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Model Inputs, Outputs, and Scripts associated with: “Combined effects of stream hydrology and land use on basin-scale hyporheic zone denitrification in the Columbia River Basin”

This data package is associated with the publication “Combined effects of stream hydrology and land use on basin‐scale hyporheic zone denitrification in the Columbia River Basin”, published in Water Resource Research (Son et al.2022) available at https://doi.org/10.1029/2021WR031131. This data package includes the key model inputs/outputs of the river corridor model for the Columbia River Basin (CRB) and the model source codes used in the manuscript. The model is a carbon-nitrogen-coupled river corridor model (RCM), and the model is used to quantify hyporheic zone (HZ) denitrification at the NHDPLUS stream reach scales. The RCM used in this study combines empirical substrate models derived from observations and three microbially driven reactions, including two-step denitrification and aerobic respiration, are considered within the HZ. The key input data of the model are exchange flux, residence time, and stream solute (dissolved organic carbon (DOC), dissolved oxygen (DO), and nitrate concentrations). These inputs are constant over time and represent long-term averaged values. This study uses the RCM to explore the spatial patterns of HZ denitrification across reaches with different sizes and land use in the CRB. Our main objective is to use the RCM as a virtual reality model, and the machine-learning models as surrogates that encapsulate the complexities of the physics-based model while identifying the importance of different variables that are not evident in the model conceptualization. We do not include a direct comparison of the modeled HZ denitrification and measurements; however, the RCM can capture the overall spatial patterns of the HZ denitrification because the model inputs and its reaction networks are based on well-established theory and a physical-based model. The combination of the model-based predictions and a machine-learning approach (e.g., random forest) is used to improve our understanding of what variables of the model are associated with spatial patterns of the modeled denitrification across reaches with different sizes and land uses, and to develop a proxy model using measurable variables to reproduce the simulated patterns.This dataset contains five folders: (1) model_inputs, (2) model_outputs, (3) Rscripts, (4) figures, and (5) model_codes. It also contains a readme, file level metadata (FLMD), and data dictionary (dd). Please see the FLMD for a list of all the files contained in this data package and descriptions for each. The model_inputs folder contains the model inputs used to drive the model simulations. The model_outputs folder contains key model output files from the river corridor model. The Rscripts folder contains the Rscripts for pre- and post- processing model results. The figures folder contains the raw figures associated with the manuscript. The model_codes folder includes key model source codes/input files. All files are .jpg, .jpeg, .out, .e, .od, .dat, .sub, .F90, .0, .R, .sbx, .cpg, .sbn, .shx, .shp, .dbf, .prj, .tfw, .tif, .xml, .pdf, or .csv.

54 ENVIRONMENTAL SCIENCES↗

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

Recovering individual genomes from metagenomic datasets allows access to uncultivated microbial populations that may have important roles in natural and engineered ecosystems. Understanding the roles of these uncultivated populations has broad application in ecology, evolution, biotechnology and medicine. Accurate binning of assembled metagenomic sequences is an essential step in recovering the genomes and understanding microbial functions. We have developed a binning algorithm, MaxBin, which automates the binning of assembled metagenomic scaffolds using an expectation-maximization algorithm after the assembly of metagenomic sequencing reads. Binning of simulated metagenomic datasets demonstrated that MaxBin had high levels of accuracy in binning microbial genomes. MaxBin was used to recover genomes from metagenomic data obtained through the Human Microbiome Project, which demonstrated its ability to recover genomes from real metagenomic datasets with variable sequencing coverages. Application of MaxBin to metagenomes obtained from microbial consortia adapted to grow on cellulose allowed genomic analysis of new, uncultivated, cellulolytic bacterial populations, including an abundant myxobacterial population distantly related to Sorangium cellulosum that possessed a much smaller genome (5 MB versus 13 to 14 MB) but has a more extensive set of genes for biomass deconstruction. For the cellulolytic consortia, the MaxBin results were compared to binning using emergent self-organizing maps (ESOMs) and differential coverage binning, demonstrating that it performed comparably to these methods but had distinct advantages in automation, resolution of related genomes and sensitivity. The automatic binning software that we developed successfully classifies assembled sequences in metagenomic datasets into recovered individual genomes. The isolation of dozens of species in cellulolytic microbial consortia, including a novel species of myxobacteria that has the smallest genome among all sequenced aerobic myxobacteria, was easily achieved using the binning software. This work demonstrates that the processes required for recovering genomes from assembled metagenomic datasets can be readily automated, an important advance in understanding the metabolic potential of microbes in natural environments. MaxBin is available at https://sourceforge.net/projects/maxbin/.

