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At least 1,315 records · Page 73

TRACER Overview 200220 [Slides]

The Atmospheric Radiation Measurement (ARM) User Facility is a U.S. Department of Energy Office of Science asset to be used by scientists to further our scientific knowledge about the atmosphere. The DOE ARM program has maintained facilities for use by the scientific community for 25 years. Data is freely available at www.arm.gov. The ARM science objective is to provide a detailed and accurate description of the Earth’s atmosphere to resolve uncertainties in earth system models. This report provides information on TRACER: TRacking Aerosol Convection Interations Experiment.

54 ENVIRONMENTAL SCIENCES↗

Integrating multimodal data through interpretable heterogeneous ensembles

Motivation: Integrating multimodal data represents an effective approach to predicting biomedical characteristics, such as protein functions and disease outcomes. However, existing data integration approaches do not sufficiently address the heterogeneous semantics of multimodal data. In particular, early and intermediate approaches that rely on a uniform integrated representation reinforce the consensus among the modalities but may lose exclusive local information. The alternative late integration approach that can address this challenge has not been systematically studied for biomedical problems. Results: We propose Ensemble Integration (EI) as a novel systematic implementation of the late integration approach. EI infers local predictive models from the individual data modalities using appropriate algorithms and uses heterogeneous ensemble algorithms to integrate these local models into a global predictive model. We also propose a novel interpretation method for EI models. We tested EI on the problems of predicting protein function from multimodal STRING data and mortality due to coronavirus disease 2019 (COVID-19) from multimodal data in electronic health records. We found that EI accomplished its goal of producing significantly more accurate predictions than each individual modality. It also performed better than several established early integration methods for each of these problems. The interpretation of a representative EI model for COVID-19 mortality prediction identified several disease-relevant features, such as laboratory test (blood urea nitrogen and calcium) and vital sign measurements (minimum oxygen saturation) and demographics (age). These results demonstrated the effectiveness of the EI framework for biomedical data integration and predictive modeling.

59 BASIC BIOLOGICAL SCIENCES↗

CheKiPEUQ Intro 1: Bayesian Parameter Estimation Considering Uncertainty or Error from both Experiments and Theory**

A common goal is extraction of physico-chemical parameter values such as pre-exponentials and activation energies from experiment. Ever increasing knowledge from experiments and computations is enabling semi-quantitative prior predictions of such values. When prior knowledge of physically realistic ranges is available, a method named Bayesian parameter estimation (BPE) enables more physically realistic parameter estimation relative to unsophisticated fitting by seeking the most probable value when considering together the uncertainties from prior knowledge, experimental data, and approximations in the model. An impediment to widespread use of BPE is a lack of understanding, training, and user-friendly software. Along with this invited publication, a general software package for BPE is being released that is user-friendly and that does not require understanding of the math behind the methodology. Overall, two previously unpublished catalysis science examples are provided along with considerations and guidelines for successful application of BPE. Following this work, BPE can become more widespread to enable extraction of physically meaningful parameter values.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Combustion machine learning: Principles, progress and prospects

Progress in combustion science and engineering has led to the generation of large amounts of data from large-scale simulations, high-resolution experiments, and sensors. This corpus of data offers enormous opportunities for extracting new knowledge and insights—if harnessed effectively. Machine learning (ML) techniques have demonstrated remarkable success in data analytics, thus offering a new paradigm for data-intense analyses and scientific investigations through combustion machine learning (CombML). While data-driven methods are utilized in various combustion areas, recent advances in algorithmic developments, the accessibility of open-source software libraries, the availability of computational resources, and the abundance of data have together rendered ML techniques ubiquitous in scientific analysis and engineering. This article examines ML techniques for applications in combustion science and engineering. Starting with a review of sources of data, data-driven techniques, and concepts, we examine supervised, unsupervised, and semi-supervised ML methods. Various combustion examples are considered to illustrate and to evaluate these methods. Next, we review past and recent applications of ML approaches to problems in combustion, spanning fundamental combustion investigations, propulsion and energy-conversion systems, and fire and explosion hazards. Challenges unique to CombML are discussed and further opportunities are identified, focusing on interpretability, uncertainty quantification, robustness, consistency, creation and curation of benchmark data, and the augmentation of ML methods with prior combustion-domain knowledge.

