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At least 1,495 records · Page 83

Development and transferability of neural-network models for plasma-surface interactions

Plasma-surface interactions are increasingly critical to modern technologies; yet, accurate molecular dynamics simulations remain limited by the capabilities of interatomic potentials. Deep Potentials (DPs) promise to revolutionize the field by providing a systematic method for producing accurate interatomic potentials. The primary challenge of DP development is selecting a dataset, which efficiently spans the set of atomic environments one expects to encounter in the subsequent molecular dynamics simulations. The computational cost of density functional theory calculations, which are the typical basis for DP development, makes it impossible to directly verify the quality of a given DP. To address this challenge, we explore the development of a deep-learned interatomic potential, “DeepREBO,” trained to reproduce the behavior of the REBO2 empirical potential, enabling direct validation of training methodology and transferability. Using an active learning framework, we begin with a minimal dataset and iteratively expand it to train a Deep Potential-Smooth Edition model that faithfully reproduces REBO2 results for 25 eV hydrogen bombardment of diamond (001), a particularly challenging case. We show that small, carefully curated datasets can outperform large, unguided ones, with effective models requiring fewer than 15 000 snapshots. Subsequent transferability tests demonstrate that while DeepREBO generalizes well to diamond (111) surfaces, performance degrades for amorphous carbon or higher-energy impacts, highlighting the need for use-case-specific training data. We also evaluate methods to improve short-range repulsion. This study outlines best practices for training robust deep potentials and underscores the importance of dataset design for predictive plasma simulations.

Ab-initio molecular dynamics↗

PDC VOL Connector (PDCVOL) v0.1

PDCVOL is an extension software originated from the Proactive Data Containers (PDC) software (LBNL Track Code 2017-098), it is an HDF5 VOL connector that allows HDF5 applications to store and access data with the PDC system without the need to modify their code. The application can take advantage of the PDC optimization features and achieve better I/O performance.

Byna, Suren↗

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations

Publicly available collections of drug-like molecules have grown to comprise tens of billions of compounds due to advances in combinatorial chemistry. Traditional methods for identifying "hit" molecules from a large collection of potential drug-like candidates have relied on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have the major drawback that they require exceptional computing capabilities for even relatively small collections of molecules. Hyperdimensional Computing (HDC) is a recently-proposed learning paradigm that represents data with high-dimension binary vectors; this allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas. We consider existing HDC approaches for molecular property classification and introduce two novel encodings of a commonly-used molecular representation, the extended connectivity fingerprint (ECFP). We show that HDC-based inference methods are as much as 91 times more efficient than traditional machine learning methods, and achieve an acceleration of nearly nine orders of magnitude compared to molecular docking. Our results show that HDC accelerated methods retain competitive accuracy on a number of well-studied tasks such as molecular property predictions using the MoleculeNet dataset, and bind/no-bind activity classification using the DUD-E and LIT-PCBA datasets. Our work thus motivates further investigation into molecular representation learning to develop ultraefficient pre-screening tools.

Jones, William↗

NetGraf: An End-to-End Learning NetworkMonitoring Service (NetGraf) v1

NetGraf is a novel end-to-end learning monitoring system that utilizes current monitoring tools, merges multiple data sources into one dashboard for easy use, and provides machine learning libraries to analyze the data and perform real-time anomaly findings. Using a database backend, NetGraf can learn performance trends and show users if network performance has degraded. We demonstrate how NetGraf can easily be deployed through automation services and linked to multiple monitoring sources to collect data. Via the machine learning innovation and merging various data sources, NetGraf aims to fulfill the need for holistic learning network telemetry monitoring. To the best of our knowledge, this is the first-ever end-to-end learning monitoring service. We demonstrate its use on two network setups to showcase its impact.

Mohammed, Bashir↗

CTGAN-TVAE

SAND2026-18914O CTGAN-TVAE (Conditional Tabular Generative Adversarial Networks-Tabular Variational Autoencoders) generates extensive sets of variable generation data through a hybrid framework. It enhances latent space representation by combining TVAE's robust feature-embedding with CTGAN's ability to condition categorical variables such as time. CTGAN-TVAE employs a fully connected neural network within a conditional generative adversarial network framework to manage continuous and categorical data effectively, capturing complex feature interactions without needing sequential modeling. This was developed as part of NNSA-MSIPP: Minority Serving Institution Partnership Program, Grant Number DE-NA0004016. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy's National Nuclear Security Administration under contract DE-NA0003525.