59 BASIC BIOLOGICAL SCIENCES↗

Towards Next-Generation Urban Decision Support Systems through AI-Powered Construction of Scientific Ontology Using Large Language Models—A Case in Optimizing Intermodal Freight Transportation

The incorporation of Artificial Intelligence (AI) models into various optimization systems is on the rise. However, addressing complex urban and environmental management challenges often demands deep expertise in domain science and informatics. This expertise is essential for deriving data and simulation-driven insights that support informed decision-making. In this context, we investigate the potential of leveraging the pre-trained Large Language Models (LLMs) to create knowledge representations for supporting operations research. By adopting ChatGPT-4 API as the reasoning core, we outline an applied workflow that encompasses natural language processing, Methontology-based prompt tuning, and Generative Pre-trained Transformer (GPT), to automate the construction of scenario-based ontologies using existing research articles and technical manuals of urban datasets and simulations. From these ontologies, knowledge graphs can be derived using widely adopted formats and protocols, guiding various tasks towards data-informed decision support. The performance of our methodology is evaluated through a comparative analysis that contrasts our AI-generated ontology with the widely recognized pizza ontology, commonly used in tutorials for popular ontology software. We conclude with a real-world case study on optimizing the complex system of multi-modal freight transportation. Our approach advances urban decision support systems by enhancing data and metadata modeling, improving data integration and simulation coupling, and guiding the development of decision support strategies and essential software components.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Comparison of numerical predictions with CO{sub 2} pipeline release datasets of relevance to carbon capture and storage applications

Predicting the correct multi-phase fluid flow behaviour during the discharge process in the near-field of sonic CO{sub 2} jets is of particular importance in assessing the risks associated with transport aspects of carbon capture and storage schemes, given the very different hazard profiles of CO{sub 2} in the gaseous and solid states. In this paper, we apply our state-of-the-art mathematical model implemented in an efficient computational method to available data. Compared to previous applications, an improved equation of state is used. We also compare to all the available data, rather than just subsets as previously, and demonstrate both the improved performance of the fluid flow model and the variation between the available datasets. The condensed phase fraction at the vent, puncture or rupture release point is revealed to be of key importance in understanding the near-field dispersion of sonic CO{sub 2}.

54 ENVIRONMENTAL SCIENCES↗

Diagnosing nuclear power plant pipe wall thinning due to flow accelerated corrosion using a passive, thermal non-destructive evaluation method: Feasibility assessment via numerical experiments

Flow accelerated corrosion (FAC) in nuclear power plant pipes is one of the leading causes of accidents, fatalities, damage and outages. Current FAC identification methods employ expensive sensing technology and are “active” methods, where the response of the piping system to an externally-generated thermal, mechanical or optical excitation must be measured. As a result, these techniques require a disruptive and time-consuming setup. Here we propose a method that utilizes pipe surface temperature measurements to passively monitor for FAC-induced pipe wall thinning without the need for expensive equipment or post-installation setup time. This diagnostic method utilizes a simulation data-driven diagnostic model to estimate the amount of thickness reduction in a pipe based on changes in measured steady-state pipe temperatures. In order to reduce the computational burden of generating large, simulation-based datasets, the behavior of the insulation of the pipe was modeled using a suitably calibrated heat transfer boundary parameter. Additionally, global sensitivity analysis was performed to determine system parameter(s), such as the temperature of water flowing inside the pipe, which significantly affect the steady state pipe wall temperature and could cause errors in diagnosis. Two diagnostic models, one using only the change in steady-state temperature as an indicator for FAC-induced pipe wall thinning and the other using water temperature as an additional diagnostic model input were evaluated for their ability to estimate thickness reductions in a pipe using simulated pipe wall temperature data. For the numerical experiments conducted in this work, both models estimated wall thickness with errors within 0.5 mm, indicating that the proposed technique can potentially be used as a low-cost, first-pass method for FAC monitoring.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Technical Note: Development of a 3D printed subresolution sandwich phantom for validation of brain SPECT analysis

