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At least 1,369 records · Page 76

Predicting the oxidation states of Mn ions in the oxygen-evolving complex of photosystem II using supervised and unsupervised machine learning

Abstract Serial Femtosecond Crystallography at the X-ray Free Electron Laser (XFEL) sources enabled the imaging of the catalytic intermediates of the oxygen evolution reaction of Photosystem II (PSII). However, due to the incoherent transition of the S-states, the resolved structures are a convolution from different catalytic states. Here, we train Decision Tree Classifier and K-means clustering models on Mn compounds obtained from the Cambridge Crystallographic Database to predict the S-state of the X-ray, XFEL, and CryoEM structures by predicting the Mn’s oxidation states in the oxygen-evolving complex. The model agrees mostly with the XFEL structures in the dark S 1 state. However, significant discrepancies are observed for the excited XFEL states (S 2 , S 3, and S 0 ) and the dark states of the X-ray and CryoEM structures. Furthermore, there is a mismatch between the predicted S-states within the two monomers of the same dimer, mainly in the excited states. We validated our model against other metalloenzymes, the valence bond model and the Mn spin densities calculated using density functional theory for two of the mismatched predictions of PSII. The model suggests designing a more optimized sample delivery and illumiation systems are crucial to precisely resolve the geometry of the advanced S-states to overcome the noncoherent S-state transition. In addition, significant radiation damage is observed in X-ray and CryoEM structures, particularly at the dangler Mn center (Mn4). Our model represents a valuable tool for investigating the electronic structure of the catalytic metal cluster of PSII to understand the water splitting mechanism.

Plant Sciences↗

A Parallel Kinetic Model for Surface and Bulk Charge Storage in ε -MnO 2 Pseudocapacitors

Pseudocapacitive materials such as manganese dioxide (MnO 2 ) are attractive for energy storage applications due to their ability to combine the fast kinetics of capacitors with the higher energy density of battery-type systems. However, the electrochemical behavior of MnO 2 remains difficult to interpret mechanistically, in part because existing models often fail to distinguish between surface-based redox processes and bulk intercalation mechanisms. In this work, we develop a physics-based model that represents MnO 2 pseudocapacitance as a linear combination of two independent, parallel electrochemical processes: (i) the surface or near-surface redox storage and (ii) lithium ion intercalation into the bulk material. These two processes are treated with distinct kinetic and thermodynamic parameters and are assumed to proceed independently. The total measured current is assumed to be the sum of these two partial currents. We validate the model using rate-dependent cyclic voltammetry experiments, demonstrating that it captures key trends and provides physically interpretable parameters reflecting the relative contributions of surface and bulk processes. By enabling a clear separation between these mechanisms, the model offers a useful framework for analyzing pseudocapacitive materials and can guide the rational design of high-performance energy storage electrodes.

Energy - Storage↗

Projecting the Thermal Response in a HTGR-Type System during Conduction Cooldown Using Graph-Laplacian Based Machine Learning

Accurate prediction of an off-normal event in a nuclear reactor is dependent upon the availability of sensory data, reactor core physical condition, and understanding of the underlying phenomenon. This work presents a method to project the data from some discrete sensory locations to the overall reactor domain during conduction cooldown scenarios similar to High Temperature Gas-cooled Reactors (HTGRs). The existing models for conductive cooldown in a heterogeneous multi-body system, such as an assembly of prismatic blocks or pebble beds relies on knowledge of the thermal contact conductance, requiring significant knowledge of local thermal contacts and heat transport possibilities across those contacts. With a priori knowledge of bulk geometry features and some discrete sensors, a machine learning approach was devised. The presented work uses an experimental facility to mimic conduction cooldown with an assembly of 68 cylindrical rods initially heated to 1200 K. High-fidelity temperature data were collected using an infrared (IR) camera to provide training data to the model and validate the predicted temperature data. The machine learning approach used here first converts the macroscopic bulk geometry information into Graph-Laplacian, and then uses the eigenvectors of the Graph-Laplacian to develop Kernel functions. Support vector regression (SVR) was implemented on the obtained Kernels and used to predict the thermal response in a packed rod assembly during a conduction cooldown experiment. The usage of SVR modeling differs from most models today because of its representation of thermal coupling between rods in the core. When trained with thermographic data, the average normalized error is less than 2% over 400 s, during which temperatures of the assembly have dropped by more than 500 K. The rod temperature prediction performance was significantly better for rods in the interior of the assembly compared to those near the exterior, likely due to the model simplification of the surroundings.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Quantifying thermal barrier coating delamination through luminescence modeling

