:177-192. Groffman, P.M., C.O. Williams, R.V. Pouyat, L.E. Band and I.C. Yesilonis. 2009. Nitrate leaching and nitrous oxide flux in urban forests and grasslands. Journal of Environmental Quality 38:1848-1860. Groffman, P.M. and R.V. Pouyat. 2009. Methane uptake in urban forests and lawns. Environmental Science and Technology 43:5229-5235. DOI: 10.1021/es803720h. Ni, X. and P.M. Groffman. 2018. Declines in methane uptake in forest soils. Proceedings of the National Academies of Science of the United States of America 115:8587-8590. Savva, Y., K. Szlavecz, R. V. Pouyat, P. M. Groffman, and G. Heisler. 2010. Effects of land use and vegetation cover on soil temperature in an urban ecosystem. Soil Science Society of America Journal 74:469-480. Templeton, L., M.L. Cadenasso, J. Sullivan, M. Neel and P.M. Groffman. 2019. Changes in vegetation structure and composition of urban and rural forest patches in Baltimore from 1998 to 2015. Forest Ecology and Management. In press. Waters, E.R., J.L. Morse, N.D. Bettez and P.M. Groffman. 2014. Differential carbon and nitrogen controls of denitrification in riparian zones and streams along an urban to exurban gradient. Journal of Environmental Quality 43:955–963.

Groffman, Peter M↗
DOE OSTI2021

KS4A-Omics1.0_FspDS682

Soil fungi facilitate the translocation of inorganic nutrients from soil minerals to other microorganisms and plants. This ability is particularly advantageous in impoverished soils, because fungal mycelial networks can bridge otherwise spatially disconnected and inaccessible nutrient hotspots. However, the molecular mechanisms underlying fungal mineral weathering and transport through soil remains poorly understood. Here, we addressed this knowledge gap by directly visualizing nutrient acquisition and transport through fungal hyphae in a mineral doped soil micromodel using a multimodal imaging approach. Here, we observed how a representative of common saprotrophic soil fungi, Fusarium sp. DS 682, exhibited a mechanosensory response (thigmotropism) around obstacles and through pore spaces (~12 μm) in the presence of minerals.This study establishes the significance of fungal biology and nutrient translocation mechanisms in maintaining fungal growth under water and nutrient limitations in a soil-like microenvironment, using a high-throughput multi-omic analysis approach. Data package KS4A-Omics.1.0_FspDS682 (Publication: Fungal Mineral Weathering Mechanisms Revealed Through Direct Molecular Visualization) contents reported here are the first version (1.0) and contain pre- and post-processed data using high throughput data capture technologies for multi-omic analysis and integration, this data package contains raw and post-processed experimental data for X-Ray Absorption Near Edge Structure Spectroscopy (XANES/XRF), Optical Microscopy, Proteomics, Scanning Electron Microscope (SEM), Time-of-Flight Secondary Ion Mass Spectroscopy (ToF-SIMS), X-Ray Diffraction Spectroscopy (XRD) files, and X- Ray Photoelectron Spectroscopy (XPS) using EMSL capabilities. This data package DOI contains a comprehensive collection of high-throughput multi-omics data and process metadata catalog. Support files include additional data download contents “Read Me” with dataset descriptor information and data source method application ontologies (see data dictionary section). Reported data download content is structured for compliance with reported guidelines provided by community standard initiatives and publisher stakeholder policies supporting FAIR data principles.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Ridgelines: Department of Interior Definition

This dataset represents ridgelines as defined by the Department of Interior (DOI): "Areas within 660 feet of the top of the ridgeline, where a ridgeline has at least 150 feet of vertical elevation gain with a minimum average slope of 10 percent between the ridgeline and the base." The dataset was created using the Geomorphons package from the University of Guelph, which can be found here: Geomorphons Package, and the 3DEP 1/3 arc-second digital elevation model. A TIF data file and a PNG map of the data are provided.

Array↗
DOE OSTI2021

Stream discharge and water quality data for East Fork Poplar Creek beginning 2012

This data note describes 15-min discharge and in situ water quality data at two locations along East Fork Poplar Creek in east Tennessee, USA. Data records include temperature, gauge height, water surface elevation above mean sea level, and volumetric discharge. Water quality measurements include temperature, specific conductance, pH, dissolved oxygen (percent saturation and concentration), turbidity, and less extensive fDOM data at one site. The data records begin in 2012 at one site and 2015 at the second site; monitoring at both sites is ongoing (as of 2021). The goal of this data collection is to improve understanding of watershed functions, hydrologic dynamics, and material flux. The data will contribute to site conceptual and numerical models, exposure and risk evaluation, remediation selection and design, and performance monitoring. The data are publicly available and can be accessed via unique url or DOI.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Genarris 2.0: A Random Structure Generator for Molecular Crystals