Purpose: To make an adaptable, head shaped radionuclide phantom to simulate molecular imaging of the brain using clinical acquisition and reconstruction protocols. This will allow the characterization and correction of scanner characteristics, and improve the accuracy of clinical image analysis, including the application of databases of normal subjects. Methods: A fused deposition modeling 3D printer was used to create a head shaped phantom made up of transaxial slabs, derived from a simulated MRI dataset. The attenuation of the printed polylactide (PLA), measured by means of the Hounsfield unit on CT scanning, was set to match that of the brain by adjusting the proportion of plastic filament and air (fill ratio). Transmission measurements were made to verify the attenuation of the printed slabs. The radionuclide distribution within the phantom was created by adding {sup 99m}Tc pertechnetate to the ink cartridge of a paper printer and printing images of gray and white matter anatomy, segmented from the same MRI data. The complete subresolution sandwich phantom was assembled from alternate 3D printed slabs and radioactive paper sheets, and then imaged on a dual headed gamma camera to simulate an HMPAO SPECT scan. Results: Reconstructions of phantom scans successfully used automated ellipse fitting to apply attenuation correction. This removed the variability inherent in manual application of attenuation correction and registration inherent in existing cylindrical phantom designs. The resulting images were assessed visually and by count profiles and found to be similar to those from an existing elliptical PMMA phantom. Conclusions: The authors have demonstrated the ability to create physically realistic HMPAO SPECT simulations using a novel head-shaped 3D printed subresolution sandwich method phantom. The phantom can be used to validate all neurological SPECT imaging applications. A simple modification of the phantom design to use thinner slabs would make it suitable for use in PET.

60 APPLIED LIFE SCIENCES↗

Using spatio-temporal graph neural networks to estimate fleet-wide photovoltaic performance degradation patterns

Accurate estimation of photovoltaic (PV) system performance is crucial for determining its feasibility as a power generation technology and financial asset. PV-based energy solutions offer a viable alternative to traditional energy resources due to their superior Levelized Cost of Energy (LCOE). A significant challenge in assessing the LCOE of PV systems lies in understanding the Performance Loss Rate (PLR) for large fleets of PV systems. Estimating the PLR of PV systems becomes increasingly important in the rapidly growing PV industry. Precise PLR estimation benefits PV users by providing real-time monitoring of PV module performance, while explainable PLR estimation assists PV manufacturers in studying and enhancing the performance of their products. However, traditional PLR estimation methods based on statistical models have notable drawbacks. Firstly, they require user knowledge and decision-making. Secondly, they fail to leverage spatial coherence for fleet-level analysis. Additionally, these methods inherently assume the linearity of degradation, which is not representative of real world degradation. To overcome these challenges, we propose a novel graph deep learning-based decomposition method called the Spatio-Temporal Graph Neural Network for fleet-level PLR estimation (PV-stGNN-PLR). PV-stGNN-PLR decomposes the power timeseries data into aging and fluctuation components, utilizing the aging component to estimate PLR. PV-stGNN-PLR exploits spatial and temporal coherence to derive PLR estimation for all systems in a fleet and imposes flatness and smoothness regularization in loss function to ensure the successful disentanglement between aging and fluctuation. We have evaluated PV-stGNN-PLR on three simulated PV datasets consisting of 100 inverters from 5 sites. Experimental results show that PV-stGNN-PLR obtains a reduction of 33.9% and 35.1% on average in Mean Absolute Percent Error (MAPE) and Euclidean Distance (ED) in PLR degradation pattern estimation compared to the state-of-the-art PLR estimation methods.

