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At least 271 records · Page 15

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

Abstract Substantial progresses in protein structure prediction have been made by utilizing deep‐learning and residue‐residue distance prediction since CASP13. Inspired by the advances, we improve our CASP14 MULTICOM protein structure prediction system by incorporating three new components: (a) a new deep learning‐based protein inter‐residue distance predictor to improve template‐free (ab initio) tertiary structure prediction, (b) an enhanced template‐based tertiary structure prediction method, and (c) distance‐based model quality assessment methods empowered by deep learning. In the 2020 CASP14 experiment, MULTICOM predictor was ranked seventh out of 146 predictors in tertiary structure prediction and ranked third out of 136 predictors in inter‐domain structure prediction. The results demonstrate that the template‐free modeling based on deep learning and residue‐residue distance prediction can predict the correct topology for almost all template‐based modeling targets and a majority of hard targets (template‐free targets or targets whose templates cannot be recognized), which is a significant improvement over the CASP13 MULTICOM predictor. Moreover, the template‐free modeling performs better than the template‐based modeling on not only hard targets but also the targets that have homologous templates. The performance of the template‐free modeling largely depends on the accuracy of distance prediction closely related to the quality of multiple sequence alignments. The structural model quality assessment works well on targets for which enough good models can be predicted, but it may perform poorly when only a few good models are predicted for a hard target and the distribution of model quality scores is highly skewed. MULTICOM is available at https://github.com/jianlin-cheng/MULTICOM_Human_CASP14/tree/CASP14_DeepRank3 and https://github.com/multicom-toolbox/multicom/tree/multicom_v2.0 .

59 BASIC BIOLOGICAL SCIENCES↗

High-Current Density Durability of Pt/C and PtCo/C Catalysts at Similar Particle Sizes in PEMFCs

The durability of carbon supported PtCo-alloy based nanoparticle catalysts play a key role in the longevity of proton-exchange membrane fuel cells (PEMFC) in electric vehicle applications. To improve its durability, it is important to understand and mitigate the various factors that cause PtCo-based cathode catalyst layers (CCL) to lose performance over time. These factors include i) electrochemical surface area (ECSA) loss, ii) specific activity loss, iii) H + /O 2 -transport changes and iv) Co 2+ contamination effects. We use a catalyst-specific accelerated stress test (AST) voltage cycling protocol to compare the durability of Pt and PtCo catalysts at similar average nanoparticle size and distribution. Our studies indicate that while Pt and PtCo nanoparticle catalysts suffer from similar magnitudes of electrochemical surface area (ECSA) losses, PtCo catalyst shows a significantly larger cell voltage loss at high current densities upon durability testing. The distinctive factor causing the large cell voltage loss of PtCo catalyst appears to be the secondary effects of the leached Co 2+ cations that contaminate the electrode ionomer. A 1D performance model has been used to quantify the cell voltage losses arising from various factors causing degradation of the membrane electrode assembly (MEA).

08 HYDROGEN↗

Updating and Evaluating Anthropogenic Emissions for NOAA’s Global Ensemble Forecast Systems for Aerosols (GEFS-Aerosols): Application of an SO 2 Bias-Scaling Method

We updated the anthropogenic emissions inventory in NOAA’s operational Global Ensemble Forecast for Aerosols (GEFS-Aerosols) to improve the model’s prediction of aerosol optical depth (AOD). We used a methodology to quickly update the pivotal global anthropogenic sulfur dioxide (SO 2 ) emissions using a speciated AOD bias-scaling method. The AOD bias-scaling method is based on the latest model predictions compared to NASA’s Modern-Era Retrospective analysis for Research and Applications, version 2 (MERRA2). The model bias was subsequently applied to the CEDS 2019 SO 2 emissions for adjustment. The monthly mean GEFS-Aerosols AOD predictions were evaluated against a suite of satellite observations (e.g., MISR, VIIRS, and MODIS), ground-based AERONET observations, and the International Cooperative for Aerosol Prediction (ICAP) ensemble results. The results show that transitioning from CEDS 2014 to CEDS 2019 emissions data led to a significant improvement in the operational GEFS-Aerosols model performance, and applying the bias-scaled SO 2 emissions could further improve global AOD distributions. The biases of the simulated AODs against the observed AODs varied with observation type and seasons by a factor of 3~13 and 2~10, respectively. The global AOD distributions showed that the differences in the simulations against ICAP, MISR, VIIRS, and MODIS were the largest in March–May (MAM) and the smallest in December–February (DJF). When evaluating against the ground-truth AERONET data, the bias-scaling methods improved the global seasonal correlation (r), Index of Agreement (IOA), and mean biases, except for the MAM season, when the negative regional biases were exacerbated compared to the positive regional biases. The effect of bias-scaling had the most beneficial impact on model performance in the regions dominated by anthropogenic emissions, such as East Asia. However, it showed less improvement in other areas impacted by the greater relative transport of natural emissions sources, such as India. The accuracies of the reference observation or assimilation data for the adjusted inputs and the model physics for outputs, and the selection of regions with less seasonal emissions of natural aerosols determine the success of the bias-scaling methods. A companion study on emission scaling of anthropogenic absorbing aerosols needs further improved aerosol prediction.