33 ADVANCED PROPULSION SYSTEMS↗

Application of Systems Engineering Principles and Techniques in Biological Big Data Analytics: A Review

In the past few decades, we have witnessed tremendous advancements in biology, life sciences and healthcare. These advancements are due in no small part to the big data made available by various high-throughput technologies, the ever-advancing computing power, and the algorithmic advancements in machine learning. Specifically, big data analytics such as statistical and machine learning has become an essential tool in these rapidly developing fields. As a result, the subject has drawn increased attention and many review papers have been published in just the past few years on the subject. Different from all existing reviews, this work focuses on the application of systems, engineering principles and techniques in addressing some of the common challenges in big data analytics for biological, biomedical and healthcare applications. Specifically, this review focuses on the following three key areas in biological big data analytics where systems engineering principles and techniques have been playing important roles: the principle of parsimony in addressing overfitting, the dynamic analysis of biological data, and the role of domain knowledge in biological data analytics.

dynamic analysis↗

The impact of multi-sensor land data assimilation on river discharge estimation

River discharge is one of the most critical renewable water resources. Accurately estimating river discharge with land surface models (LSMs) remains challenging due to the difficulty in estimating land water storages such as snow, soil moisture, and groundwater. While data assimilation (DA) ingesting optical, microwave, and gravity measurements from space can help constrain theses storage states, its impacts on runoff and eventually river discharge are not fully understood. In this study, by taking advantage of recently published land DA results that jointly assimilate eight different combinations of observations from the Moderate Resolution Imaging Spectroradiometer (MODIS), Gravity Recovery and Climate Experiment (GRACE), and Advanced Microwave Scanning Radiometer for EOS (AMSR-E), we quantify to what degree multi-sensor land DA improves the river discharge simulation skills over 40 global river basins, and investigate the complementary strengths of different satellite measurements on river discharge. To be more specific, river discharge is updated by feeding gridded runoff from the eight multi-sensor DA simulations into a vector-based river routing model named the Routing Application for Parallel computatIon of Discharge (RAPID). Our modeling results, including 7-year simulations at 177,458 river reaches globally, are used to study the seasonal to interannual variability of river discharge. It is found that assimilating GRACE has the greatest impact on global runoff patterns, leading to the most pronounced improvements in spatial river discharge in the middle and high latitudes with the R 2 increased by 0.16. The seasonal variation of spatial discharge is most skillful during the boreal summer. However, our evaluation also shows model and DA still struggle to generate reasonable variability and averaged discharge over permafrost regions. Finally, by assessing how different satellites add value to discharge forecasts, this study paves the way for more advanced multi-sensor satellite data assimilation to predict the terrestrial hydrological cycle.

54 ENVIRONMENTAL SCIENCES↗

express: Extensible, high-level workflows for swifter ab initio materials modeling

In this work, we introduce an open-source Julia project, express, an extensible, lightweight, high-throughput, high-level workflow framework that aims to automate ab initio calculations for the materials science community. express is shipped with well-tested workflow templates, including structure optimization, equation of state (EOS) fitting, phonon spectrum (lattice dynamics) calculation, and thermodynamic property calculation in the framework of the quasi-harmonic approximation (QHA). It is designed to be highly modularized so that its components can be reused across various occasions, and customized workflows can be built on top of that. Users can also track the status of workflows in real-time, and rerun failed jobs thanks to the data lineage feature express provides. Finally, two working examples, i.e., all workflows applied to lime and akimotoite, are also presented in the code and this paper.

36 MATERIALS SCIENCE↗

Toward data assimilation of ship-induced aerosol–cloud interactions

Satellite imagery can detect temporary cloud trails or ship tracks formed from aerosols emitted from large ships traversing our oceans, a phenomenon that global climate models cannot directly reproduce. Ship tracks are observable examples of marine cloud brightening, a potential solar climate intervention that shows promise in helping combat climate change. In this paper, we demonstrate a simulation-based approach in learning the behavior of ship tracks based upon a novel stochastic emulation mechanism. Our method uses wind fields to determine the movement of aerosol–cloud tracks and uses a stochastic partial differential equation (SPDE) to model their persistence behavior. This SPDE incorporates both a drift and diffusion term which describes the movement of aerosol particles via wind and their diffusivity through the atmosphere, respectively. We first present our proposed approach with examples using simulated wind fields and ship paths. We then successfully demonstrate our tool by applying the approximate Bayesian computation method-sequential Monte Carlo for data assimilation.

