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Correction to “COCOMO2: A Coarse-Grained Model for Interacting Folded and Disordered Proteins”

Biomolecular interactions are essential in many biological processes, including complex formation and phase separation processes. Coarse-grained computational models are especially valuable for studying such processes via simulation. Here, we present COCOMO2, an updated residue-based coarse-grained model that extends its applicability from intrinsically disordered peptides to folded proteins. This is accomplished with the introduction of a surface exposure scaling factor, which adjusts interaction strengths based on solvent accessibility, to enable the more realistic modeling of interactions involving folded domains without additional computational costs. COCOMO2 was parametrized directly with solubility and phase separation data to improve its performance on predicting concentration-dependent phase separation for a broader range of biomolecular systems compared to the original version. COCOMO2 enables new applications including the study of condensates that involve IDPs together with folded domains and the study of complex assembly processes. COCOMO2 also provides an expanded foundation for the development of multiscale approaches for modeling biomolecular interactions that span from residue-level to atomistic resolution.

Molecular interactions↗

Learning Physically Interpretable Atmospheric Models From Data With WSINDy

The multiscale and turbulent nature of Earth's atmosphere has historically rendered accurate weather modeling a hard problem. Recently, there has been an explosion of interest surrounding data-driven approaches to weather modeling, which in many cases show improved forecasting accuracy and computational efficiency when compared to traditional methods. However, many of the current data-driven approaches employ highly parameterized neural networks, often resulting in uninterpretable models and limited gains in scientific understanding. In this work, we address the interpretability problem by explicitly discovering partial differential equations governing atmospheric phenomena, identifying symbolic mathematical models with direct physical interpretations. The purpose of this paper is to demonstrate that, in particular, the weak-form sparse identification of nonlinear dynamics (WSINDy) algorithm can learn effective atmospheric models from both simulated and assimilated data. Our approach adapts the standard WSINDy algorithm to work with high-dimensional fluid data of arbitrary spatial dimension.

58 GEOSCIENCES↗

Task-oriented machine learning surrogates for tipping points of agent-based models

We present a machine learning framework bridging manifold learning, neural networks, Gaussian processes, and Equation-Free multiscale approach, for the construction of different types of effective reduced order models from detailed agent-based simulators and the systematic multiscale numerical analysis of their emergent dynamics. The specific tasks of interest here include the detection of tipping points, and the uncertainty quantification of rare events near them. Our illustrative examples are an event-driven, stochastic financial market model describing the mimetic behavior of traders, and a compartmental stochastic epidemic model on an Erdös-Rényi network. We contrast the pros and cons of the different types of surrogate models and the effort involved in learning them. Importantly, the proposed framework reveals that, around the tipping points, the emergent dynamics of both benchmark examples can be effectively described by a one-dimensional stochastic differential equation, thus revealing the intrinsic dimensionality of the normal form of the specific type of the tipping point. This allows a significant reduction in the computational cost of the tasks of interest.

97 MATHEMATICS AND COMPUTING↗

State of the art, gaps, and prospects in fusion materials theory and modelling

Advancing the theory and simulation of materials for fusion applications remains a key component of global roadmaps aimed at delivering much-needed fusion power. Especially as the drive for commercial application increases, prototypes must be designed against radiation damage before the relevant experimental data can be collected and cost reductions that are possible by testing materials in silico become even more important. Here, we summarise the state of the art as it emerged during the 7 th Fusion Materials Theory & Modelling Workshop that took place in 2024, with the aim to highlight present gaps and future directions for the fusion materials modelling community. Of particular interest were the effects of transmutations, chemical complexity with the development of novel alloys and interatomic potentials, advancements in modelling high-dose microstructures, comparison with experimental data and multiscale models for structural assessment relying on high-performance computing and virtual reality.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Beyond Magic Barrels: Digital manufacturing for crystallization, process development and optimization of explosive materials: Part II Resveratrol Exemplar