Thermal barrier coatings (TBCs) are widely used in the hot sections of gas turbine systems as they are remarkably efficient in insulating the underlying superalloys, leading to higher operating temperatures and therefore enhancing the performance of the engines. However, this benefit is only possible if the integrity of the TBC under aggressive thermo-mechanical environments is ensured. Delamination is a common but hard to detect failure mode. We present, in this work, supported by experimentation, the implementation of a modeling approach applying the Kubelka-Munk theory to provide numerical quantification of luminescence contrast and intensity due to top coat delamination in TBCs. The method relies on the drastic change in reflectivity when a delamination forms, exploiting it for high-contrast luminescence mapping. Two distinct TBC configurations containing an erbium-doped yttria-stabilized zirconia (YSZ:Er 3+ ) layer for delamination sensing were used to validate this model. A delamination zone induced by Rockwell indentation was successfully tracked by measuring an increase of the intensity of the erbium emission line at 562 nm. Luminescence-based methods for delamination detection can provide a revolutionary non-invasive technique, with potential for both off-line and on-line engine monitoring.

36 MATERIALS SCIENCE↗

Autodifferentiable Spectrum Model for High-dispersion Characterization of Exoplanets and Brown Dwarfs

We present an autodifferentiable spectral modeling of exoplanets and brown dwarfs. This model enables a fully Bayesian inference of the high-dispersion data to fit the ab initio line-by-line spectral computation to the observed spectrum by combining it with the Hamiltonian Monte Carlo in recent probabilistic programming languages. An open-source code, ExoJAX, developed in this study, was written in Python using the GPU/TPU compatible package for automatic differentiation and accelerated linear algebra, JAX. We validated the model by comparing it with existing opacity calculators and a radiative transfer code and found reasonable agreements for the output. As a demonstration, we analyzed the high-dispersion spectrum of a nearby brown dwarf, Luhman 16 A, and found that a model including water, carbon monoxide, and H 2 /He collision-induced absorption was well fitted to the observed spectrum (R = 10 5 and 2.28-2.30 μm). As a result, we found that T0 = 1295$^{-32}_{+35}$ K at 1 bar and C/O = 0.62 ± 0.03, which is slightly higher than the solar value. This work demonstrates the potential of a full Bayesian analysis of brown dwarfs and exoplanets as observed by high-dispersion spectrographs and also directly imaged exoplanets as observed by high-dispersion coronagraphy.

79 ASTRONOMY AND ASTROPHYSICS↗

Measuring binary fluidization of nonspherical and spherical particles using machine learning aided image processing

Abstract The binary fluidization of Geldart D type nonspherical wood particles and spherical low density polyethylene (LDPE) particles was investigated in a laboratory‐scale bed. The experiment was performed for varying static bed height, wood particles count, as well as superficial gas velocity. The LDPE velocity field were quantified using particle image velocimetry (PIV). The wood particles orientation and velocity are measured using particle tracking velocimetry (PTV). A machine learning pixel‐wise classification model was trained and applied to acquire wood and LDPE particle masks for PIV and PTV processing, respectively. The results show significant differences in the fluidization behavior between LDPE only case and binary fluidization case. The effects of wood particles on the slugging frequency, mean, and variation of bed height, and characteristics of the particle velocities/orientations were quantified and compared. This comprehensive experimental dataset serves as a benchmark for validating numerical models.

