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At least 235 records · Page 13

Knowledge-guided graph machine learning for spatially distributed prediction of daily discharge and nitrogen export dynamics

Spatially distributed prediction of streamflow and nitrogen export dynamics is essential for precision management of agricultural watersheds. While temporal deep learning models such as Long Short-Term Memory (LSTM) have shown strong performance at basin scales, their ability to generalize spatially is limited by insufficient representation of spatial dependencies and flow paths, particularly under data-scarce conditions. To address this gap, we propose HydroGraphNet, a knowledge-guided graph machine learning framework that integrates process-based knowledge and explicit spatial learning into temporal modeling. This framework incorporates directed graph topology to encode watershed connectivity and upstream inflows, with mass balance constraints to improve physical consistency. To enhance generalization in sparsely monitored regions, HydroGraphNet is pretrained on synthetic data generated by the SWAT+ (Soil and Water Assessment Tool Plus) model. We evaluated HydroGraphNet in the Upper Sangamon River Basin (44 HUC-12 subwatersheds, 2001–2020) against two LSTM baselines: a lumped basin-level model and a distributed variant. When benchmarked on SWAT+ simulations in pretraining, HydroGraphNet improved test NSEs by 8.9% (discharge) and 13.7% (NO₃–N load) in temporal extrapolation, and by 27.1% and 34.7% in spatial extrapolation, relative to the Lumped LSTM baseline. After fine-tuning with USGS monitoring data, the model achieved mean test NSE (KGE) scores of 0.768 (0.861) for discharge and 0.626 (0.664) for NO₃–N load, substantially outperforming baselines. Attribution analysis further highlighted the importance of upstream inflow representation and graph-based spatial learning in capturing cross-subwatershed dependencies. The model also reproduced seasonal hydrological and biogeochemical patterns consistent with known processes, demonstrating its robustness and process fidelity for spatially distributed prediction. Altogether, HydroGraphNet advances the integration of physical knowledge and spatially explicit learning in hydrological modeling, offering a generalizable framework for distributed modeling to support spatially targeted water quality management in data-scarce watersheds.

54 ENVIRONMENTAL SCIENCES↗

Full wave modeling of radio-frequency beams in tokamaks in the electron cyclotron frequency range

Simulation of full wave, without paraxial approximation, high-resolution solution of wave equations in frequency domain in the electron cyclotron resonance (ECR) frequency range for realistic Tokamak plasma parameters became possible by using recently formulated hybrid iterative algorithm [Svidzinski et al., Phys. Plasmas 25, 082509 (2018)] for numerically solving discretized wave equations. This approach combines time evolution and iterative relaxation techniques into iteration cycles. This algorithm is implemented in 2D code FullWave, solving wave equations in Tokamaks in cold and hot plasma models, and it has been tested in 3D full wave iterative RF beams simulation tool, which is presently being developed to model 3D ECRH RF beams in fusion devices using dynamic grid adaptation. The results of 2D full wave modeling, assuming specified toroidal mode number, of ECRH RF beams in DIII-D plasma, performed in the cold and hot plasma models for outboard and top launch scenarios using FullWave are presented. Nonlocal hot plasma response model, based on accurate numerical solution of linearized Vlasov equation, is used to model beam propagation and absorption in the 2nd electron cyclotron harmonic region. Demonstration of capability of the hybrid iterative algorithm to model ECRH RF beams in 3D is made by simulating a substantial part of realistic beam in DIII-D, launched from outboard side of the machine. All relevant physics of RF beam propagation, most of which is not captured in paraxial approximation, such as beam's divergence, interference between the X and O modes in the beam, X-O mode conversion, beam splitting into the X and O mode beams, transformation of beam's cross section, and absorption at the 2nd electron cyclotron harmonic, is captured in the simulations. A numerical technique to find an optimal beam polarization at the launcher to launch a nearly pure X or O mode beam in plasma is developed and tested.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