This SAND report summarizes work supported by an Engineering Sciences Research Foundation (ESRF) Lab Directed Research and Development (LDRD) project entitled “Beyond Magic Barrels: Digital manufacturing for crystallization, process development and optimization of explosive materials.” This SAND report is written in two parts with Part 1 discusses recrystallization of our explosive exemplar and Part 2 summarizing our work with recrystallization of resveratrol. We have studied resveratrol recrystallization with a multiscale approach combining experiments, modeling and simulation. At the single crystal scale, microscopy experiments illuminate crystal time-dependent growth rates using advanced image analysis. Bench scale experiments were carried out to look at growth of multiple particles in a small reactor creating thousands of particles and analyzing the results with microscopy and μCT. For the modeling we combine kinetic Monte Carlo (kMC) models with subscale information from density functional theory (DFT) or molecular dynamics. This work is discussed in Part 1 and can also be found in a paper from the project discussing a coarse-grained kMC model specifically developed for resveratrol. For well-mixed systems, we have population balance equations (PBE) linked with species mass conservation forming a set of ordinary differential equations that can be solved quickly. For more complicated geometries, such as the vat crystallization used throughout the complex, a coupled computational fluid dynamic (CFD)/PBE method was developed to account for gradients in temperature and concentration and differences in crystallization rates throughout the domain. These simulations are more complex and require high performance computing. We present results for two cases: 5% seed fast cool with parameters fit to the well-mixed case and 5% seed slow cool using the same parameters. We show reasonable agreement with experiments though are particles are significantly larger than the experiments.

36 MATERIALS SCIENCE↗

Group-Additivity–Embedded Multiscale Modeling for Electric Field-Enhanced Nanocatalysis

Elucidating structure-performance relationships remains a central challenge in field-enhanced catalysis, where nanoparticles exhibit nonuniform surface sites with site-dependent responses to electric fields. Low-coordination sites (edges, corners, and tips) are particularly electric field-sensitive (EF), leading to nonuniform charge distribution, adsorption energies, and catalytic activity. Here, using ammonia decomposition on a ruthenium cluster as a model system, we develop a transferable multiscale framework integrating density functional theory, group additivity (GA), Brønsted-Evans-Polanyi scaling, and microkinetic modeling to predict EF-dependent activity across nonuniform cluster sites. Across sites and fields, the nitrogen adsorption energy (E N ) emerges as the governing descriptor, yielding robust volcano relationships whose optimum shifts systematically with field: negative fields strengthen N binding via electron accumulation, while positive fields weaken N binding via charge depletion, moving the optimal E N toward weaker binding. Microkinetic analysis shows that N≡N bond formation remains the key kinetic bottleneck over most conditions; positive fields lower the effective barrier and, critically, increase the fraction of near-optimal active sites, leading to a net enhancement in overall activity relative to zero-field and negative-field cases. By capturing EF- and site-dependent energetics with high accuracy and low computational cost, this GA-embedded multi-scale simulation workflow provides a physically interpretable route to predict and design field-enhanced nanocatalysis.

ammonia decomposition↗

AK112: Full Waveform Inversion Tomography of Alaska Improves Waveform Fits While Imaging Crustal, Mantle, and Slab Structure

We report a full waveform inversion tomography model of Alaska and the surrounding regions, inferring radially anisotropic shear and isotropic compressional wavespeeds by fitting complete waveforms from 120 regional earthquakes. Our multiscale approach inverted time–frequency phase misfits (maximum period of 100 s), starting with a minimum period of 40 s and ending at 20 s in 7 stages and 112 total iterations. The model (AK112) was evaluated by computing the misfits for 36 independent validation events. We find that misfit reductions were large and equal (∼55%) for both the inversion and validation data sets, providing confidence in the model. AK112 also provides much better waveform fits compared to other reported models for the region, including an isotropic version of itself, highlighting the importance of anisotropy. The model resolves known crustal, upper mantle, and slab structure to depths of 100 km with new detail: sedimentary basins in the Alaskan Shelf, Cook Inlet, and Colville basins, among others; discontinuous lithospheric structure across major terrane boundaries; and subducting slab geometry and back‐arc volcanic sources. In addition to tectonic interpretations, the model enables full waveform simulations for long‐period earthquake ground motions and source characterization (e.g., moment tensor and finite‐fault inversion).