54 ENVIRONMENTAL SCIENCES↗

A Multi-Instrument Cloud Condensation Nuclei Spectrum Product (Final Technical Report)

A wealth of observational data exists on the characteristics of atmospheric particulate matter, over multiple years, at the DOE ARM Southern Great Plains (SGP) Central Facility site. This site is located in a region of the country that frequently experiences weather extremes, and that is removed from many local sources of pollution but is affected by transported smoke, dust, and urban emissions. The relationships between particulate matter, cloud formation and evolution, and precipitation are therefore of strong interest, and are being explored via modeling on a variety of scales. These models require as input detailed information on the characteristics of particles capable of serving as the nuclei for cloud formation. Sufficient data exist to be able to put together a picture of the nature of the total aerosol and the cloud condensation nuclei (CCN) subset, and their variability, through merged data products. This study was aimed at exploiting the multiple measurement types at SGP to develop the first such multi-year estimates. Further, the resulting data were analyzed to understand temporal patterns ranging from hourly to seasonal, thereby gaining insights into the particle sources affecting the atmosphere in this region. DOE-funded datasets that were analyzed in this study include total particle number concentrations, submicron aerosol scattering coefficients, dry aerosol size distributions, and more recently, time-resolved submicron aerosol chemical composition. Data are also available for the number concentrations of particles that are activated in a cloud condensation nucleus instrument at a series of setpoint supersaturations, providing direct observations of the number concentrations of “CCN”. This variable is the quantity that is generally desired for inclusion in numerical models that seek to represent and predict the impacts of varying aerosol characteristics on the formation and microphysical properties of clouds. One limitation of the use of direct CCN observations is that they are not available for supersaturations larger than about 1%, which is insufficient for deep convection and may be insufficient even for shallow convection, depending on the nature of the available CCN and the dynamics of the cloud. We developed a data-based approach to representing the full aerosol size spectrum with size-dependent hygroscopicity, and used this to extrapolate CCN spectra beyond the limited measurements. Five years of SGP aerosol data (2009 -2013) were analyzed. As a side product of our work, we identified and communicated several previously-unflagged data quality issues. The resulting merged aerosol distributions, along with fits for seasonal averages, were published and submitted to the ARM archive as a special value-added product (VAP; submitted as a PI product). CCN spectra were computed for the same data period and will similarly be published and submitted to the archive for use by the community. We also note that our methodologies and findings have been discussed at several Joint ARM User Facility/Atmospheric System Research (ASR) Principal Investigators Meetings and that recent ARM/ASR aerosol data reporting strategies have included similar ideas for data merging, indicating that this work has had a lasting impact on ARM aerosol data acquisition and reporting. The proposed work advances the science of the interactions of aerosols, clouds and precipitation, with direct application to improve representation of such interactions for clouds in regional and global climate models. The archived data will continue to serve research studies in the future.

54 ENVIRONMENTAL SCIENCES↗

Label-based Virtual Directories In dCache

Traditional filesystems organize data in directories. These directories are typically a collection of files whose grouping is based on a single criterion, e.g., the starting date of an experiment, experiment name, beamline ID, measurement device, or instrument. However, each file in a directory can belong to several logical groups, such as a special event type, experiment condition, or a part of a selected dataset. dCache is a storage system developed to store large amounts of scientific data, used by many HEP and Photon Science experiments. With recent developments in dCache, we have introduced a concept of file tagging, which dynamically groups files with the same label into virtual directories. The file labels can be added, removed, renamed, and deleted through the admin interface or via REST API. The files in virtual directories are exposed through all protocols supported by dCache. This contribution will describe the details of the implementation for file tagging in dCache and present our future development plans on automatic metadata extractions, a feature that will significantly simplify data management. Additionally, we are exploring the future use of virtual directories as a way to translate scientific data catalogs into filesystem views for direct data analysis.

