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At least 217 records · Page 12

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DOE OSTI2026

Full-wave modeling of RF waves in fusion plasmas with finite element method: Progress in past decades and its future role

This paper reviews the progress in computing radio frequency (RF) wave fields in fusion plasmas, specifically focusing on simulations utilizing the finite element method (FEM) over the past few decades. Computing RF wave fields in fusion plasmas presents unique challenges due to large simulation domains, complex antenna structures, non-local dielectric properties, and wide ranges of spatial scales. It highlights key developments and outlines future directions, primarily addressing waves in the ion cyclotron (IC) to lower hybrid (LH) frequency range. We begin with briefly revisiting earlier developments before the widespread availability of modern computer-aided engineering (CAE) software based on FEM. This historical perspective illuminates early progress and the physics difficulties that motivated ongoing work within the community. Modern wave simulations for RF antennas based on FEM are characterized by the use of detailed 3D antenna model geometry generated from engineering CAD software and localized wave dielectric model. Significant advancements have also been made in improving physics models to include phenomena such as RF sheath rectification and wave scattering. FEM-based RF simulations have also been applied to compute wave propagation in the core region, where the inclusion of non-local dielectric response is crucial. This is a challenging goal, and several promising approaches have been proposed in this area. Additionally, RF simulation development initiatives based on open-source libraries have gained popularity, demonstrating scalability and flexibility in extending physics models. This paper will discuss the advantages and disadvantages of using such a publicly available FEM library.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2024

Estradiol associations with brain functional connectivity in postmenopausal women

Abstract Objective Previous studies have found that estrogens play a role in functional connectivity in the brain; however, little research has been done regarding how estradiol is associated with functional connectivity in postmenopausal women. The purpose of this study was to examine the relationship between estradiol and functional connectivity in postmenopausal women. Methods Structural and blood oxygenation level–dependent resting-state magnetic resonance imaging scans of 88 cognitively healthy postmenopausal individuals were obtained along with blood samples collected the same day as the magnetic resonance imaging to assess hormone levels. We generated connectivity values in CONN toolbox version 20.b, an SPM-based software. Results A regression analysis was run using estradiol level and regions of interest (ROI), including the hippocampus, parahippocampus, dorsolateral prefrontal cortex, and precuneus. Estradiol level was found to enhance parahippocampal gyrus anterior division left functional connectivity during ROI-to-ROI regression analysis. Estradiol enhanced functional connectivity between the parahippocampal gyrus anterior division left and the precuneus as well as the parahippocampal gyrus anterior division left and parahippocampal gyrus posterior division right. An exploratory analysis showed that years since the final menstrual period was related to enhanced connectivity between regions within the frontoparietal network. Conclusions These results illustrated the relationship between estradiol level and functional connectivity in postmenopausal women. They have implications for understanding how the functioning of the brain changes for individuals after menopause that may eventually lead to changes in cognition and behavior in older ages.

Obstetrics & Gynecology↗

DOE OSTI2025

Atomate2: modular workflows for materials science

High-throughput density functional theory (DFT) calculations have become a vital element of computational materials science, enabling materials screening, property database generation, and training of “universal” machine learning models. While several software frameworks have emerged to support these computational efforts, new developments such as machine learned force fields have increased demands for more flexible and programmable workflow solutions. This manuscript introduces atomate2, a comprehensive evolution of our original atomate framework, designed to address existing limitations in computational materials research infrastructure. Key features include the support for multiple electronic structure packages and interoperability between them, along with generalizable workflows that can be written in an abstract form irrespective of the DFT package or machine learning force field used within them. Our hope is that atomate2's improved usability and extensibility can reduce technical barriers for high-throughput research workflows and facilitate the rapid adoption of emerging methods in computational material science.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

AI-assisted object condensation clustering for calorimeter shower reconstruction at CLAS12

Several nuclear physics studies using the CLAS12 detector rely on the accurate reconstruction of neutrons and photons from its forward angle calorimeter system. These studies often place restrictive cuts when measuring neutral particles due to an overabundance of false clusters created by the existing calorimeter reconstruction software. In this work, we present a new AI approach to clustering CLAS12 calorimeter hits based on the object condensation framework. The model learns a latent representation of the full detector topology using GravNet layers, serving as the positional encoding for an event’s calorimeter hits which are processed by a Transformer encoder. This unique structure allows the model to contextualize local and long range information, improving its performance. Evaluated on one million simulated $e^-$ $+$ $p$ collision events, our method significantly improves cluster trustworthiness: the fraction of reliable neutron clusters, increasing from 8.88% to 30.73%, and photon clusters, increasing from 51.07% to 64.73%. In conclusion, our study also marks the first application of AI clustering techniques for hodoscopic detectors, showing potential for usage in many other experiments.