Li, Cheng↗

Analysis of gas storage and transport in Eagle Ford shale using pressure pulse decay measurements with He, Kr and CO 2

Detailed characterization of gas transport and storage in low-permeability and organic-rich shales is associated with an array of challenges due to the complex morphology of the pore space, representing a broad range of pore sizes, combined with the heterogeneous fabric of the shale matrix. These factors, and their interplay during gas transport and sorption, complicate a) the analysis of shale samples at the laboratory scale (~ up to a ft. In length), and b) the prediction of natural gas production and carbon sequestration potential at larger scales. Here, in this work, tandem experiments with inert (helium – He) and adsorbing (krypton - Kr and carbon dioxide - CO 2 ) gases were performed and analyzed to develop an efficient workflow for characterizing and modeling transport and sorption at the laboratory scale. In particular, pressure pulse-decay (PPD) measurements were conducted on an Eagle Ford shale core sample at room temperature using He, Kr, and CO 2 . PPD measurements with He (a non-sorbing gas) were employed to probe the overall porosity, including natural fractures, microcracks, mesopores, and micropores. A triple-porosity model (TPM) was adopted to interpret the gas transport in the shale sample: The pore space is represented by three interacting continua, including macropores (larger fractures), mesopores (including microcracks), and micropores. To facilitate the application of the TPM, a modified analytical approach is introduced to extract effective transport parameters (in terms of the characteristic time for transport at relevant porosity levels) directly from the PPD measurements with He. To validate the modeling approach, model parameters extracted from two He PPD measurements are demonstrated to provide excellent agreement with a 3rd He PPD measurement performed at a higher pressure. The effective transport parameters, extracted from the He experiments, were subsequently converted for application to the Kr and CO 2 PPD experiments, by accounting for relevant transport modes and differences in fluid properties. Excess adsorption isotherms were extracted from the equilibrium pressures of the Kr and CO 2 PPD experiments using the He pore volume as a baseline. These adsorption isotherms were then integrated into the TPM to predict combined gas transport and sorption for Kr and CO 2 , with transport coefficients translated from the He measurements. The predictions for Kr and CO 2 are demonstrated to be in excellent agreement with the experimental observations. This, in turn, demonstrates that the proposed analytical approach provides for an effective characterization of mass transfer rates in shales, that can be applied directly in a TPM representation of mass transfer and sorption.

58 GEOSCIENCES↗

Automated annotation of scientific texts for ML-based keyphrase extraction and validation

Advanced omics technologies and facilities generate a wealth of valuable data daily; however, the data often lack the essential metadata required for researchers to find, curate, and search them effectively. The lack of metadata poses a significant challenge in the utilization of these data sets. Machine learning (ML)–based metadata extraction techniques have emerged as a potentially viable approach to automatically annotating scientific data sets with the metadata necessary for enabling effective search. Text labeling, usually performed manually, plays a crucial role in validating machine-extracted metadata. However, manual labeling is time-consuming and not always feasible; thus, there is a need to develop automated text labeling techniques in order to accelerate the process of scientific innovation. This need is particularly urgent in fields such as environmental genomics and microbiome science, which have historically received less attention in terms of metadata curation and creation of gold-standard text mining data sets. In this paper, we present two novel automated text labeling approaches for the validation of ML-generated metadata for unlabeled texts, with specific applications in environmental genomics. Our techniques show the potential of two new ways to leverage existing information that is only available for select documents within a corpus to validate ML models, which can then be used to describe the remaining documents in the corpus. The first technique exploits relationships between different types of data sources related to the same research study, such as publications and proposals. The second technique takes advantage of domain-specific controlled vocabularies or ontologies. In this paper, we detail applying these approaches in the context of environmental genomics research for ML-generated metadata validation. Our results show that the proposed label assignment approaches can generate both generic and highly specific text labels for the unlabeled texts, with up to 44% of the labels matching with those suggested by a ML keyword extraction algorithm.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Edge ML for CAN bus intrusion detection in AVs