54 ENVIRONMENTAL SCIENCES↗

Comparison of Model Predictions and Performance Test Data for a Prototype Thermal Energy Storage Module

Although model predictions of thermal energy storage (TES) performance have been explored in previous investigations, relevant test data that enable experimental validation of performance models have been limited. This is particularly true for high-performance TES designs that facilitate fast input and extraction of energy. In this paper, we present a summary of experimental tests of a high-performance TES unit using lithium nitrate trihydrate phase change material as a storage medium. Performance data are presented for complete dual-mode cycles consisting of extraction (melting) followed by charging (freezing). These tests simulate the cyclic operation of a TES unit for asynchronous cooling in a variety of applications. Finally, the model analysis is found to agree reasonably well, within 10%, with the experimental data except for conditions very near the initiation of freezing, a consequence of subcooling that is required to initiate solidification.

25 ENERGY STORAGE↗

Isomeric effects on the reactivity of branched alkenes: An experimental and kinetic modeling study of methylbutenes

Here, a detailed experimental study of the low-to-intermediate temperature combustion of methylbutene isomers, i.e., branched C 5 alkenes, has been undertaken with multiple experimental facilities. Ignition delay times were measured at equivalence ratios 0.5–2.0, 685–1020 K and up to 45 bar condition from two rapid compression machines and showed slight deviation from an Arrhenius behavior for all three isomers, while their reactivity order differs as temperature changes. Sampled intermediates formed during the oxidation process of mixtures at 900–1150 K and 0.82 bar from a flow reactor and at 730 K and 20 bar from a rapid compression machine were analyzed using gas chromatography techniques. Trends in the formation and consumption of sampled intermediates were modeled using a kinetic model developed in this work for all three isomers. Rate of production and sensitivity analyses emphasize the role of double bond-specific reactions governing the global reactivity of these fuels. Additional studies of the addition reactions of HO 2 radicals to the double bond and to allylic radicals may improve the model performance.

2-Methyl-1-butene↗

Semisupervised Learning for Seismic Monitoring Applications

The impressive performance that deep neural networks demonstrate on a range of seismic monitoring tasks depends largely on the availability of event catalogs that have been manually curated over many years or decades. However, the quality, duration, and availability of seismic event catalogs vary significantly across the range of monitoring operations, regions, and objectives. Semisupervised learning (SSL) enables learning from both labeled and unlabeled data and provides a framework to leverage the abundance of unreviewed seismic data for training deep neural networks on a variety of target tasks. We apply two SSL algorithms (mean-teacher and virtual adversarial training) as well as a novel hybrid technique (exponential average adversarial training) to seismic event classification to examine how unlabeled data with SSL can enhance model performance. In general, we find that SSL can perform as well as supervised learning with fewer labels. We also observe in some scenarios that almost half of the benefits of SSL are the result of the meaningful regularization enforced through SSL techniques and may not be attributable to unlabeled data directly. Lastly, the benefits from unlabeled data scale with the difficulty of the predictive task when we evaluate the use of unlabeled data to characterize sources in new geographic regions. Finally, in geographic areas where supervised model performance is low, SSL significantly increases the accuracy of source-type classification using unlabeled data.