Sahakyan, Marina [DESY]↗

Model, data, and code for paper "Modeling of streamflow in a 30-kilometer-long reach spanning 5 years using OpenFOAM 5.x"

The data package includes data, model, and code that support the analyses and conclusions in the paper titled “modeling of streamflow in a 30-kilometer-long reach spanning 5 years using OpenFOAM 5.x”. The primary goal of this paper is to demonstrate that key streamflow properties such as water depth, flow velocity, and dynamic pressure in a natural river at 30-kilometer scale over 5 years can be reliably and efficiently modeled using the computational framework presented in this paper. To support the paper, various data types from remote sensing, field observations, and computational models are used. Specific details are described as follows. Firstly, the river bathymetry data was obtained from a Light Detection and Ranging (LiDAR) survey. This data is then converted to a triangulated surface format, STL, for mesh generation in OpenFOAM. The STL data can be found in Model_Setups/BaseCase_2013To2015/constant/triSurface. The OpenFOAM mesh generated using this STL file can be found in constant/polyMesh. Other model setups, boundary and initial conditions can be found in /system and /0.org under folder BaseCase_2013To2015. A similar data structure can also be found in BaseCase_2018To2019 for the simulations during 2018 and 2019. Secondly, the OpenFOAM simulations need the upstream discharge and water depth information at the upstream boundary to drive the model. These data are generated from a one-dimensional hydraulic model and the data can be found under the folder Model_Setups /1D model Mass1 data. The mass1_65.csv and mass1_191.csv files include the results of the 1D model at the model inlet and outlet, respectively. The Matlab source code Mass1ToOFBC20182019.m is used to convert these data into OpenFOAM boundary condition setups.With the above OpenFOAM model, it can generate data for water surface elevation, flow velocity, and dynamic pressure. In this paper, the water surface elevation was measured at 7 locations during different periods between 2011 and 2019. The exact survey locations (see Fig1_SurveyLocations.txt) can be found in folder Fig_1. The variation of water stage over time at the 7 locations can be found in folder /Observation_WSE. The data type include .txt, .csv, .xlsx, and .mat. The .mat data can be loaded by Matlab.We also measured the flow velocities at 12 cross-sections along the river. At each cross-section, we recorded the x, y locations, depth, three velocity components u,v,w. These data are saved to a Matlab format which can be found under folder /Observation_Velocity and /Fig_1. The relative locations of velocity survey locations to the river bathymetry can be found in Figure 1c.The water stage data at the 7 locations from OpenFOAM, 1D, and 2D hydraulic models are also provided to evaluate the long-term performance of 3D models vs 1D/2D models. The water stage data for the 7 locations from OpenFOAM have been saved to .mat format and can be found in /OpenFOAM_WSE. The water stage data from the 1D model are saved in .csv format and can be found in /Mass1_WSE. The water stage from the 2D model is saved as .mat format and can be found in / Mass2_WSEIn addition, the OpenFOAM model outputs the information of hydrostatic and hydrodynamic pressure. They are saved as .mat format under folder /Fig_11/2013_1. As the files are too large, we only uploaded the data for January 2013. The area of different ratio of dynamic pressure to static pressure for all simulation range, i.e., 2013-2015, are saved to .mat format. They can be found in /Fig_11/PA. Further, the data of wall clock time versus the solution time of the OpenFOAM modeling are also saved to .mat format under folder /Fig_13/LogsMat. In summary, the data package contains seven data types, including .txt, .csv, .xlsx, .dat, .stl, .m, and .mat. The former 4 types can be directly open using a text editor or Microsoft Office. The .mat format needs to be read by Matlab. The Matlab source code .m files need to be run with Matlab. The OpenFOAM setups can be visualized in ParaView. The .stl file can be opened in ParaView or Blender. The data in subfolders Fig_1 to Fig_10 and Fig_12 are copied from the aforementioned data folders to generate specific figures for the paper. A readME.txt file is included in each subfolder to further describe how the data in each folder are generated and used to support the paper.Please use the data package's DOI to cite the data package. Please contact yunxiang.chen@pnnl.gov if you need more data related to the paper.