An innovative and alternative approach toward gear fabrication

In this paper, we present the first demonstration of single-step gear manufacturing via an innovative in-situ friction stir forging approach. This novel process is a natural extension to the friction stir processing technique and relies on shear and normal stresses to form the complex shapes. Friction stir welding pin tool with shoulder is plunged at high revolutions per minute (rpm) into the sample to heat it to the desired temperature and enable plastic flow. Then, the tool is forged at high plunge rate to form the desired structurally-sound and defect free complex shapes. To better visualize the process the experiments are complemented by a 3D thermomechanically coupled, smoothed particle hydrodynamics (SPH) model to understand the material flow pattern both radially and through thickness in the gear teeth, plastic strain distribution, and temperature profile. We have demonstrated application of I-FSF to inherently poor formable AZ31 Mg, AA 7075-T6, and AA5083–10 vol% TiB 2 composite and fabricated 14-tooth spur gears from these materials with minimal farther machining. In conclusion, microstructure of the forged gears exhibited a directional material flow pattern due to the normal forging action and refinement of grains to 6–13 μm through dynamically recrystallization across the radial, through-thickness direction, which is in good agreement with the corresponding SPH simulation results.

42 ENGINEERING↗

From predicting to learning dissipation from pair correlations of active liquids

Active systems, which are driven out of equilibrium by local non-conservative forces, can adopt unique behaviors and configurations. Towards designing such materials, an important challenge is to precisely connect the static structure of active systems to the dissipation of energy induced by the local driving. Here, we use tools from liquid-state theories and machine learning to take on these challenges. We first demonstrate analytically for an isotropic active matter system that dissipation and pair correlations are closely related when driving forces behave like an active temperature. We then extend a nonequilibrium mean-field framework for predicting these pair correlations which, unlike most existing approaches, is applicable even for strongly interacting particles and far from equilibrium, to predict dissipation in these systems. Based on this theory, we reveal analytically a robust relation between dissipation and structure which holds even as the system approaches a nonequilibrium phase transition. Finally, we construct a neural network which maps static configurations of particles to their dissipation rate without any prior knowledge of the underlying dynamics. Furthermore, our results open novel perspectives on the interplay between dissipation and organization out-of-equilibrium.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Visualizing group II intron dynamics between the first and second steps of splicing

Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5’-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Machine learning mathematical models for incidence estimation during pandemics

Accurate estimates of the incidence of infectious diseases are key for the control of epidemics. However, healthcare systems are often unable to test the population exhaustively, especially when asymptomatic and paucisymptomatic cases are widespread; this leads to significant and systematic under-reporting of the real incidence. Here, we propose a machine learning approach to estimate the incidence of a pandemic in real-time, using reported cases and the overall test rate. In particular, we use Bayesian symbolic regression to automatically learn the closed-form mathematical models that most parsimoniously describe incidence. We develop and validate our models using COVID-19 incidence values for nine different countries, confirming their ability to accurately predict daily incidence. Remarkably, despite the differences in epidemic trajectories and dynamics across countries, we find that a single model for all countries offers a more parsimonious description and is more predictive of actual incidence compared to separate models for each country. Our results show the potential to accurately model incidence in real-time using closed-form mathematical models, providing a valuable tool for public health decision-makers.

Fajardo-Fontiveros, Oscar (ORCID:0000000207058972)↗

Persistent Protein Motions in a Rugged Energy Landscape Revealed by Normal Mode Ensemble Analysis

Proteins are allosteric machines that couple motions at distinct, often distant, sites to control biological function. Low-frequency structural vibrations are a mechanism of this long-distance connection and are often used computationally to predict correlations, but experimentally identifying the vibrations associated with specific motions has proved challenging. Spectroscopy is an ideal tool to explore these excitations, but measurements have been largely unable to identify important frequency bands. The result is at odds with some previous calculations and raises the question what methods could successfully characterize protein structural vibrations. Here we show the lack of spectral structure arises in part from the variations in protein structure as the protein samples the energy landscape. However, by averaging over the energy landscape as sampled using an aggregate 18.5 μs of all-atom molecular dynamics simulation of hen egg white lysozyme and normal-mode analyses, we find vibrations with large overlap with functional displacements are surprisingly concentrated in narrow frequency bands. These bands are not apparent in either the ensemble averaged vibrational density of states or isotropic absorption. However, in the case of the ensemble averaged anisotropic absorption, there is persistent spectral structure and overlap between this structure and the functional displacement frequency bands. We systematically lay out heuristics for calculating the spectra robustly, including the need for statistical sampling of the protein and inclusion of adequate water in the spectral calculation. The results show the congested spectrum of these complex molecules obscures important frequency bands associated with function and reveal a method to overcome this congestion by combining structurally sensitive spectroscopy with robust normal mode ensemble analysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Multimodal super-resolution: discovering hidden physics and its application to fusion plasmas