14 SOLAR ENERGY↗

Model Evaluation of Short-Lived Climate Forcers for the Arctic Monitoring and Assessment Programme: A Multi-Species, Multi-Model Study

While carbon dioxide is the main cause for global warming, modeling short-lived climate forcers (SLCFs) such as methane, ozone, and particles in the Arctic allows us to simulate near-term climate and health impacts for a sensitive, pristine region that is warming at 3 times the global rate. Atmospheric modeling is critical for understanding the long-range transport of pollutants to the Arctic, as well as the abundance and distribution of SLCFs throughout the Arctic atmosphere. Modeling is also used as a tool to determine SLCF impacts on climate and health in the present and in future emissions scenarios. In this study, we evaluate 18 state-of-the-art atmospheric and Earth system models by assessing their representation of Arctic and Northern Hemisphere atmospheric SLCF distributions, considering a wide range of different chemical species (methane, tropospheric ozone and its precursors, black carbon, sulfate, organic aerosol, and particulate matter) and multiple observational datasets. Model simulations over 4 years (2008-2009 and 2014-2015) conducted for the 2022 Arctic Monitoring and Assessment Programme (AMAP) SLCF assessment report are thoroughly evaluated against satellite, ground, ship, and aircraft-based observations. The annual means, seasonal cycles, and 3-D distributions of SLCFs were evaluated using several metrics, such as absolute and percent model biases and correlation coefficients. The results show a large range in model performance, with no one particular model or model type performing well for all regions and all SLCF species. The multi-model mean (mmm) was able to represent the general features of SLCFs in the Arctic and had the best overall performance. For the SLCFs with the greatest radiative impact (CH4, 03, BC, and SO(sup 2-)(sub 4)), the mmm was within ±25 % of the measurements across the Northern Hemisphere. Therefore, we recommend a multi-model ensemble be used for simulating climate and health impacts of SLCFs. Of the SLCFs in our study, model biases were smallest for C"4 and greatest for OA. For most SLCFs, model biases skewed from positive to negative with increasing latitude. Our analysis suggests that vertical mixing, long-range transport, deposition, and wildfires remain highly uncertain processes. These processes need better representation within atmospheric models to improve their simulation of SLCFs in the Arctic environment. As model development proceeds in these areas, we highly recommend that the vertical and 3-D distribution of SLCFs be evaluated, as that information is critical to improving the uncertain processes in models.

Arctic Monitoring and Assessment Programme↗

E3SMv2 simulation output from sensitivity study on cloud formation

This dataset contains E3SMv2 simulation output files discussed in the manuscript approved for IR in PNNL-SA-206024. The dataset was used to examine the occurrences of ultra-low cloud droplet number concentrations in E3SMv2. Submitting the manuscript to a peer-reviewed journal will require making the model output publicly available. We plan to use DataHub for that.

Wan, Hui [PNNL] (ORCID:0000000152944116)↗

IoT Intrusion Detection Taxonomy, Reference Architecture, and Analyses

This paper surveys the deep learning (DL) approaches for intrusion-detection systems (IDSs) in Internet of Things (IoT) and the associated datasets toward identifying gaps, weaknesses, and a neutral reference architecture. A comparative study of IDSs is provided, with a review of anomaly-based IDSs on DL approaches, which include supervised, unsupervised, and hybrid methods. All techniques in these three categories have essentially been used in IoT environments. To date, only a few have been used in the anomaly-based IDS for IoT. For each of these anomaly-based IDSs, the implementation of the four categories of feature(s) extraction, classification, prediction, and regression were evaluated. We studied important performance metrics and benchmark detection rates, including the requisite efficiency of the various methods. Four machine learning algorithms were evaluated for classification purposes: Logistic Regression (LR), Support Vector Machine (SVM), Decision Tree (DT), and an Artificial Neural Network (ANN). Therefore, we compared each via the Receiver Operating Characteristic (ROC) curve. The study model exhibits promising outcomes for all classes of attacks. The scope of our analysis examines attacks targeting the IoT ecosystem using empirically based, simulation-generated datasets (namely the Bot-IoT and the IoTID20 datasets).