Autonomous Vehicles (AVs) are revolutionizing transportation, but their reliance on interconnected cyber-physical systems exposes them to unprecedented cybersecurity risks. This study addresses the critical challenge of detecting real-time cyber intrusions in self-driving vehicles by leveraging a dataset from the Udacity self-driving car project. We simulate four high-impact attack vectors, Denial of Service (DoS), spoofing, replay, and fuzzy attacks, by injecting noise into spatial features (e.g., bounding box coordinates) to replicate adversarial scenarios. We develop and evaluate two lightweight neural network architectures (NN-1 and NN-2) alongside a logistic regression baseline (LG-1) for intrusion detection. The models achieve exceptional performance, with NN-2 attaining an AUC score of 93.15% and 93.15% accuracy, demonstrating their suitability for edge deployment in AV environments. Through explainable AI techniques, we uncover unique forensic fingerprints of each attack type, such as spatial corruption in fuzzy attacks and temporal anomalies in replay attacks, offering actionable insights for feature engineering and proactive defense. Visual analytics, including confusion matrices, ROC curves, and feature importance plots, validate the models' robustness and interpretability. This research sets a new benchmark for AV cybersecurity, delivering a scalable, field-ready toolkit for Original Equipment Manufacturers (OEMs) and policymakers. By aligning intrusion fingerprints with SAE J3061 automotive security standards, we provide a pathway for integrating machine learning into safety-critical AV systems. Our findings underscore the urgent need for security-by-design AI, ensuring that AVs not only drive autonomously but also defend autonomously. This work bridges the gap between theoretical cybersecurity and life-preserving engineering, offering a leap toward safer, more secure autonomous transportation.

97 MATHEMATICS AND COMPUTING↗

Development of Training Materials for Pathologists to Provide Machine Learning Validation Data of Tumor-Infiltrating Lymphocytes in Breast Cancer

The High Throughput Truthing project aims to develop a dataset for validating artificial intelligence and machine learning models (AI/ML) fit for regulatory purposes. The context of this AI/ML validation dataset is the reporting of stromal tumor-infiltrating lymphocytes (sTILs) density evaluations in hematoxylin and eosin-stained invasive breast cancer biopsy specimens. After completing the pilot study, we found notable variability in the sTILs estimates as well as inconsistencies and gaps in the provided training to pathologists. Using the pilot study data and an expert panel, we created custom training materials to improve pathologist annotation quality for the pivotal study. We categorized regions of interest (ROIs) based on their mean sTILs density and selected ROIs with the highest and lowest sTILs variability. In a series of eight one-hour sessions, the expert panel reviewed each ROI and provided verbal density estimates and comments on features that confounded the sTILs evaluation. We aggregated and shaped the comments to identify pitfalls and instructions to improve our training materials. From these selected ROIs, we created a training set and proficiency test set to improve pathologist training with the goal to improve data collection for the pivotal study. We are not exploring AI/ML performance in this paper. Instead, we are creating materials that will train crowd-sourced pathologists to be the reference standard in a pivotal study to create an AI/ML model validation dataset. The issues discussed here are also important for clinicians to understand about the evaluation of sTILs in clinical practice and can provide insight to developers of AI/ML models.

60 APPLIED LIFE SCIENCES↗

Validation of the Fault Ride-Through Response of a Generic EMT Inverter Model by Laboratory Testing

This paper presents the validation of the fault ride-through response of a large-scale inverter model using laboratory testing of a commercial inverter. First, we present the generic inverter model specifications. The generic inverter control is developed based on the fault ride-through response performance requirements of IEEE Std 2800-2022 for inverter-based resources. Next, we present laboratory tests that emulate voltages at the inverter terminal resulting from balanced and unbalanced faults on the transmission system. The tests are performed on a commercia12.2 MVA battery storage inverter at the U.S. National Renewable Energy Laboratory. Comparisons of the model's response to the laboratory measurements show the generic model presented can predict the controlled response of the commercial equipment. The differences between the model's response and the laboratory measurements during the initial transient at fault inception are discussed.

fault ride-through↗

Modal Analysis of Ultrasonic Spot Welding for Lightweight Metals Joining

Ultrasonic spot welding (USW) represents one of the unique solid-state joining methods for lightweight materials such as magnesium alloy and aluminum alloy. However, the sonotrode vibration may have a detrimental impact on the sheet material and the existing welds, depending on the component geometry and vibration frequency. In this study, a modal analysis tool based on steady-state dynamics was developed for ultrasonic spot welding which features a cyclic load applied to the sheets during the joining process. Through predicting relative motion and shear stress at the faying surfaces, coupon geometry and weld spacing are identified as two major factors that affect the welding reliability and joint quality in USW. The model was validated via welding experiments on aluminum alloy and magnesium alloy and relevant characterization of temperature distribution, joint strength as well as fracture location.