Newlun, Cody [Sandia National Lab. (SNL-CA), Liver↗

Challenges in Clinical Trial Implementation: Results from a Survey of the National Accreditation Program of Breast Centers (NAPBC)

Background: Although the results of clinical trials often guide best practices, changing clinical practice based on clinical trial results can be challenging. The objective of this study was to examine provider-reported barriers to adopting best clinical practices according to clinical trial data. Methods: A cross-sectional survey was conducted of providers from the National Accreditation Program for Breast Centers about barriers that prevent the incorporation of trial findings. Descriptive analyses and multivariable analyses were performed to determine provider characteristics that were significantly associated with reported barriers. Results: Overall, 383 institutions participated (63.5% response rate), with a total of 1226 physicians responding to the survey (80% response rate). Providers identified national guidelines and meetings as the most compelling way to receive practice-changing information. They reported the following internal barriers to trial implementation: patient preference (45%), strongly held beliefs by partners/colleagues (37%), and insufficient time to discuss new practices (30%). External barriers preventing trial implementation included a lack of agreement from multidisciplinary tumor boards (32%), fear of reimbursement loss (23%), and resistance from clinical staff (20%). Reported barriers differed by provider specialty, with plastic surgeons and radiation oncologists reporting that strongly held beliefs by partners/colleagues and disagreement from multidisciplinary tumor boards were the most significant factors preventing clinical trial implementation. Conclusions: Physician beliefs and patient preferences are the most frequently reported barriers to clinical trial implementation. Tactics to better educate providers about how to explain new clinical trial data to their patients and colleagues are needed.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Synthetic method of analogues for emerging infectious disease forecasting

The Method of Analogues (MOA) has gained popularity in the past decade for infectious disease forecasting due to its non-parametric nature. In MOA, the local behavior observed in a time series is matched to the local behaviors of several historical time series. The known values that directly follow the historical time series that best match the observed time series are used to calculate a forecast. This non-parametric approach leverages historical trends to produce forecasts without extensive parameterization, making it highly adaptable. However, MOA is limited in scenarios where historical data is sparse. This limitation was particularly evident during the early stages of the COVID-19 pandemic, where the emerging global epidemic had little-to-no historical data. In this work, we propose a new method inspired by MOA, called the Synthetic Method of Analogues (sMOA). sMOA replaces historical disease data with a library of synthetic data that describe a broad range of possible disease trends. This model circumvents the need to estimate explicit parameter values by instead matching segments of ongoing time series data to a comprehensive library of synthetically generated segments of time series data. We demonstrate that sMOA has competitive performance with state-of-the-art infectious disease forecasting models, out-performing 78% of models from the COVID-19 Forecasting Hub in terms of averaged Mean Absolute Error and 76% of models from the COVID-19 Forecasting Hub in terms of averaged Weighted Interval Score. Additionally, we introduce a novel uncertainty quantification methodology designed for the onset of emerging epidemics. Developing versatile approaches that do not rely on historical data and can maintain high accuracy in the face of novel pandemics is critical for enhancing public health decision-making and strengthening preparedness for future outbreaks.

97 MATHEMATICS AND COMPUTING↗

Neutralization profiles of HIV-1 viruses from the VRC01 Antibody Mediated Prevention (AMP) trials

The VRC01 Antibody Mediated Prevention (AMP) efficacy trials conducted between 2016 and 2020 showed for the first time that passively administered broadly neutralizing antibodies (bnAbs) could prevent HIV-1 acquisition against bnAb-sensitive viruses. HIV-1 viruses isolated from AMP participants who acquired infection during the study in the sub-Saharan African (HVTN 703/HPTN 081) and the Americas/European (HVTN 704/HPTN 085) trials represent a panel of currently circulating strains of HIV-1 and offer a unique opportunity to investigate the sensitivity of the virus to broadly neutralizing antibodies (bnAbs) being considered for clinical development. Pseudoviruses were constructed using envelope sequences from 218 individuals. The majority of viruses identified were clade B and C; with clades A, D, F and G and recombinants AC and BF detected at lower frequencies. We tested eight bnAbs in clinical development (VRC01, VRC07-523LS, 3BNC117, CAP256.25, PGDM1400, PGT121, 10–1074 and 10E8v4) for neutralization against all AMP placebo viruses (n = 76). Compared to older clade C viruses (1998–2010), the HVTN703/HPTN081 clade C viruses showed increased resistance to VRC07-523LS and CAP256.25. At a concentration of 1μg/ml (IC80), predictive modeling identified the triple combination of V3/V2-glycan/CD4bs-targeting bnAbs (10-1074/PGDM1400/VRC07-523LS) as the best against clade C viruses and a combination of MPER/V3/CD4bs-targeting bnAbs (10E8v4/10-1074/VRC07-523LS) as the best against clade B viruses, due to low coverage of V2-glycan directed bnAbs against clade B viruses. Overall, the AMP placebo viruses represent a valuable resource for defining the sensitivity of contemporaneous circulating viral strains to bnAbs and highlight the need to update reference panels regularly. Our data also suggests that combining bnAbs in passive immunization trials would improve coverage of global viruses.