Understanding complex physical systems often requires integrating data from multiple diagnostics, each with limited resolution or coverage. We present a machine learning framework that reconstructs synthetic high-temporal-resolution data for a target diagnostic using information from other diagnostics, without direct target measurements during the inference. This multimodal super-resolution technique improves diagnostic robustness and enables monitoring even in case of measurement failures or degradation. Applied to fusion plasmas, our method targets edge-localized modes (ELMs), which can damage plasma-facing materials. By reconstructing super-resolution Thomson Scattering data from complementary diagnostics, we uncover fine-scale plasma dynamics and validate the role of resonant magnetic perturbations (RMPs) in ELM suppression through magnetic island formation. The approach provides new observation supporting the plasma profile flattening due to these islands. Our results demonstrate the framework’s ability to generate high-fidelity synthetic diagnostics, offering a powerful tool for ELM control development in future reactors like ITER. The approach is broadly transferable to other domains facing sparse, incomplete, or degraded diagnostic data, opening new avenues for discovery.

Jalalvand, Azarakhsh [Princeton Univ., NJ (United ↗

Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures

Abstract Large biomolecular structures are being determined experimentally on a daily basis using established techniques such as crystallography and electron microscopy. In addition, emerging integrative or hybrid methods (I/HM) are producing structural models of huge macromolecular machines and assemblies, sometimes containing 100s of millions of non-hydrogen atoms. The performance requirements for visualization and analysis tools delivering these data are increasing rapidly. Significant progress in developing online, web-native three-dimensional (3D) visualization tools was previously accomplished with the introduction of the LiteMol suite and NGL Viewers. Thereafter, Mol* development was jointly initiated by PDBe and RCSB PDB to combine and build on the strengths of LiteMol (developed by PDBe) and NGL (developed by RCSB PDB). The web-native Mol* Viewer enables 3D visualization and streaming of macromolecular coordinate and experimental data, together with capabilities for displaying structure quality, functional, or biological context annotations. High-performance graphics and data management allows users to simultaneously visualise up to hundreds of (superimposed) protein structures, stream molecular dynamics simulation trajectories, render cell-level models, or display huge I/HM structures. It is the primary 3D structure viewer used by PDBe and RCSB PDB. It can be easily integrated into third-party services. Mol* Viewer is open source and freely available at https://molstar.org/.

Sehnal, David↗

Advanced Modeling of Beam Physics and Performance Optimization for Nuclear Physics Colliders

High energy colliders provide a critical tool in nuclear physics study by probing the fundamental structure and dynamics of matter. To maximize the potential of scientific discovery in nuclear physics study, it is important to optimize the parameters of these colliders to attain the best performance. The performance of a collider is typically measured by its integrated luminosity of colliding beams since the probability of a new event is proportional to the integrated luminosity. However, the achievable luminosity is limited by the electromagnetic interactions (beam-beam effects) of two colliding beams at higher energy, and the interplay between the space-charge effects and the beam-beam effects at lower energy. To achieve the best performance of a collider means to attain the highest luminosity of the collider with optimized collider parameters. Optimizing the collider’s machine parameters is both computationally and experimentally expensive. A fast and robust computational framework including beam-beam and space-charge effects will be critical to attaining the best performance of the collider. In this project, we will study the beam dynamics challenges, specifically the interplay of the space-charge and the beam-beam effects, and the machine tuning models for maximizing the performance of RHIC experiments. We will develop an advanced modeling framework based on first-principles physical simulations, lattice models and the state-of-the-art machine learning methods and apply this framework to performance improvement of the RHIC in operation. We will build data manipulation packages to connect the simulation data and the experimental data with the framework, develop a self-consistent hybrid model of space-charge and beam-beam effects, study underlying physics mechanisms, build surrogate models using the labeled data, integrate the models into the advanced modeling framework, and apply the framework to RHIC luminosity (STAR and sPHENIX) optimization. The success of this project would substantially improve the performance of existing and future colliders and increase the opportunity for scientific discovery.