58 GEOSCIENCES↗

Analysis of GPU Data Access Patterns on Complex Geometries for the D3Q19 Lattice Boltzmann Algorithm

GPU performance of the lattice Boltzmann method (LBM) depends heavily on memory access patterns. When implemented with GPUs on complex domains, typically, geometric data is accessed indirectly and lattice data is accessed lexicographically. Although there are a variety of other options, no study has examined the relative efficacy between them. Here, we examine a suite of memory access schemes via empirical testing and performance modeling. We find strong evidence that semi-direct is often better suited than the more common indirect addressing, providing increased computational speed and reducing memory consumption. For the layout, we find that the Collected Structure of Arrays (CSoA) and bundling layouts outperform the common Structure of Array layout; on V100 and P100 devices, CSoA consistently outperforms bundling, however the relationship is more complicated on K40 devices. When compared to state-of-the-art practices, our recommendations lead to speedups of 10–40 percent and reduce memory consumption up to 17 percent. Using performance modeling and computational experimentation, we determine the mechanisms behind the accelerations. We demonstrate that our results hold across multiple GPUs on two leadership class systems, and present the first near-optimal strong results for LBM with arterial geometries run on GPUs.

42 ENGINEERING↗

User-defined EMT inverter model reference performance, utility-scale [Slides]

This report investigates the response of the inverter under different terminal voltage and operating conditions. The goal is to understand the control objective of the inverter (e.g., injection of reactive current for voltage dips) based on the inverter’s response. No attempt is made to determine the exact control algorithms implemented in the inverter.

14 SOLAR ENERGY↗

Comparative post-irradiation examination of high burnup U-19Pu-10Zr: Assessing steady-state irradiation behavior against historical and modeled fuel performance

Here, the development of next-generation sodium-cooled fast reactors necessitates comprehensive research on metallic fuels to maximize economic performance while ensuring safe operation. In this study, we investigated the steady-state irradiation behavior of two high burnup U-19Pu-10Zr fuel pins, DP-36 and DP-40, in preparation for planned safety testing. Post-irradiation examination (PIE) was performed to quantify fuel column elongation, regions of low-density at the top of the fuel column, pin deformation, fission product distribution, fractional fission gas release, microstructural evolution, and fuel constituent redistribution. Benchmarking against existing PIE data from U-19Pu-10Zr fuel pins irradiated in EBR-II revealed consistent patterns in fuel column elongation and cladding diametral strain. However, both pins exhibited longer low-density structures, and destructive examination of DP-36 revealed more complex constituent redistribution patterns compared to previously reported data for ternary fuel pins. The steady-state irradiation of both pins was also modeled using BISON. Comparisons of PIE results with modeled predictions showed overall agreement in fractional fission gas release but consistent overestimation of axial and radial swelling due to gaseous and solid swelling models. These findings underscore the critical importance of pre-test characterization on test and sibling pins to accurately capture steady-state fuel behavior ahead of transient testing, thus establishing a baseline for post-test comparison. Additionally, these analyses identified key data gaps that warrant further investigation to improve the understanding and prediction of fuel swelling, thereby enhancing the synergy between modeling and experimental efforts in supporting accident testing.

BISON↗

Maps of growing season gross primary production and net ecosystem exchange for Council Road Mile Marker 71, Seward Peninsula, Alaska, [2017-2023]

This data archive is in support of the Next-Generation Ecosystem Experiments in the Arctic (NGEE Arctic) publication "Integrating Characteristic Arctic Vegetation in a Land Surface Model Improves Representation of Carbon Dynamics Across a Tundra Landscape", by Murphy et al. (2025a). Murphy et al. (2025a) evaluated whether incorporating observed Arctic vegetation heterogeneity into ELM, the land model of the Department of Energy’s Energy Exascale Earth System Model (E3SM), improved simulations of tundra carbon cycling. The associated model archive can be found at Murphy et al. (2025b). The study focused on the spatial patterns and net landscape-level growing season productivity and carbon uptake. As part of this evaluation, observationally derived maps of average growing season (June–August) net ecosystem exchange (NEE) and gross primary production (GPP) were developed for the same domain. These maps, which form the dataset described here, integrate eddy covariance flux tower, remote sensing, and vegetation community data to provide spatially explicit benchmarks for model evaluation. The maps provide spatially explicit estimates of average growing season NEE and GPP across 13 tundra vegetation communities within the study domain. By combining flux tower observations with Airborne Visible-Infrared Imaging Spectrometer-Next Generation (AVIRIS-NG) hyperspectral imagery and drone-based normalized difference vegetation index (NDVI), these maps capture the heterogeneity of carbon fluxes associated with different Arctic vegetation types. While they represent average seasonal conditions rather than interannual variability, the maps provide a unique dataset for evaluating model performance, comparing vegetation community contributions to landscape-scale carbon cycling, and supporting regional analyses of Arctic carbon dynamics. This data archive contains 5 m resolution maps of vegetation communities, vegetation community average growing season GPP, and vegetation community average growing season NEE (three *.tif files), a User’s Guide (*pdf file), and Table 1 of the User’s Guide displaying vegetation community coverage and average growing season NEE and GPP values (*.csv file).