97 MATHEMATICS AND COMPUTING↗

Scale Dependence of Multiplier Distributions for Particle Concentration, Enstrophy, and Dissipation in the Inertial Range of Homogeneous Turbulence

Turbulent flows preferentially concentrate inertial particles depending on their stopping time or Stokes number, which can lead to significant spatial variations in the particle concentration. Cascade models are one way to describe this process in statistical terms. Here, we use a direct numerical simulation (DNS) dataset of homogeneous, isotropic turbulence to determine probability distribution functions (PDFs) for cascade multipliers, which determine the ratio by which a property is partitioned into subvolumes as an eddy is envisioned to decay into smaller eddies. We present a technique for correcting effects of small particle numbers in the statistics. We determine multiplier PDFs for particle number, flow dissipation, and enstrophy, all of which are shown to be scale dependent. However, the particle multiplier PDFs collapse when scaled with an appropriately defined local Stokes number. As anticipated from earlier works, dissipation and enstrophy multiplier PDFs reach an asymptote for sufficiently small spatial scales. From the DNS measurements, we derive a cascade model that is used it to make predictions for the radial distribution function (RDF) for arbitrarily high Reynolds numbers, Re, finding good agreement with the asymptotic, infinite Re inertial range theory of Zaichik and Alipchenkov [New J. Phys. 11, 103018 (2009)]. We discuss implications of these results for the statistical modeling of the turbulent clustering process in the inertial range for high Reynolds numbers inaccessible to numerical simulations.

turbulent flows↗

Application and evaluation of a pattern-based building energy model calibration method using public building datasets

Building performance simulation has been adopted to support decision making in the building life cycle. An essential issue is to ensure a building energy simulation model can capture the reality and complexity of buildings and their systems in both the static characteristics and dynamic operations. Building energy model calibration is a technique that takes various types of measured performance data (e.g., energy use) and tunes key model parameters to match the simulated results with the actual measurements. This study performed an application and evaluation of an automated pattern-based calibration method on commercial building models that were generated based on characteristics of real buildings. A public building dataset that includes high-level building attributes (e.g., building type, vintage, total floor area, number of stories, zip code) of 111 buildings in San Francisco, California, USA, was used to generate building models in EnergyPlus. Monthly level energy use calibrations were then conducted by comparing building model results against the actual buildings' monthly electricity and natural gas consumption. The results showed 57 out of 111 buildings were successfully calibrated against actual buildings, while the remaining buildings showed opportunities for future calibration improvements. Enhancements to the pattern-based model calibration method are identified to expand its use for: (1) central heating, ventilation and air conditioning (HVAC) systems with chillers, (2) space heating and hot water heating with electricity sources, (3) mixed-use building types, and (4) partially occupied buildings.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Exploring Wildfire & Energy data toward State Prioritization Index (WESPI)

Energy infrastructure can both induce and suffer risks from wildfires ranging from direct damage to energy assets such as substations and power lines to Public Safety Power Shutoffs. Recent wildfire events underscore the need for data-driven approaches that help states and utilities proactively plan for wildfire risk. Existing national tools such as Federal Emergency Management Agency (FEMA)’s National Risk Index (NRI) are valuable for community hazard planning. However, they are less suited for energy infrastructure, as they emphasize population and building exposure rather than system vulnerabilities. In this paper, we explore relationships between energy and wildfire data and present a Wildfire-Energy State Prioritization Index (WESPI). Our methodology combines data from the US Forest Service’s Fire Simulation (FSIM) dataset with energy resilience metrics, historical fire incidents, and geospatial data on transmission lines and fire stations. Correlation analyses suggest that FSIM burn probability is more strongly associated with power outage metrics (ρ = 0.32) than NRI wildfire frequency, and counties with a greater density of fire stations experience more frequent, but less intense wildfires. We further leverage data for burn probability, transmission line density, and fire station density to develop a Wildfire-Energy State Prioritization Index (WESPI) to highlight counties where wildfire hazard, infrastructure exposure, and limited suppression capacity converge. The index provides a consistent, scalable framework for state energy offices and utilities to screen counties for vegetation management, optimization of outage management system deployment, and to inform wildfire mitigation plans.