60 APPLIED LIFE SCIENCES↗

System identity and transformation in petroleum jurisdictions: A multi-method approach for the North Slope Borough, Alaska

Capturing the multidimensionality of a bounded social-environmental system (SES) presents a range of challenges to interdisciplinary researchers due to the need to integrate divergent scientific paradigms, scalar data, and social theories. Contemporary Arctic circumpolar SESs studied under conditions of rapid and unprecedented climatic, ecological, economic, and sociopolitical change, defy any singular established methodological approach that aims to schematize and interpret the system for decision-making purposes. As a small interdisciplinary team working within a large Arctic SES modeling effort, we have found that developing systems models to support resilience in the Arctic requires an understanding of system dynamics that is attentive to holistic indicators of change, measured both quantitatively and qualitatively. Using the Alaska North Slope Borough as a case study, we apply three convergent frameworks to capture significant dimensions of the system for improved problem definition in confronting the challenges of Arctic climate change. We describe contemporary “oil and gas” social-ecological system components and dynamics, the historical processes and transformations that fundamentally altered the system, and the scientific projections for the most likely catalysts of future change. This analysis results in a typology for defining subnational Arctic hydrocarbon SESs. We conclude that the future of oil and gas development as a policy pathway in different locations experiencing rapid climate change can be evaluated when difficult-to-quantify variables are included.

Lovecraft, Amy Lauren↗

FTICR, NPOC, TN, and Moisture of Variably Inundated Sediment across 48 North American Rivers

This dataset supports a broader study examining drivers of organic matter chemistry in variably inundated hyporheic zone sediments and further linking that chemistry to biogeochemical rates. The dataset provides physical and chemical sediment data collected from 48 rivers across North America. There are related data that will be published, including surficial sediment temperature time series that can be used to infer the dynamics of inundation prior to the collection of sediments. This dataset is comprised of two folders: (1) ECA2_Sediment and (2) ECA2_SitePhotos. The ECA2_Sediment folder contains: (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) non-purgeable organic carbon (NPOC), total nitrogen (TN), and sediment moisture; (5) sediment sampling protocol, (6) readme, and (7) folder of high resolution characterization of organic matter from sediment extracts via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR-MS files are .xml, and the data package includes instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All other files are .csv, .txt, or .pdf. The ECA2_SitePhotos folder contains a readme and site photographs taken in the field. All files are .txt or .jpg.

54 ENVIRONMENTAL SCIENCES↗

WHONDRS Surface Water and Sediment Non-Purgeable Organic Carbon and FTICR-MS across Glacial Features in Svalbard 2021 (v3)

This dataset supports a broader study examining land-atmosphere gas exchange associated with permafrost and glaciers in Svalbard. The dataset provides geochemistry and organic matter characterization data generated from surface water and sediment. Samples were collected from 8 spatially diverse sites across central Svalbard and also from a more comprehensive temporal and spatial study within one glacial catchment area throughout one summer melt season. Related data were collected and will be published separately in collaboration with Yde and Kleber.This data package was originally published in September 2022. It was updated in March 2023 (v2; new and modified files), and July 2025 (v3; modified files). See the change history section in the readme for details.For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved organic carbon (DOC; measure as non-purgeable organic carbon; NPOC); (5) surface water sampling protocol; (6) sediment extraction protocol; (7) readme; (8) methods codes; (9) international generic sample number (IGSN) mapping file; and (10) folder of high resolution characterization of organic matter via 7 and 12 Tesla (7T and 12T) Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR folder contains two subfolders containing the 7T and 12T .xml data files and another subfolder containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗

WHONDRS Surface Water Dissolved Organic Carbon and FTICR-MS across Glacial Features in Svalbard 2022

This dataset supports a broader study examining climatic forcing of terrestrial greenhouse gas emission through permafrost and glaciers in Svalbard. The dataset provides geochemistry and organic matter characterization data generated from surface water collected from 11 sites across central Svalbard. Data were also collected in 2021 and can be found at https://data.ess-dive.lbl.gov/view/doi:10.15485/1888571. Additional related data were collected and will be published separately in collaboration with Yde and Kleber.This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) field metadata; (4) dissolved organic carbon (DOC; measured as non-purgeable organic carbon; NPOC); (5) surface water sampling protocol; (6) readme; (7) methods codes; (8) international geo-sample number (IGSN) mapping file; (9) a folder of field photos; and (10) folder of high resolution characterization of organic matter via 7 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) generated through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory). The FTICR folder contains two subfolders, one containing the .xml data files and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .R, .ref, or .xml.