Calorimeters↗

DOE OSTI2025

MBX V1.2: Accelerating Data-Driven Many-Body Molecular Dynamics Simulations

The MBX software provides an advanced platform for molecular dynamics simulations, leveraging state-of-the-art MB-pol and MB-nrg data-driven many-body potential energy functions. Developed over the past decade, these potential energy functions integrate physics-based and machine-learned many-body terms trained on electronic structure data calculated at the "gold standard" coupled-cluster level of theory. Recent advancements in MBX have focused on optimizing its performance, resulting in the release of MBX v1.2. While the inherently many-body nature of MB-pol and MB-nrg ensures high accuracy, it poses computational challenges. MBX v1.2 addresses these challenges with significant performance improvements, including enhanced parallelism that fully harnesses the power of modern multicore CPUs. In conclusion, these advancements enable simulations on nanosecond time scales for condensed-phase systems, significantly expanding the scope of high-accuracy, predictive simulations of complex molecular systems powered by data-driven many-body potential energy functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

NFPA Distributed Energy Resources Safety Training (DERST) For Emergency Responders

The National Fire Protection Association, with support from the Department of Energy, executed a multi-year initiative to develop, enhance, and disseminate Distributed Energy Resources Safety Training (DERST) tools for U.S. emergency responders. As Distributed Energy Resources (DER)—such as solar photovoltaics, battery energy storage systems (ESS), electric vehicles (EVs), and associated infrastructure—become increasingly prevalent, the NFPA identified a critical need for up-to-date standardized, accessible, and effective safety training tailored for the fire service and related public safety professionals. The project delivered a comprehensive suite of educational resources to improve responders’ abilities to safely manage DER-related incidents. This included: • Revised Modular Training Courses: Updated classroom-based DER safety courses, now modular and accessible nationwide through fire academies and the North American Fire Training Directors (NAFTD) network. • Live Burn Testing & Research: A full-scale controlled burn of a DER-equipped residential structure provided real-world data and insights, forming the basis for updated best practices. • A Gamified Simulation Tool – Firefighters Incident Response Simulation Tool (FIRST): A first-of-its-kind, multiplayer, scenario-based simulation using the Unreal Engine 5.0 to train responders in a realistic virtual, multi-DER incident environment. • Field Familiarization Software Tools & Prop Guide: Digital DER field familiarization evolutions software guide and a prop development manual to support field-based DER training exercises, enhancing responders' hands-on familiarity with DER infrastructure and collaboration on virtual incident responses. • National Dissemination Strategy: Strategic partnerships with NAFTD, Vector Solutions, and others enabled wide-scale distribution, with over 5,000 departments accessing resources and 1,100+ departments adopting the simulator in the first seven months. Also provided a web portal for easy access to all training and simulation programs developed under this grant for the U.S. responder community. Key findings from the project—particularly from the burn test—led to paradigm shifts in fire response tactics. For example, traditional approaches to garage fires may be hazardous if DERs are present, due to explosive off gassing and thermal runaway risks. The new training emphasizes scene assessment, stand-off approaches, thermal imaging verification, and careful post-incident cooling of DER components to prevent reignition. This initiative has had a significant national impact, raising awareness, enhancing preparedness, and supporting safer DER incident response practices. Significant engagement from the media, public safety organizations, and PBS coverage has further amplified the reach and adoption of NFPA’s DER safety training, tools, and simulations.