54 ENVIRONMENTAL SCIENCES↗

1000 Soils Pilot Dataset, version 8, May 2025

This record hosts data generated by the 1000 Soils Pilot. Data will be updated as more become available. Please see the most recent data upload for current data. A beta visualization tool is available for some data types at https://shinyproxy.emsl.pnnl.gov/app/1000soils. Please submit any suggestions or comments through the 'contact' tab. We are actively working to improve visualizations and value all feedback. Data completed include: Geochemistry, texture, respiration, and enzyme activities FTICR-MS organic matter chemistry Microbial biomass C and N TOC/TDN of water-extractable OM X-ray computed tomography (derived metrics available here, raw data available upon request) Metagenomes; a variety of data formats are available upon request Soil hydraulic properties Data in progress: LC-MS/MS in development, timeline TBD, inquire for status 1000S_processed_BGC_summary.csv contains all available biogeochemical data; microbial biomass C and N; and TOC/TDN of water-extractable OM; and 1000S_Tomography.xslx contains a summary of data generated via X-ray computed tomography. icr_v2_corems2.csv contains FTICR-MS data processed by CoreMS version 2. These data are merged by formula across instrument runs to enable cross-sample comparisons. Technical replicates are merged by retaining peaks present in 2 out of 3 replicates. 1000Soils_Metadata_Site_Mastersheet_v1.csv contains site information. Soil Hydraulics_corrected_02042025.xlsx contains soil hydraulics information. Readme File_v4.xlsx is the readme file. Please contact the MONet project (monet.emsl@pnnl.gov) or Emily Graham (emily.graham@pnnl.gov) with questions. The following file and all raw data are available upon request: icr_by_mass_for_single_sample_analysis_only.csv contains FTICR-MS data processed by CoreMS and is intended for usage in the calculation of biochemical transformations within samples only. These data are not acceptable for cross-sample comparison of masses because they are from multiple instrument runs. For more information, please see: https://www.emsl.pnnl.gov/monet and https://sc-data.emsl.pnnl.gov/monet Acknowledgment: Soil data were provided by the Molecular Observation Network (MONet) at the Environmental Molecular Sciences Laboratory (https://ror.org/04rc0xn13), a DOE Office of Science user facility sponsored by the Biological and Environmental Research program under Contract No. DE-AC05-76RL01830. The work (proposal: 10.46936/10.25585/60008970) conducted by the U.S. Department of Energy, Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science user facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. The Molecular Observation Network (MONet) database is an open, FAIR, and publicly available compilation of the molecular and microstructural properties of soil. Data in the MONet open science database can be found at https://sc-data.emsl.pnnl.gov/.

biogeochemistry↗

The Colorado East River Community Observatory Data Collection

Abstract The U.S. Department of Energy's (DOE) Colorado East River Community Observatory (ER) in the Upper Colorado River Basin was established in 2015 as a representative mountainous, snow‐dominated watershed to study hydrobiogeochemical responses to hydrological perturbations in headwater systems. The ER is characterized by steep elevation, geologic, hydrologic and vegetation gradients along floodplain, montane, subalpine, and alpine life zones, which makes it an ideal location for researchers to understand how different mountain subsystems contribute to overall watershed behaviour. The ER has both long‐term and spatially‐extensive observations and experimental campaigns carried out by the Watershed Function Scientific Focus Area (SFA), led by Lawrence Berkeley National Laboratory, and researchers from over 30 organizations who conduct cross‐disciplinary process‐based investigations and modelling of watershed behaviour. The heterogeneous data generated at the ER include hydrological, genomic, biogeochemical, climate, vegetation, geological, and remote sensing data, which combined with model inputs and outputs comprise a collection of datasets and value‐added products within a mountainous watershed that span multiple spatiotemporal scales, compartments, and life zones. Within 5 years of collection, these datasets have revealed insights into numerous aspects of watershed function such as factors influencing snow accumulation and melt timing, water balance partitioning, and impacts of floodplain biogeochemistry and hillslope ecohydrology on riverine geochemical exports. Data generated by the SFA are managed and curated through its Data Management Framework. The SFA has an open data policy, and over 70 ER datasets are publicly available through relevant data repositories. A public interactive map of data collection sites run by the SFA is available to inform the broader community about SFA field activities. Here, we describe the ER and the SFA measurement network, present the public data collection generated by the SFA and partner institutions, and highlight the value of collecting multidisciplinary multiscale measurements in representative catchment observatories.