54 ENVIRONMENTAL SCIENCES↗

Surface Water Disinfection Byproducts and Organic Matter Characterization Data Associated with: “Disinfection byproducts formed during drinking water treatment reveal an export control point for dissolved organic matter in a subalpine headwater stream”

This dataset is associated with the publication “Disinfection byproducts formed during drinking water treatment reveal an export control point for dissolved organic matter in a subalpine headwater stream” published in Water Research X (Leonard et al. 2022; https://doi.org/10.1016/j.wroa.2022.100144). The associated study analyzed temporal trends from the Town of Crested Butte water treatment facility and synoptic sampling at Coal Creek in Crested Butte, Colorado, US. This work demonstrates how drinking water quality archives combined with synoptic sampling and targeted analyses can be used to identify and understand export control points for dissolved organic matter. This dataset is comprised of one main data folder containing (1) file-level metadata; (2) data dictionary; (3) metadata and international geo-sample number (IGSN) mapping file; (4) dissolved organic carbon (DOC), ultraviolet absorbance at 254 nanometers (UV254), total nitrogen (TN), and specific ultraviolet absorbance (SUVA) data; (5) disinfection bioproduct formation potential (DBP-FP) data; (6) readme; (7) methods codes; (8) water collection protocol; (9) folder of high resolution characterization of organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory); and (10) folder of excitation emissions matrix (EEM) spectra. The FTICR folder contains a file of DOC (measured as non-purgeable organic carbon; NPOC) used for FTICR sample preparation. The FTICR folder also contains three subfolders: one subfolder containing the raw .xml data files, one containing the processed data, and the other containing instructions for using Formularity (https://omics.pnl.gov/software/formularity) and an R script to process the data based on the user's specific needs. All files are .csv, .pdf, .dat, .R, .ref, or .xml

54 ENVIRONMENTAL SCIENCES↗

Benchmarking Demand Flexibility in Commercial Buildings and Flattening the Duck – Addressing Baseline and Commissioning Challenges

With the transition from our traditional electric grid to a cleaner grid with renewable power generation, there is a need to enable building loads to be flexible. Load shedding and shifting will be essential for flattening the “Duck” for decarbonization. This paper explored the trend in the timing of DR events as a reflection of the grid’s needs using recent four years of event data from 203 retail stores in 11 states. The events are becoming significantly shorter with 2-hour duration being the most popular; shifting to late afternoon and early evening is another trend beyond California. Benchmarking will be essential for accounting DF as a reliable grid resource. This paper addresses a challenging aspect of benchmarking – inaccuracies in counterfactual baseline methods can introduce significant DF metrics variations in addition to weather and building characteristics related factors. The conventional “10/10” with adjustment baseline method has inherent limitation by design for load shifting applications. Therefore, it is imperative to identify alternative methods. This study compared three hourly regression baseline methods with “10/10” methods using two groups of commercial buildings that participated in DR programs: (1) 121 big-box retail stores, and (2) 11 office buildings in CA. The 14-day hourly outdoor temperature regression method was found to produce least error in the tested datasets and is promising for load shifting. The paper also pointed out that commissioning issues can also be a significant barrier for achieving consistent DF performance, which building managers and utilities should be aware of.

Liu, Jingjing↗

Insights into cosmological structure formation with machine learning.