Murphy, Bailey [ORNL] (ORCID:0000000203995221)↗

AGR-5/6/7 Irradiation As Run Predictions Using PARFUME

The PARticle FUel ModEl (PARFUME), a fuel performance modeling code used for high-temperature gas-cooled reactors, was used to model the Advanced Gas Reactor (AGR)-5/6/7 irradiation test using as-run physics and thermal data. The AGR-5/6/7 irradiation test consists of the combined fifth, sixth, and seventh planned irradiations of the AGR Fuel Development and Qualification Program. The AGR-5/6/7 test train is a multi-capsule, instrumented experiment that is designed for irradiation in the 133.4-mm diameter northeast flux trap position of the Advanced Test Reactor (ATR) at Idaho National Laboratory. Each capsule contains compacts filled with uranium oxycarbide unaltered fuel particles. This report documents the calculations performed to predict the failure probability of tristructural isotropic (TRISO)-coated fuel particles during the AGR-5/6/7 experiment. In addition, this report documents the calculated fission product release fraction from the fuel. The calculations include modeling of the AGR 5/6/7 irradiation that occurred from February 2018 to July 2020 over nine ATR cycles, including six normal cycles and three power axial locator mechanism cycles, for a total of approximately 376 effective full power days (EFPD). The irradiation conditions and material properties of the AGR-5/6/7 test predicted zero fuel particle failures in Capsules 1, 3, and 4. Fuel particle failures were predicted in two of the compacts in Capsule 2 and one particle failure is predicted in each one of the compacts in Capsule 5. All compacts that exhibited fuel particle failures predicted by PARFUME were caused by localized stress concentrations in the silicon carbide (SiC) layer caused by cracking in the inner pyrolytic (IPyC) layer. In addition, shrinkage of the buffer and IPyC layer during irradiation resulted in formation of a buffer-IPyC gap. Compacts with a lower irradiation temperature and fluence experienced the smallest buffer-IPyC gap formation. Conversely, higher irradiated temperature compacts with a high fluence experienced the largest buffer-IPyC gap formation. Compact 3-6-3 experienced the largest buffer IPyC gap formation of just under 21.7 µm. The release fraction of fission products silver (Ag), cesium (Cs), and strontium (Sr) vary depending on capsule location and irradiation temperature. The maximum release fraction of Ag occurs in Capsule 3, reaching up to 59.5% for the TRISO fuel particles (compact 3-6-3). The release fraction of the other two fission products, Cs and Sr, are much smaller. A maximum Cs release fraction of 1.1% occurred in compact 3-4-3 and 4.4% for Sr in compact 3-6-3.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

The Water Balance Representation in Urban‐PLUMBER Land Surface Models

Abstract Urban Land Surface Models (ULSMs) simulate energy and water exchanges between the urban surface and atmosphere. However, earlier systematic ULSM comparison projects assessed the energy balance but ignored the water balance, which is coupled to the energy balance. Here, we analyze the water balance representation in 19 ULSMs participating in the Urban‐PLUMBER project using results for 20 sites spread across a range of climates and urban form characteristics. As observations for most water fluxes are unavailable, we examine the water balance closure, flux timing, and magnitude with a score derived from seven indicators expecting better scoring models to capture the latent heat flux more accurately. We find that the water budget is only closed in 57% of the model‐site combinations assuming closure when annual total incoming fluxes (precipitation and irrigation) fluxes are within 3% of the outgoing (all other) fluxes. Results show the timing is better captured than magnitude. No ULSM has passed all water balance indicators for any site. Models passing more indicators do not capture the latent heat flux more accurately refuting our hypothesis. While output reporting inconsistencies may have negatively affected model performance, our results indicate models could be improved by explicitly verifying water balance closure and revising runoff parameterizations. By expanding ULSM evaluation to the water balance and related to latent heat flux performance, we demonstrate the benefits of evaluating processes with direct feedback mechanisms to the processes of interest.