36 MATERIALS SCIENCE↗

Seismicity-constrained fault detection and characterization with a multitask machine learning model

Geological fault detection and characterization are crucial for understanding subsurface dynamics across scales. While methods for fault delineation based on either seismicity location analysis or seismic image reflector discontinuity are well-established, a systematic approach that integrates both data types remains absent. We develop a novel machine learning model that unifies seismic reflector images and seismicity location information to automatically identify geological faults and characterize their geometrical properties. The model encodes a seismic image and a seismicity location image separately, and fuses the encoded features with a spatial-channel attention fusion module to improve the learning of important features in both inputs. We design an automated strategy to generate high-quality synthetic training data and labels. To improve the realism of the seismicity location image, we include random seismicity noise and missing seismicity location associated with some of the faults. We validate the model’s efficacy and accuracy using synthetic data examples and two field data examples. Moreover, we show that fine-tuning the trained model with a small, domain-specific dataset enhances its fidelity for field data applications. The results demonstrate that integrating seismicity location and seismic images into a unified framework allows the end-to-end neural network to achieve higher fidelity and accuracy in delineating subsurface faults and their geometrical properties compared with image-only fault detection methods. Our approach offers an adaptive data-driven tool for geological fault characterization and seismic hazard mitigation, bridging the gap between seismicity location and image-based fault detection methods.

58 GEOSCIENCES↗

Statistically-informed deep learning for gravitational wave parameter estimation

We introduce deep learning models to estimate the masses of the binary components of black hole mergers, $(m_1,m_2)$, and three astrophysical properties of the post-merger compact remnant, namely, the final spin, $a_\mathrm f$, and the frequency and damping time of the ringdown oscillations of the fundamental $\ell = m = 2$ bar mode, $(\omega_\mathrm R, \omega_\mathrm I)$. Our neural networks combine a modified WaveNet architecture with contrastive learning and normalizing flow. We validate these models against a Gaussian conjugate prior family whose posterior distribution is described by a closed analytical expression. Upon confirming that our models produce statistically consistent results, we used them to estimate the astrophysical parameters $(m_1,m_2, a_\mathrm f, \omega_\mathrm R, \omega_\mathrm I)$ of five binary black holes: GW150914, GW170104, GW170814, GW190521 and GW190630. We use PyCBC Inference to directly compare traditional Bayesian methodologies for parameter estimation with our deep learning based posterior distributions. Our results show that our neural network models predict posterior distributions that encode physical correlations, and that our data-driven median results and 90% confidence intervals are similar to those produced with gravitational wave Bayesian analyses. This methodology requires a single V100 NVIDIA GPU to produce median values and posterior distributions within two milliseconds for each event. Furthermore, this neural network, and a tutorial for its use, are available at the Data and Learning Hub for Science.

79 ASTRONOMY AND ASTROPHYSICS↗

Quantitative Analysis of the Effects of Natural and Human Factors on a Hydrological System in Zhangweinan Canal Basin

Drought is a water deficit state caused by large-scale climate change that cannot be avoided by a water resource management system. Water scarcity refers to the unsustainable utilization of water resources over a long time, which is the result of water management policies. However, water deficits caused by drought and water scarcity often occur simultaneously and are indistinguishable. This study proposes a model-based simulation framework that can quantitatively distinguish natural factors (drought) from human factors (water scarcity) in a hydrological system. The simulation was applied to the Zhangweinan Canal Basin, based on the runoff sequences from 1950 to 2004. The results show that the runoff curve number, soil depth, soil available water, soil evaporation compensation coefficient, base runoff α coefficient and the maximum canopy interception have the highest sensitivity to runoff, and that the calibrated and validated SWAT model can effectively simulate the runoff process in the Zhangweinan Canal Basin and similar areas. Abrupt changes in human activities in 1975 and water scarcity led to the disappearance of the summer peak runoff period in both wet and dry years. Human factors are the main reason for the change in the hydrological system in the study area; the runoff loss caused by human factors is four times that caused by natural factors according to the proposed variable threshold. This study proposes a model-based simulation framework that can help water resource managers to distinguish the effects of drought and water scarcity in water-stressed areas and adjust management accordingly.