43 PARTICLE ACCELERATORS↗

Data from: "Towards CONUS-Wide ML-Augmented Conceptually-Interpretable Modeling of Catchment-Scale Precipitation-Storage-Runoff Dynamics"

This data package was generated to support the manuscript “Towards CONUS-Wide Machine Learning-Augmented Conceptually Interpretable Modeling of Catchment-Scale Precipitation-Storage-Runoff Dynamics.” It provides input files, model outputs, plotting data, scripts, notebooks, and documentation used to develop, evaluate, and reproduce Mass-Conserving Perceptron (MCP)-based hydrologic modeling experiments across 513 selected Catchment Attributes and Meteorology for Large-sample Studies in the United States (CAMELS-US) basins. The files are organized by modeling component and analysis purpose, including rainfall–runoff experiments, snow module experiments, coupled hydrologic-snow experiments, Long Short-Term Memory (LSTM) benchmark results, model skill metrics, initialization and epoch records, cell-state normalization files, Akaike Information Criterion (AIC)-based model comparison files, and data used to generate manuscript figures. Tabular files can be opened using standard spreadsheet software or Python/R data-analysis tools. Python scripts, Jupyter notebooks, and selected MATLAB scripts are included for model execution, postprocessing, plotting, and statistical analysis. Quality assurance and quality control were conducted through the source-data selection and modeling workflow. Meteorological forcing, streamflow, and static catchment attributes were derived from the CAMELS-US dataset, and snow water equivalent data were derived from the University of Arizona (UA) Snow Water Equivalent dataset. Selected basins and time periods were screened during the associated research workflow to avoid missing observations or poor-quality cases. Static geospatial features were processed primarily using Quantum Geographic Information System (QGIS) and Geospatial Data Abstraction Library (GDAL) workflows. Additional details are provided in the associated manuscript and documentation.

ESS-DIVE CSV File Formatting Guidelines Reporting ↗

Validation of Phasor-Domain Transmission and Distribution Co-simulation Against Electromagnetic Transient Simulation

The rapid deployment of renewable energy resources has led to the widespread use of power electronics in modern power systems. As these systems transition from being dominated by large synchronous machines to increasingly incorporating inverter-based resources (IBRs), traditional methods are becoming inadequate. Addressing this challenge, this paper introduces a scalable phasor-domain T\&D co-simulation framework based on open-source software. It focuses on the framework's validation against the PSCAD Electromagnetic Transient (EMT) analysis tool. The validation results demonstrate the framework's high-fidelity and a computational time speed-up of 60 to 100 times, marking a pioneering validation effort in T\&D co-simulation research.

Inverter-based resources, co-simulation, Electroma↗

Robust Real-Time Modeling of Distribution Systems with Data-Driven Grid-Wise Observability (Final Technical Report)

The overall objective of this project is to leverage existing and emerging sensor measurements to develop data-driven observability enhancement algorithms as well as robust state estimation and parameter identification techniques to enable real-time grid-wise monitoring and modeling of loads and distributed energy resources (DERs). The project resulted in a holistic framework with the following key components: 1) data-driven and machine learning-based grid-edge visibility enhancement, 2) robust branch-current-based state estimation (BCSE), and 3) robust real-time steady-state and dynamic-state modeling of loads and DERs. The research outcomes have provided utility companies better network visibility, higher-fidelity load/DER models, and more accurate assessment of DERs’ impacts, thus, facilitating the integration of renewable energy sources. The synergistic collaborative project among Iowa State University (ISU), Argonne National Laboratory (ANL), Electric Power Research Center (EPRC), SIEMENS Industry, Alliant Energy, Cedar Falls Utilities (CFU), and Maquoketa Valley Electric Cooperative (MVEC) to leverage the team’s extensive expertise and experience in power distribution systems, state estimation, online modeling and identification, and DER integrations. The proposed frameworks have been verified with industry adopted software and attempted integrated with existing tool wherever possible