Jongen, H. J.↗

Performance evaluation of automated data-driven feature extraction and selection methods for practical and scalable building energy consumption prediction models

Here, this study quantifies the impact of automated feature engineering methods (feature extraction and selection) on the quality and accuracy of machine learning models that predict building energy consumption. The case study compares model performance for three main scenarios: baseline (no feature extraction and selection), feature extraction only, and feature extraction combined with feature selection (filter and/or wrapper methods) for fully trained machine learning models for 200 metered/sub-metered energy measurements across 118 real buildings. For consistency, the same machine learning model architecture (a black box deep learning neural network with probabilistic forecast output) was used for all scenarios. Based on results, all feature engineering methods provided noticeable prediction accuracy improvements (e.g., 29%-68% median prediction improvement) compared to baseline scenarios. However, in this application, feature selection methods provide little practical value due to their limited performance gains and high computational cost. Smarter algorithm development supported by better computational environments will be needed before feature selection methods can reliably and efficiently improve predictive model performance.

97 MATHEMATICS AND COMPUTING↗

Radon-222 Charcoal Canister Steady State Model Calibrations Performed in a Highly Controlled Environmental Chamber and a Natural Indoor Environment

Charcoal canisters are a common method of 222 Rn screening. The calibrations of different batches of activated charcoal used in different canister designs are typically performed in large volume controlled environmental chambers with known and controlled radon concentration, temperature, and humidity. Radon screening could be facilitated in locations without ready access to environmental chambers if canisters could be accurately calibrated and undergo quality control in less controlled environments. This study compares charcoal canister calibrations from a highly controlled radon chamber with calibrations from a basement storage area experiencing temporally varying radon. In addition, the impacts of exposure time and spectral region of interest selection on calibration accuracy are investigated by comparing calibrations calculated using three different choices. Approximately 30 mo after calibrations were completed, groups of canisters were exposed for different durations of time to investigate measurement accuracy and calibration validity over an extended time. A digital simulation of charcoal canister kinetics was also performed to establish limits on how stable radon must be in a space for equilibrium-based calibration to be performed there. Overall, the accuracy of measurements using calibrations from each space differed by less than 10% after 2 d exposure time, showing that carefully controlled conditions are not necessary for the accurate calibration of charcoal canisters. Furthermore, measurement accuracy differed by less than 2% for different spectral region selections. Accuracy improved slightly with canister exposure duration. Simulations suggest that radon instability is most tolerable near the beginning of canister calibration exposures, but this merits further experimental study.

07 ISOTOPE AND RADIATION SOURCES↗

Enhancing Electron Microscopy Image Classification Using Data Augmentation

Manual labeling for machine learning tasks such as image classification is tedious and labor-intensive; as a result, scientific datasets suitable for deep learning applications are scarce and limited. While data augmentation techniques have shown promise for extending image datasets, very little work has been done to understand the impact of combining multiple augmentation methods sequentially or the limits of their effectiveness when combined. Our work addresses this gap by examining how standard and combinatorial data augmentation affects the performance of machine learning models when trained on small datasets for label classification tasks. For our analysis, we generate single, double and quadruple-augmented datasets for a microscopy image classification task using six standard augmentation methods, and compare the resultant improvements observed in binary classification accuracy with three standard image classification models (DenseNet169, MobileNetV2, ResNet101V2). Our experiments show a non-monotonic relationship between the number of simultaneous augmentation methods and classification accuracy, indicating that there is a trade-off between the degree of augmentation and the model performance. These findings suggest that the optimal number of augmentation methods will vary by domain and use case. We also find that the order in which augmentation methods are applied to a limited dataset matters when combining augmentation schemes, with our use case showing performance differences up to 2.6% when the augmentation order is reversed for double-augmented datasets. Our work offers insights to the limits of data augmentation when working on image classification tasks with limited datasets.

Welsman, Jordan A↗