14 SOLAR ENERGY↗

DOE OSTI2025

Benders Decomposition Using Graph Modeling and Multi-Parametric Programming

Benders decomposition is a widely used method for solving large and structured optimization problems, but its performance is affected by the repeated solution of subproblems. We propose a flexible and modular algorithmic framework for accelerating Benders decomposition. Specifically, we express the problem structure by using a graph-theoretic modeling abstraction in which nodes represent optimization subproblems and edges represent connectivity between subproblems. A key innovation of our approach is that we embed multiparametric programming (mp) surrogates for node subproblems, which maps the exact analytical map of the subproblem solution space. The use of mp surrogates allows us to replace subproblem solves with fast look-ups and function evaluations for primal and dual variables during the iterative Benders process. We formally show the equivalence between classical Benders cuts and those derived from the mp solution. We implement our framework in the open-source PlasmoBenders.jl software package. To demonstrate the capabilities of the proposed framework, we apply it to a two-stage stochastic programming problem, which aims to make optimal capacity expansion decisions under market uncertainty. We evaluate both single-cut and multicut variants of Benders decomposition and show that the use of mp surrogates achieves substantial speedups in subproblem solve time, while preserving the convergence guarantees of Benders decomposition. We highlight advantages in solution analysis and interpretability that is enabled by mp critical region tracking; specifically, we show that these reveal how decisions evolve geometrically across the Benders search. Our results aim to demonstrate that combining surrogate modeling with graph modeling offers a promising and extensible foundation for structure-exploiting decomposition. In addition, by decomposing the problem into more tractable subproblems, the proposed approach also aims to overcome scalability issues of mp. Finally, the use of mp surrogates provides a unifying and modular optimization framework that enables the representation of heterogeneous node subproblems as modeling objects with a homogeneous structure.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Real-time single-element-detection structured illumination optical metrology for laser powder bed fusion

Laser powder bed fusion (LPBF) is a type of metal additive manufacturing which could benefit from improved process monitoring to improve quality control. We demonstrate, for the first time to our knowledge, the coaxial monitoring of melt track formation in steel powder with spatial frequency modulation imaging (SPIFI), an enhanced-resolution imaging technique which uses a photodiode to record one-dimensional images. Using a custom live-display software and a high-speed SPIFI geometry, we offset the SPIFI field of view from the fusing beam to monitor different regions of the LPBF melt pool and surrounding area. This demonstrates the potential of SPIFI to monitor spatial features within the melt pool in real-time with increased data efficiency.

Hunter, Scott (ORCID:0009000886150312)↗

DOE OSTI2024

Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment

Force Field X (FFX) is an open-source software package for atomic resolution modeling of genetic variants and organic crystals that leverages advanced potential energy functions and experimental data. FFX currently consists of nine modular packages with novel algorithms that include global optimization via a many-body expansion, acid–base chemistry using polarizable constant-pH molecular dynamics, estimation of free energy differences, generalized Kirkwood implicit solvent models, and many more. Applications of FFX focus on the use and development of a crystal structure prediction pipeline, biomolecular structure refinement against experimental datasets, and estimation of the thermodynamic effects of genetic variants on both proteins and nucleic acids. The use of Parallel Java and OpenMM combines to offer shared memory, message passing, and graphics processing unit parallelization for high performance simulations. Overall, the FFX platform serves as a computational microscope to study systems ranging from organic crystals to solvated biomolecular systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Smart Adaptive Structures for an Ocean Wave Energy Converter

Ocean wave energy converters face significant challenges including cost-effectiveness, minimizing maintenance requirements, and withstanding extreme conditions. However, by utilizing smart materials, these converters could overcome these challenges. Such energy harvesters could use dielectric elastomer generators to convert ocean wave energy into electricity through their dynamic straining. Conversely, by applying electricity to these generators, they become actuators - dielectric elastomer actuators - thereby enabling them to alter their stiffness and adapt to the ever-changing ocean energy environments. Such active adaptation could enhance the converter's ability to: reach resonance with ocean waves and protect itself from dangerous waves. This study utilizes numerical analyses through the COMSOL software framework to evaluate the potential energy that could be harvested by a conceptual ocean wave energy converter based upon dielectric elastomer generators/actuators. The converter is composed of an external hull (that is a hollow cylinder), an inertial mass (that is a hollow cylinder and concentric with the hull), and 'spokes' - made of dielectric elastomer generators/actuators - that connect the hull to the inertial mass. Results of the numerical analyses include those outcomes arising from the conceptual converter being simulated via a sinusoidal motion analogous to ocean waves. That motion, therefore, causes relative motion between the converter's hull and inertial mass thereby dynamically stretching the corresponding connecting elastomers. The stretching of the elastomers enables them to 'gain elastic strain energy' and is, therefore, considered to be the theoretical limit of possible electrical energy conversion for the dielectric elastomer generator/actuator spokes. Additionally, the elastomer material properties of the spokes were altered to simulate the actuation of those same elastomers; with overall strain energy being subsequently investigated. Ultimately this is a preliminary study exploring the ability of such smart materials - electricity-generating and self-actuating elastomers - to actively adapt an ocean wave energy converter's structure to address and overcome the aforementioned challenges.