54 ENVIRONMENTAL SCIENCES↗

TSDC: Transportation Secure Data Center: Real-World Data for Planning, Modeling, and Analysis

The Transportation Secure Data Center is a centralized repository for high-resolution transportation data from hundreds of travel and transit surveys and studies. It makes vital transportation data broadly available to users while preserving the privacy of survey participants. It houses surveys and studies conducted by state departments of transportation, metropolitan planning organizations, transit agencies, cities, and other public agencies. Meanwhile, the Livewire Data Platform empowers research, industry, and academic partners to easily and securely preserve, maintain, share, discover, and gain access to transportation and mobility data. Livewire accommodates a range of datasets, including behavioral, experimental, model, analytical, and raw data at the vehicle, traveler, and system levels. Datasets support mobility research and planning spanning urban science, connected and automated vehicles, fueling and charging infrastructure, mobility decision science, multimodal transportation, vehicle efficiency, and more.

33 ADVANCED PROPULSION SYSTEMS↗

Kinetic Measurements in Heterogeneous Catalysis

This contribution is about the experimental determination of the rate of a heterogeneous catalytic reaction and the analysis of kinetic data. In this case, the reaction rate can be defined as the frequency at which the closed sequence of elementary steps transforming reactants into products is occurring. However, the rate of chemical reaction is not directly observed; rather, one records the rate of substance change. The rate of chemical reaction is calculated based on the rate of substance change and assumed stoichiometry of the reaction. In order to make this an intensive quantity (i.e., independent of the volume in which the reaction is performed, this frequency is divided by the latter or by a quantity proportional to the latter). As the focus of what follows is on heterogeneously catalyzed reactions this can be the catalyst mass, the catalyst surface area or the total number of active sites present in the reaction volume confined by the walls of a chemical reactor. For example, the rate may be reported as one of the following: Net rate of consumption/production of component i mol m-3 s-1 Net specific rate of consumption/production of component i mol kg-1 s-1 Rate of substance change (per unit volume of catalyst) mol m-3 s-1 Specific reaction rate (per unit mass of catalyst) mol kg-1 s-1 Net rate of consumption/production of component i mol m-2 s-1 The turnover frequency (TOF) is a characteristic originally introduced by Boudart [1] is expressed as TOF=R/G_tot , where R is the steady-state rate of reactant consumption or product generation and G_totis the total areal density of active sites [mol m-2]. The latter is typically taken from experimental chemisorption data obtained at low temperature. The advancement of a chemical reaction leads to changes in the amounts of reactants and products which, for a stoichiometric single reaction, are connected by the stoichiometric coefficients. In many cases, for the sake of simplicity, we will assume that the investigated reaction proceeds according to a single reaction pathway, so that the net production rate of a reaction component is directly proportional to the reaction rate and that the latter equals the net production rate of any of the involved components when divided by the appropriate stoichiometric coefficient. For complex stoichiometric reactions the net production rates of the involved components are linear combinations of the reaction rates. Different goals for kinetic measurements can be formulated: Catalyst testing, i.e., obtaining the kinetic dependences for the development and discrimination of efficient catalytic materials. Precise kinetic characterization of active materials via high-throughput screening is a part of such activity. Detailed kinetics, i.e., revealing the detailed mechanism of complex catalytic reaction via systematic kinetic studies, both steady-state and non-steady-state Industrial kinetics, i.e., obtaining data and relationships for describing and predicting the behaviour of catalytic reactors and processes at industrial scale Finally, mathematical modeling and analysis where kinetic measurements provide data for understanding complex kinetic phenomena, e.g., oscillations, non-linear self-organization, etc.

36 MATERIALS SCIENCE↗