Critical infrastructure↗

An initial exploration of Bayesian model calibration for estimating the composition of rocks and soils on Mars

The Mars Curiosity rover carries an instrument, ChemCam, designed to measure the composition of surface rocks and soil using laser-induced breakdown spectroscopy (LIBS). The measured spectra from this instrument must be analyzed to identify the component elements in the target sample, as well as their relative proportions. This process, which we call disaggregation, is complicated by so-called matrix effects, which describe nonlinear changes in the relative heights of emission lines as an unknown function of composition due to atomic interactions within the LIBS plasma. In this work, we explore the use of the plasma physics code ATOMIC, developed at Los Alamos National Laboratory, for the disaggregation task. ATOMIC has recently been used to model LIBS spectra and can robustly reproduce matrix effects from first principles. The ability of ATOMIC to predict LIBS spectra presents an exciting opportunity to perform disaggregation in a manner not yet tried in the LIBS community, namely via Bayesian model calibration. However, using it directly to solve our inverse problem is computationally intractable due to the large parameter space and the computation time required to produce a single output. Therefore, we also explore the use of emulators as a fast solution for this analysis. We discuss a proof of concept Gaussian process emulator for disaggregating two-element compounds of sodium and copper. The training and test datasets were simulated with ATOMIC using a Latin hypercube design. After testing the performance of the emulator, we successfully recover the composition of 25 test spectra with Bayesian model calibration.

97 MATHEMATICS AND COMPUTING↗

The interactive indoor-outdoor building energy modeling for enhancing the predictions of urban microclimates and building energy demands

There is a lack of an urban building energy modeling framework that considers the influence of surrounding buildings and local urban climate on building thermal performance. This can lead to inaccurate results since the thermal performance of individual buildings is heavily influenced by their surrounding built and climatic environment. This study establishes an interactive indoor-outdoor building energy modeling method to enhance the predictions of urban microclimates and building energy demands by coupling an urban physics model with a physics-based building energy model. Validation of the interactive coupling scheme uses field measurement datasets. Parametric simulation and analysis are conducted to understand the influence of the roof-to-canyon width ratio, canyon orientation, and ground vegetation fraction on canyon temperature, building energy consumption, and energy demand. Furthermore, the impacts of building energy model complexity (e.g., detailed vs. simplified building models) and coupling approaches on canyon temperature and building energy profiles are demonstrated using two case study buildings. In comparison with the one-way coupling approach, cooling energy consumption predicted with the dynamic two-way coupling approach varies by 3.5% and 0.5% for the detailed medium office building model and high-rise building model, respectively, and peak cooling demand varies by 8.4% and 7.0% for the detailed medium office building model and high-rise building model, respectively. Here this study also suggests that adopting a complex two-way coupling approach with environmental data exchange at various elevations is necessary for modeling tall buildings at the urban scale.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Neural networks for parameter estimation in intractable models

The goal is to use deep learning models to estimate parameters in statistical models when standard likelihood estimation methods are computationally infeasible. For instance, inference for max-stable processes is exceptionally challenging even with small datasets, but simulation is straightforward. Data from model simulations are used to train deep neural networks and learn statistical parameters from max-stable models. The proposed neural network-based method provides a competitive alternative to current approaches, as demonstrated by considerable accuracy and computational time improvements. Finally, it serves as a proof of concept for deep learning in statistical parameter estimation and can be extended to other estimation problems.

97 MATHEMATICS AND COMPUTING↗

Revealing the complex chemistry of grain boundaries in K-doped BaFe 2 As 2 with atom probe tomography

Iron-based superconductors have attractive properties for high-field applications, but there is a lack of understanding of the effect of grain boundary chemistry on the in-field performance. The near atomic-scale resolution, ppm sensitivity and 3D analysis offered by atom probe tomography make it a powerful tool to investigate the nanoscale structure and chemistry of these defects in fine-grained K-doped BaFe 2 As 2 samples. A computational method to systematically extract and compare the Gibbsian interfacial excess of chemical species across grain boundaries has been explored in this work. The robustness of the method has been tested by evaluating the effects of selected variables on simulated APT datasets. The accuracy and precision of the calculated Gibbsian interfacial excess were found to be stable over a range of analysis conditions: varying grain boundary widths and detection efficiencies, spatial precisions below 1.5 nm, and bin widths between 1.2 and 1.6 nm. For the K-doped BaFe 2 As 2 samples studied, segregation of As, Ba, K and impurities of O, Na, and Sb were found at grain boundaries. The Gibbsian excess values were found to vary widely between different boundaries, showing the complexity of the grain boundary chemistry in this material. Possible links between the observed critical current density (Jc) of these samples and their nano- and micro-structure have also been investigated and discussed.

36 MATERIALS SCIENCE↗