active materials↗

DOE OSTI2024

Robust Iterative Method for Symmetric Quantum Signal Processing in All Parameter Regimes

Here, this paper addresses the problem of solving nonlinear systems in the context of symmetric quantum signal processing (QSP), a powerful technique for implementing matrix functions on quantum computers. Symmetric QSP focuses on representing target polynomials as products of matrices in SU(2) that possess symmetry properties. We present a novel Newton’s method tailored for efficiently solving the nonlinear system involved in determining the phase factors within the symmetric QSP framework. Our method demonstrates rapid and robust convergence in all parameter regimes, including the challenging scenario with ill-conditioned Jacobian matrices, using standard double precision arithmetic operations. For instance, solving symmetric QSP for a highly oscillatory target function α cos(1000x) (polynomial degree ≈ 1433) takes 6 iterations to converge to machine precision when α = 0.9, and the number of iterations only increases to 18 iterations when α = 1 – 10 -9 with a highly ill-conditioned Jacobian matrix. Leveraging the matrix product state structure of symmetric QSP, the computation of the Jacobian matrix incurs a computational cost comparable to a single function evaluation. Moreover, we introduce a reformulation of symmetric QSP using real-number arithmetics, further enhancing the method’s efficiency. Extensive numerical tests validate the effectiveness and robustness of our approach, which has been implemented in the QSPPACK software package.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Three-dimensional modeling of hyphal fusion, branching, and nutrient transport in filamentous fungi

Fungi exhibit behaviors distinct from other microbes. Filamentous fungi grow by extending complex networks of branched filaments collectively referred to as the mycelium. These networks can expand over large distances and traverse low-nutrient areas by translocating nutrients through the filament network. This spatial characteristic makes filamentous fungi crucial for soil ecosystems, supporting stable microbial communities and promoting plant growth. However, simulating these behaviors is complex. The elongated nature of fungal compartments results in different mechanical interactions compared to the commonly modeled spherical bacteria. These detailed hyphal mechanics require specialized consideration and are often excluded from conventional fungal simulation packages. Additionally, the extensive fungal networks in nature demand computationally intensive simulations, necessitating high-performance algorithms. Therefore, realistic fungi simulations require specialized software. Here, we introduce a fungal modeling expansion to the high-performance biological modelling and interface exchange (bmx) software suite. bmx leverages adaptive mesh refinement in AMReX for chemical diffusion and incorporates a full mechanical model for bacterial cells, accelerated by GPUs. By extending bmx to model filamentous particles, we demonstrate the formation of complex filament networks through interactions like hyphal branching and fusion (anastomosis). We show that the networks produced match real-world fungal structures through various metrics. This work supports computational studies of fungal growth dynamics and can be adapted to investigate the growth of other filamentous structures in biology or materials science. The expanded-BMX package is open-sourced and is available online.

Cell mechanics↗

DOE OSTI2024

Bridging the time scale in exascale computing of chemical systems (Final Technical Report)

This report summarizes the work carried out with support of the United States Department of Energy under Award DE-SC0019441. The theme of this project was to develop and apply methods that allowed for the acceleration of atomistic calculations, particularly in challenging areas such as multiphase systems, electrified interfaces, uncertainty estimation, and applications requiring chemical accuracy, which tend to be applications where simulation time is severely bottlenecked by the computational time requirements. Much of the focus was on the application of emerging machine-learning methodologies, although a wide range of methodologies were employed. This report has two major sections. The first focuses on the methodological advances themselves. Within this part, we report a number of major advances, a few examples of which are described here. We report the first machine-learning scheme for the acceleration of electronically grand-canonical calculations (that is, those applicable to electrochemistry). We report new methods of performing transfer learning, in which physics-based priors can be used to provide predictions, often with uncertainty estimates, of images well outside of training sets; we also offer ways to fine-tune these transfer-learning models. We provide a new systematic means to generate and apply minimal training data sets to very large (10,000’s of atoms) systems, with only small training sets appropriate for electronic structure. We developed new methodologies to integrate surface vibrations into surface adsorption calculations. We made advances to the applicability of diffusion Monte Carlo methods to allow (learned) force prediction, finite-size error correction, and force-free means of searching for transition states. We integrated machine-learned atomistic predictions into mechanism generation codes. Additionally, we released new software including AmpTorch, a modernized version of our original atomistic machine-learning code Amp. The second part of this report focuses on the scientific applications that accompanied, and were often enabled by, the methodological advances described earlier. A few examples follow, but full details are in the individual chapters of the report. For example, we developed a general theory of phonon-induced friction on molecular adsorbates. We showed fundamentally how solvent influences the adsorption and desorption process and how it differs from the processes typically involved at the solid–gas interface, making aqueous-phase and electrocatalysis different from traditional thermocatalysis. We examined how metal–insulator and magnetic transitions can be probed, and accelerated exciton dynamics via Frenkel Hamiltonian parameters. We showed that the nearsighted force-training approach, developed within this project, can predict both the stability and reactivity of large nanoparticles, and can also lead to insights on catalyst coverage on binding energies and entropies. These applied studies, which generally integrated with our method development, allowed us to push forward the theoretical understanding of several reaction classes.