Genarris is an open source Python package for generating random molecular crystal structures with physical constraints for seeding crystal structure prediction algorithms and training machine learning models. Here we present a new version of the code, containing several major improvements. A MPI-based parallelization scheme has been implemented, which facilitates the seamless sequential execution of user-defined workflows. A new method for estimating the unit cell volume based on the single molecule structure has been developed using a machine-learned model trained on experimental structures. A new algorithm has been implemented for generating crystal structures with molecules occupying special Wyckoff positions. A new hierarchical structure check procedure has been developed to detect unphysical close contacts efficiently and accurately. New intermolecular distance settings have been implemented for strong hydrogen bonds. To demonstrate these new features, we study two specific cases: benzene and glycine. Genarris finds the experimental structures of the two polymorphs of benzene and the three polymorphs of glycine. Program summary Program Title: Genarris 2.0 Program Files doi: http://dx.doi.org/10.17632/grx6mz4pjn.1 Licensing provisions: BSD-3 Clause Programming language: Python, C External routines/libraries: Spglib, ASE, pymatgen, SciPy, mpi4py, scikit-learn, PyTorch, FHI-aims. Nature of problem: Molecular crystal structure prediction. Solution method: Genarris 2.0 generates molecular crystal structures over the 230 space groups, on general and special Wyckoff positions, using physical constraints. Down-sampling of the generated structures may be performed subsequently, based on molecular crystal packing descriptors and an unsupervised machine learning algorithm. Lastly, ab initio structure relaxation may be performed for the final pool. Depending on the user-defined workflow implemented, Genarris may be used to generate diverse molecular crystal datasets to seed evolutionary algorithms or to train machine learning algorithms or as a standalone crystal structure prediction method. Restrictions: For crystal structure generation, the molecule of interest must be semi-rigid with no bond rotational degrees of freedom. Unusual features: Genarris 2.0 is a highly distributed program, making use of MPI for Python parallelization. The user has the ability to design and implement workflows by executing a user-defined list of procedures. Genarris 2.0 offers new features including a machine learning model for estimating the molecular volume in the solid state from the single molecule structure, structure generation in special Wyckoff positions of space groups, hierarchical structure checks including rigorous treatment of non-orthogonal structures, and clustering and down-selection workflows combining first principles simulations with machine learning. (C) 2020 Elsevier B.V. All rights reserved.

Crystal structure prediction↗
DOE OSTI2022

PDFDataExtractor: A Tool for Reading Scientific Text and Interpreting Metadata from the Typeset Literature in the Portable Document Format

The layout of portable document format (PDF) files is constant to any screen, and the metadata therein are latent, compared to mark-up languages such as HTML and XML. No semantic tags are usually provided, and a PDF file is not designed to be edited or its data interpreted by software. However, data held in PDF files need to be extracted in order to comply with opensource data requirements that are now government-regulated. In the chemical domain, related chemical and property data also need to be found, and their correlations need to be exploited to enable data science in areas such as data-driven materials discovery. Such relationships may be realized using text-mining software such as the “chemistry-aware” natural-language-processing tool, ChemDataExtractor; however, this tool has limited data-extraction capabilities from PDF files. This study presents the PDFDataExtractor tool, which can act as a plug-in to ChemDataExtractor. It outperforms other PDF-extraction tools for the chemical literature by coupling its functionalities to the chemical-named entityrecognition capabilities of ChemDataExtractor. The intrinsic PDF-reading abilities of ChemDataExtractor are much improved. The system features a template-based architecture. This enables semantic information to be extracted from the PDF files of scientific articles in order to reconstruct the logical structure of articles. While other existing PDF-extracting tools focus on quantity mining, this template-based system is more focused on quality mining on different layouts. PDFDataExtractor outputs information in JSON and plain text, including the metadata of a PDF file, such as paper title, authors, affiliation, email, abstract, keywords, journal, year, document object identifier (DOI), reference, and issue number. With a self-created evaluation article set, PDFDataExtractor achieved promising precision for all key assessed metadata areas of the document text.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

QuantumScents: Quantum-Mechanical Properties for 3.5k Olfactory Molecules

Quantitative structure–odor relationships are critically important for studies related to the function of olfaction. Current literature data sets contain expert-labeled molecules but lack feature data. This paper introduces QuantumScents, a quantum mechanics augmented derivative of the Leffingwell data set. QuantumScents contains 3.5k structurally and chemically diverse molecules ranging from 2 to 30 heavy atoms (CNOS) and their corresponding 3D coordinates, total PBE0 energy, molecular dipole moment, and per-atom Hirshfeld charges, dipoles, and ratios. The authors demonstrate that Hirshfeld charges and ratios contain sufficient information to perform molecular classification by training a Message Passing Neural Network with chemprop (Heid, E.; et al. ChemRxiv, 2023, DOI: 10.26434/chemrxiv-2023-3zcfl) to predict scent labels. Finally, the QuantumScents data set is freely available on Zenodo along with the authors’ code, example models, and data set generation workflow (https://zenodo.org/doi/10.5281/zenodo.8239853).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Ultrafast X-ray Spectroscopy of Intersystem Crossing in Hexafluoroacetylacetone: Chromophore Photophysics and Spectral Changes in the Face of Electron-Withdrawing Groups