24 POWER TRANSMISSION AND DISTRIBUTION↗

Landscaper v1

Understanding the inner workings of machine learning models through their loss landscapes offers crucial insights into model properties, optimization dynamics, and generalizability. However, accessing these insights has traditionally required specialized mathematical expertise, limiting broader adoption. Landscaper is an open-source Python package designed to bridge this gap. Landscaper seamlessly integrates a suite of multi-dimensional loss landscape analyses with cutting-edge topological data analysis (TDA) methods. This powerful combination makes both fundamental loss landscape analysis and advanced TDA techniques accessible to the broader scientific ML community, without requiring deep pre-existing mathematical knowledge. Landscaper offers three key functionalities: * Construction: Builds detailed loss landscape representations through versatile low and high-dimensional sampling techniques. * Quantification: Applies advanced metrics, including a novel topological data analysis (TDA) based smoothness metric, enabling new perspectives on model behavior. * Visualization: Offers intuitive tools to visualize and interpret loss landscapes, providing actionable insights beyond traditional performance metrics.

Weber, Gunther [Lawrence Berkeley National Laborat↗

Multi-Timescale Integrated Dynamics and Scheduling for Solar (MIDAS-Solar) (Final Technical Report)

Solar photovoltaic (PV) installations have experienced unprecedented growth in the United States. PV will become not only an energy producer but also a necessary provider of ancillary services at multiple timescales. Conventional methods to simulate power systems operations - such as long-term production simulation (which typically considers schedules from hours to minutes by using an optimization framework) and short-term transient studies (which simulate dynamics from seconds to sub-seconds using state variables and differential equations) - are not sufficient for studying the multiple-timescale variation of solar generation and its impact on system reliability. Long-term system economics and short-term system dynamics are highly coupled, particularly when the penetration level of renewable generation is extremely high, because the uncertainty and variability of solar generation will impact both power system steady-state and dynamic performance. This project helps meet and exceed the U.S. Department of Energy Office of Energy Efficiency and Renewable Energy Solar Energy Technologies Office goal of systems integration by directly addressing this stability and reliability challenge for power grid planning and operation. We have developed a temporally comprehensive, closed-loop simulation model, named Multi-timescale Integrated Dynamics and Scheduling (MIDAS), that seamlessly simulates power system operations from economic scheduling (day-ahead to hours) to dynamic response analysis (seconds to sub-seconds). For schedules with very high levels of inverter-based resources (IBRs), up to and including 100%, the stability of grid controls has been evaluated through electromagnetic transient (EMT) simulations and power-hardware-in-the-loop (PHIL) simulations of key transient events at key schedule points. Specifically, MIDAS provides: 1) a closed-loop simulation framework for simulating timescales from economic scheduling to dynamic stability analysis; 2) machine learning-based stability assessment; 3) EMT modeling and analysis for large-scale power systems; 4) MIDAS PHIL test bed. We worked with Hawaii Electric Companies to apply the MIDAS study framework to a Maui grid study. The entire island's transmission system was modeled in detail - from a yearly scheduling model, to a second-level frequency dynamic model, down to a sub-second-scale EMT model to address critical stability issues. The project demonstrated how MIDAS can help system planners and operators assess system reliability and stability while the power grid is marching toward a high-renewable, high-IBR future. In this Maui grid study, we found that 100% instantaneous IBR operation is achievable in EMT simulation and PHIL testing, and grid planners and operators might need new analysis/simulation tools to assess grid reliability and stability in the scheduling stage. MIDAS will bring Maui and other systems closer to 100% clean and stable energy futures. (In this study, we examined transient stability. Other topics necessary for 100% IBR operation, such as protection and resource adequacy, were not examined.)