Our modern understanding of cosmological structure formation posits that small matter density fluctuations present in the early Universe, as traced by the cosmic microwave background, grow via gravitational instability to form extended haloes of dark matter. A theoretical understanding of the structure, evolution and formation of dark matter haloes is an essential step towards unravelling the intricate connection between halo and galaxy formation, needed to test our cosmological model against data from upcoming galaxy surveys. Physical understanding of the process of dark matter halo formation is made difficult by the highly non-linear nature of the haloes' evolution. I describe a new approach to gain physical insight into cosmological structure formation based on machine learning. This approach combines the ability of machine learning algorithms to learn non-linear relationships, with techniques that enable us to physically interpret the learnt mapping. I describe applicatio ns of th e method, with the aim of investigating which aspects of the early universe density field impact the later formation of dark matter haloes. First I present a case where the process of halo formation is turned into a binary classification problem; the algorithm predicts whether or not dark matter `particles' in the initial conditions of a simulation will collapse into haloes of a given mass range. Second, I present its generalization to regression, where the algorithm infers the final mass of the halo to which each particle will later belong. I show that the initial tidal shear does not play a significant role compared to the initial density field in establishing final halo masses. Finally, I demonstrate that extending the framework to deep learning algorithms such as convolutional neural networks allows us to explore connections between the early universe and late time haloes beyond those studied by existing analytic approximations of halo collapse.

79 ASTRONOMY AND ASTROPHYSICS↗

Electric Vehicle and Infrastructure Systems Modeling in Washington D.C. and Baltimore

This report documents the Argonne-Exelon effort to develop and utilize an agent-based model (ATEAM) of charging demand and infrastructure expansion applicable to the Washington, DC–Baltimore, MD consolidated metropolitan area. This study extends the ATEAM model time horizon to 10 years (from 2020 to 2030), expands agent behavior modeling capabilities, incorporates more granular and extensive empirical data on charging behavior, and analyzes charging needs for a much larger population of PEVs, in keeping with regional goals for significant adoption of ZEVs. With given targets for annual BEV adoption, five scenarios were developed to examine public infrastructure needs and resulting charging load, considering different home charging availabilities, as well as different PEV consumer profiles and public charging infrastructure deployment strategies. Scenario results show that if new chargers (both L2 and DCFC) are spread more widely (as with ubiquitous deployment strategies), there will be less variation in the number of chargers added to each census tract in the study area. More importantly, widespread public charging infrastructure with ubiquitous deployment strategies reduces unmet charging demand and improves charging success, even with heavy reliance on public charging. About 80 percent of BEV drivers can charge on their first attempt in scenarios with ubiquitous deployment strategies. Moreover, widespread public charging infrastructure better meets the demand for more charging, and in return, increases BEV adoption. Low home charging availability produces higher charging loads in public locations, especially during the early morning (around 8:00 a.m.) and late afternoon (around 6:00 p.m.). The evening peak load indicates that drivers are taking advantage of public charging before heading home. Study results also indicate that even with 20 percent home charging availability in 2030, just 20 percent of drivers attempt to charge on a given day. With their relatively high electric range (200+ miles), the BEVs expected to be on the road in 2030 can handle daily commutes without re-charging for a couple of days.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Accelerating Multiscale Materials Modeling with Machine Learning

The focus of this project is to accelerate and transform the workflow of multiscale materials modeling by developing an integrated toolchain seamlessly combining DFT, SNAP, LAMMPS, (shown in Figure 1-1) and a machine-learning (ML) model that will more efficiently extract information from a smaller set of first-principles calculations. Our ML model enables us to accelerate first-principles data generation by interpolating existing high fidelity data, and extend the simulation scale by extrapolating high fidelity data (10 2 atoms) to the mesoscale (10 4 atoms). It encodes the underlying physics of atomic interactions on the microscopic scale by adapting a variety of ML techniques such as deep neural networks (DNNs), and graph neural networks (GNNs). We developed a new surrogate model for density functional theory using deep neural networks. The developed ML surrogate is demonstrated in a workflow to generate accurate band energies, total energies, and density of the 298K and 933K Aluminum systems. Furthermore, the models can be used to predict the quantities of interest for systems with more number of atoms than the training data set. We have demonstrated that the ML model can be used to compute the quantities of interest for systems with 100,000 Al atoms. When compared with 2000 Al system the new surrogate model is as accurate as DFT, but three orders of magnitude faster. We also explored optimal experimental design techniques to choose the training data and novel Graph Neural Networks to train on smaller data sets. These are promising methods that need to be explored in the future.

36 MATERIALS SCIENCE↗

The Quick Rise and Fall of LK-99 as a Room Temperature Superconductor [Slides]

A swift determination of superconductivity vs non-superconductivity of LK-99 demonstrates the importance of reproducibility in science. This has benefited from 4 decades study of high-temperature cuprate mechanism. Holy grail of room-temperature ambient-pressure superconductor remains to be pursued. Caution is needed about DFT calculations. Crucial old experimental data should be referenced. With the existing amount of experimentally discovered superconductors, could data science make a stride?

36 MATERIALS SCIENCE↗