Intersystem crossings between singlet and triplet states represent a crucial relaxation pathway in photochemical processes. Herein, we probe the intersystem crossing in hexafluoro-acetylacetone with ultrafast X-ray transient absorption spectroscopy at the carbon K-edge. In this study, we observe the excited state dynamics following excitation with 266 nm UV light to the 1 ππ* (S 2 ) state with element and site-specificity using a broadband soft X-ray pulse produced by high harmonic generation. These results are compared to X-ray spectra computed from orbital optimized density functional theory methods. It is found that the electron-withdrawing fluorine atoms decongest the X-ray absorption spectrum by enhancing separation between features originating from different carbon atoms. This facilitates the elucidation of structural and electronic dynamics at the chromophore. The evolution of the core-to-valence resonances at the carbon K-edge reveals an ultrafast population transfer between the 1 nπ* (S 1 ) and 3 ππ* (T 1 ) states on a 1.6 ± 0.4 ps time scale, which is similar to the 1.5 ps time scale earlier observed for acetylacetone [ J. Am. Chem. Soc. 2017, 139, 16576—16583, DOI: 10.1021/jacs.7b07532]. It therefore appears that terminal fluorination has little influence on the intersystem crossing rate of the acetylacetone chromophore. In addition, the significant role of hydrogen-bond opened and twisted rotational isomers is elucidated in the excited state dynamics by comparison of the experimental transient X-ray spectra with theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Colloidal Stability of PFSA-Ionomer Dispersions. Part I. Single-Ion Electrostatic Interaction Potential Energies

Charged colloidal particles neutralized by a single counterion are increasingly important for many emerging technologies. Attention here is paid specifically to hydrogen fuel cells and water electrolyzers whose catalyst layers are manufactured from a perfluorinated sulfonic acid polymer (PFSA) suspended in aqueous/alcohol solutions. Partially dissolved PFSA aggregates, known collectively as ionomers, are stabilized by the electrostatic repulsion of overlapping diffuse double layers consisting of only protons dissociated from the suspended polymer. We denote such double layers containing no added electrolyte as "single ion". Size-distribution predictions build upon interparticle interaction potential energies from the Derjaguin-Landau-Verwey-Overbeek (DLVO) formalism. However, when only a single counterion is present in solution, classical DLVO electrostatic potential energies no longer apply. Accordingly, here a new formulation is proposed to describe how single-counterion diffuse double layers interact in colloidal suspensions. Part II (Srivastav, H.; Weber, A. Z.; Radke, C. J. Langmuir 2024 DOI: 10.1021/acs.langmuir.3c03904) of this contribution uses the new single-ion interaction energies to predict aggregated size distributions and the resulting solution pH of PFSA in mixtures of n-propanol and water. A single-counterion diffuse layer cannot reach an electrically neutral concentration far from a charged particle. Consequently, nowhere in the dispersion is the solvent neutral, and the diffuse layer emanating from one particle always experiences the presence of other particles (or walls). Thus, in addition to an intervening interparticle repulsive force, a backside osmotic force is always present. With this new construction, we establish that single-ion repulsive pair interaction energies are much larger than those of classical DLVO electrostatic potentials. The proposed single-ion electrostatic pair potential governs dramatic new dispersion behavior, including dispersions that are stable at a low volume fraction but unstable at a high volume fraction and finite volume-fraction dispersions that are unstable with fine particles but stable with coarse particles. Finally, the proposed single-counterion electrostatic pair potential provides a general expression for predicting colloidal behavior for any charged particle dispersion in ionizing solvents with no added electrolyte.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Scaling of Electron Heating by Magnetization During Reconnection and Applications to Dipolarization Fronts and Super-Hot Solar Flares

Electron ring velocity space distributions have previously been seen in numerical simulations of magnetic reconnection exhausts and have been suggested to be caused by the magnetization of the electron outflow jet by the compressed reconnected magnetic fields (Shuster et al., 2014, https://doi. org/10.1002/2014GL060608). Here, we present a theory of the dependence of the major and minor radii of the ring distributions solely in terms of upstream (lobe) plasma conditions, thereby allowing a prediction of the associated temperature and temperature anisotropy of the rings in terms of upstream parameters. We test the validity of the prediction using 2.5-dimensional particle-in-cell (PIC) simulations with varying upstream plasma density and temperature, finding excellent agreement between the predicted and simulated values. We confirm the Shuster et al. suggestion for the cause of the ring distributions, and also find that the ring distributions are located in a region marked by a plateau, or shoulder, in the reconnected magnetic field profile. The predictions of the temperature are consistent with observed electron temperatures in dipolarization fronts, and may provide an explanation for the generation of plasma with temperatures in the 10s of MK in super-hot solar flares. A possible extension of the model to dayside reconnection is discussed. Since ring distributions are known to excite whistler waves, the present results should be useful for quantifying the generation of whistler waves in reconnection exhausts.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