54 ENVIRONMENTAL SCIENCES↗

MULTIPHYSICS-MODELING OF FIRE-INDUCED URANIUM AEROSOL FORMATION – A-POSTERIORI BENCHMARKING OF EXPERIMENTS

The formulation and solution of a model that properly described the temperature profiles of uranium in fire conditions was prepared, verified and validated, to support a-posteriori benchmarking of historical experiments. Data from the multi-physics model combined with data regression from the experiments provides a useful tool for exploring sources of potential bias in historical experiments. The approaches used are augmented by visual observations and photographic evidence allowing for correlations between various phenomena, independent of whether or not that specific phenomena are part of the validated model. In this manner, the validated model is a tool for a-posteriori benchmarking, and not a model designed to replicate the experimental output exactly for any specific experiment. For experiments like the Clark (2015) experiments, this integrated model (including chemistry) demonstrated that the largest bias was associated in the metallurgy of the coupons. The model developed does serve as a basis for defending which of the historical alloys tested are the most appropriate for any other alloy being considered (e.g., one that has not yet been tested). The model identifies key reactions that impact uranium chemistry and can significantly bias experimental results. Through use of the model and energy balances, data from historical experiments by Elder and Tinkle (1980) were regressed and benchmarked. This study identifies that all uranium alloys are not equal and that there are distinct differences between the dominant alloys representing distinct metallurgical phases.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Predictive turbulence-driven flux model of scrape-off layer widths across confinement regimes in tokamaks

Reliable scrape-off layer (SOL) profile decay lengths predictions are needed to design and operate future tokamaks. The present manuscript describes a new model based on turbulent transport that is able to predict SOL widths for both L-mode and H-mode plasmas. The model is based upon the sheared-spectral filament paradigm (Peret et al (WEST Team) 2022 Phys. Plasmas 29 072306), however, incorporating the effects of thermal transport in order to calculate the parallel heat fluxes. The effects of magnetic shear and ExB shear on the cross-field transport are crucial to explain the shorter SOL decay lengths found in H-mode. The model is validated against a database of thousands of DIII-D L-mode and H-mode SOL profiles. We also calculate SOL decay length predictions in terms of plasma and engineer control parameters, which are in agreement with the multi-machine empirical H-mode scaling (Eich et al (ASDEX Upgrade Team and JET EFDA Contributors) 2013 Nucl. Fusion 53 093031), however, with an additional device geometry dependence. ITER SOL width predictions by the model are 3 times higher than the empirical scaling.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

TULIP: An RNA-seq-based Primary Tumor Type Prediction Tool Using Convolutional Neural Networks

Background: With cancer as one of the leading causes of death worldwide, accurate primary tumor type prediction is critical in identifying genetic factors that can inhibit or slow tumor progression. There have been efforts to categorize primary tumor types with gene expression data using machine learning, and more recently with deep learning, in the last several years. Methods In this paper, we developed four 1-dimensional (1D) Convolutional Neural Network (CNN) models to classify RNA-seq count data as one of 17 highly represented primary tumor types or 32 primary tumor types regardless of imbalanced representation. Additionally, we adapted the models to take as input either all Ensembl genes (60,483) or protein coding genes only (19,758). Unlike previous work, we avoided selection bias by not filtering genes based on expression values. RNA-seq count data expressed as FPKM-UQ of 9,025 and 10,940 samples from The Cancer Genome Atlas (TCGA) were downloaded from the Genomic Data Commons (GDC) corresponding to 17 and 32 primary tumor types respectively for training and validating the models. Results: All 4 1D-CNN models had an overall accuracy of 94.7% to 97.6% on the test dataset. Further evaluation indicates that the models with protein coding genes only as features performed with better accuracy compared to the models with all Ensembl genes for both 17 and 32 primary tumor types. For all models, the accuracy by primary tumor type was above 80% for most primary tumor types. Conclusions: We packaged all 4 models as a Python-based deep learning classification tool called TULIP (TUmor CLassIfication Predictor) for performing quality control on primary tumor samples and characterizing cancer samples of unknown tumor type. Further optimization of the models is needed to improve the accuracy of certain primary tumor types.

Jones, Sara↗