08 HYDROGEN↗

DOE OSTI2024

Annotation of DOM metabolomes with an ultrahigh resolution mass spectrometry molecular formula library

Current approaches to analyzing metabolomic data often rely on matching MS/MS fragmentation data to sparse libraries or databases. This approach results in limited identification of features, often with less than 10% of the dataset being annotated. A complementary approach is to assign molecular formula to features based on accurate mass measurements, but the platforms commonly used for metabolomics do not have the needed accuracy or resolving power to do this robustly, particularly for larger molecules. Using our newly modified analysis tool, CoreMS, we generated a library of molecular formula from pooled samples analyzed with LC-21T FT-ICR MS. This library successfully annotated approximately 53.2% of features identified from the exometabolome of marine diatom Phaeodactylum tricornutum – a nearly ten-fold increase over the 5.9% annotation rate achieved using a conventional MS/MS library matching approach. Using this FT-ICR MS library approach, we were able to differentiate differences in the exometabolome of P. tricornutum in iron replete and iron limited conditions, with 668 metabolites being differentially expressed (p < 0.05, 2 x intensity difference) under these conditions. The traditional MS/MS fragmentation-based annotation approach only annotated 61 of these metabolites, while our novel pipeline annotated 450 metabolites and revealed 12 metabolites that were significantly more abundant under low iron conditions. Our results demonstrate the utility of ultrahigh resolution mass spectrometry for generating more comprehensive and confident molecular annotations.

21T-FTICR-MS, CoreMS↗

DOE OSTI2026

“Frameworks, Algorithms and Scalable Technologies for Mathematics (FASTMath) SciDAC Institute” (Final Technical Report)

SMU personnel formed a portion of the overall “Time Integration” team within the FASTMath SciDAC-5 Institute, and we interacted very closely with team members from collaborating institutions. The major goals of our team within the FASTMath institute may be categorized into two groups: the development of advanced and application-aware time integration methods and software, and close interactions with DOE application scientists to facilitate their use of these new methods and software. The two goals are intimately linked, since our research and development of novel tools is informed by the needs of our application partners, who in turn benefit from subsequent mathematical and software advances. While the SMU personnel collaborated with the rest of the Time Integration FASTMath team on most of our shared deliverables within the larger FASTMath institute, SMU personnel primarily contributed to the following subset of those goals: ● expanding capabilities for higher-order and solve-decoupled multirate methods, ● enhancing support for temporal adaptivity within multirate methods, and ● adding structure-aware time integration methods. Each of these goals focused both on intellectual contributions through journal articles or research presentations, and on enhancements to the open-source SUNDIALS library of time integrators and nonlinear solvers, of which the SMU PI Reynolds is a core developer.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

cclib 2.0: An updated architecture for interoperable computational chemistry

Interoperability in computational chemistry is elusive, impeded by the independent development of software packages and idiosyncratic nature of their output files. The cclib library was introduced in 2006 as an attempt to improve this situation by providing a consistent interface to the results of various quantum chemistry programs. The shared API across programs enabled by cclib has allowed users to focus on results as opposed to output and to combine data from multiple programs or develop generic downstream tools. Initial development, however, did not anticipate the rapid progress of computational capabilities, novel methods, and new programs; nor did it foresee the growing need for customizability. Here, we recount this history and present cclib 2, focused on extensibility and modularity. We also introduce recent design pivots—the formalization of cclib’s intermediate data representation as a tree-based structure, a new combinator-based parser organization, and parsed chemical properties as extensible objects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Sierra/SD – User's Manual – 5.22

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high-fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a user’s guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Sierra/SD – User's Manual (V.5.24)

42 ENGINEERING↗