100% Renewables↗

Panoramic Mapping of Phonon Transport from Ultrafast Electron Diffraction and Scientific Machine Learning

Abstract One central challenge in understanding phonon thermal transport is a lack of experimental tools to investigate frequency‐resolved phonon transport. Although recent advances in computation lead to frequency‐resolved information, it is hindered by unknown defects in bulk regions and at interfaces. Here, a framework that can uncover microscopic phonon transport information in heterostructures is presented, integrating state‐of‐the‐art ultrafast electron diffraction (UED) with advanced scientific machine learning (SciML). Taking advantage of the dual temporal and reciprocal‐space resolution in UED, and the ability of SciML to solve inverse problems involving coupled Boltzmann transport equations, the frequency‐dependent interfacial transmittance and frequency‐dependent relaxation times of the heterostructure from the diffraction patterns are reliably recovered. The framework is applied to experimental Au/Si UED data, and a transport pattern beyond the diffuse mismatch model is revealed, which further enables a direct reconstruction of real‐space, real‐time, frequency‐resolved phonon dynamics across the interface. The work provides a new pathway to probe interfacial phonon transport mechanisms with unprecedented details.

36 MATERIALS SCIENCE↗

Asynchronous Reciprocal Coupling of Martini 2.2 Coarse-Grained and CHARMM36 All-Atom Simulations in an Automated Multiscale Framework

The appeal of multiscale modeling approaches is predicated on the promise of combinatorial synergy. However, this promise can only be realized when distinct scales are combined with reciprocal consistency. Here, we consider multiscale molecular dynamics (MD) simulations that combine the accuracy and macromolecular flexibility accessible to fixed-charge all-atom (AA) representations with the sampling speed accessible to reductive, coarse-grained (CG) representations. AA-to-CG conversions are relatively straightforward because deterministic routines with unique outcomes are achievable. Conversely, CG-to-AA conversions have many solutions due to a surge in the number of degrees of freedom. While automated tools for biomolecular CG-to-AA transformation exist, we find that one popular option, called Backward, is prone to stochastic failure and the AA models that it does generate frequently have compromised protein structure and incorrect stereochemistry. Although these shortcomings can likely be circumvented by human intervention in isolated instances, automated multiscale coupling requires reliable and robust scale conversion. In this work, we detail an extension to Multiscale Machine-learned Modeling Infrastructure (MuMMI), including an improved CG-to-AA conversion tool called sinceCG. This tool is reliable (~98% weakly correlated repeat success rate), automatable (no unrecoverable hangs), and yields AA models that generally preserve protein secondary structure and maintain correct stereochemistry. We describe how the MuMMI framework identifies CG system configurations of interest, converts them to AA representations, and simulates them at the AA scale while on-the-fly analyses provide feedback to update CG parameters. Application to systems containing the peripheral membrane protein RAS and proximal components of RAF kinase on complex eight-component lipid bilayers with ~1.5 million atoms is discussed in the context of MuMMI.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Neural lumped parameter differential equations with application in friction-stir processing

Lumped parameter methods aim to simplify the evolution of spatially-extended or continuous physical systems to that of a “lumped” element representative of the physical scales of the modeled system. For systems where the definition of a lumped element or its associated physics may be unknown, modeling tasks may be restricted to full-fidelity physics simulations. Here, in this work, we consider data-driven modeling tasks with limited point-wise measurements of otherwise continuous systems. We build upon the notion of the Universal Differential Equation (UDE) to construct data-driven models for reducing dynamics to that of a lumped parameter and inferring its properties. The flexibility of UDEs allow for composing various known physical priors suitable for application-specific modeling tasks, including lumped parameter methods. The motivating example for this work is the plunge and dwell stages for friction-stir welding; specifically, (i) mapping power input into the tool to a point-measurement of temperature and (ii) using this learned mapping for process control.

97 MATHEMATICS AND COMPUTING↗