Rodgers, Arthur [Lawrence Livermore National Labor↗

Coupled Climate Simulations With E3SM‐MMF

Simulations of the recent historical period from 1950 to 2014 are conducted with E3SM‐MMF, which uses an embedded 2D cloud resolving model that runs efficiently on GPUs in place of traditional parameterizations for cloud and turbulence. Analysis of the climate and variability reveal several aspects where E3SM‐MMF produces smaller biases compared to E3SMv2, including better agreement with the observed evolution of global mean surface temperature, although the representation of ENSO is too weak and fast. Three idealized abrupt CO 2 experiments were also conducted to assess climate sensitivity and feedbacks. These yield three estimates of effective climate sensitivity (4.38, 5.21, and 6.06 K), with a corresponding spread in the shortwave cloud feedbacks. These estimates are on the higher end of sensitivity estimates from CMIP ensembles, and the spread indicates substantial state‐dependent feedbacks. These results demonstrate how multiscale modeling framework (MMF) models can be used for climate relevant experiments and projections by leveraging modern GPU enabled computational platforms. The unique qualities of E3SM‐MMF shown in previous literature are largely still present, but various instances of reduced biases suggest that MMF models have utility in improving future projections.

E3SM↗

MuSIKAL: Multiphysics Simulations and Knowledge Discovery through AI/ML Technologies

Under the MuSiKAL project, we developed a framework for a coastal digital twin (DT) platform capable of integrating diverse data resources, configuring multiscale model simulations, performing SciML‐accelerated predictions, with applications primarily driven by storm surge and heavily rainfall events impacting the Gulf Coast of the U.S.

54 ENVIRONMENTAL SCIENCES↗

Revealing EDL-driven reduction mechanisms in binary, ternary, and quaternary fluorinated electrolytes via an integrated MD–DFT–ML framework

Accurately predicting solid electrolyte interphase (SEI) formation requires explicitly resolving the electric double layer (EDL) structure, which deviates significantly from that of the bulk electrolyte. Although an established molecular dynamics (MD) and Density Functional Theory (DFT) framework can model SEI formation by evaluating reduction reactions of local clusters in the EDL, it suffers from a combinatorial computational bottleneck. To overcome this limitation, we introduce a machine-learning-accelerated simulation workflow (MD–DFT–ML), integrating a gradient-boosted regression model trained on EDL composition data to efficiently predict reduction potentials. We apply this framework to seven fluorinated electrolytes comprising fluorinated anions, a fluorinated ester solvent, two types of diluent (ion-solvating ester vs. non-solvating ether), and an FEC additive. The analysis shows that the EDL selectively accumulates cation-binding species; consequently, the non–cation-binding ether diluent rarely enters the EDL and makes minimal contributions to SEI formation. DFT calculations on statistically representative EDL clusters provide reduction potentials and fluorine-release pathways, while the ML model, which substantially reduces the DFT workload, predicts cluster reduction energies with a mean absolute error of 0.1 eV. The combined MD–DFT–ML approach also quantifies contributions from different sources to LiF formation in the SEI. This methodology establishes a generalizable route for multiscale modeling electrolyte and interphase design for next-generation electrochemical energy-storage systems.

DFT-MD-ML workflow↗

Accelerating multiscale electronic stopping power predictions with time-dependent density functional theory and machine learning

Knowing the rate at which particle radiation releases energy in a material, the “stopping power,” is key to designing nuclear reactors, medical treatments, semiconductor and quantum materials, and many other technologies. While the nuclear contribution to stopping power, i.e., elastic scattering between atoms, is well understood in the literature, the route for gathering data on the electronic contribution has for decades remained costly and reliant on many simplifying assumptions, including that materials are isotropic. We establish a method that combines time-dependent density functional theory (TDDFT) and machine learning to reduce the time to assess new materials to hours on a supercomputer and provide valuable data on how atomic details influence electronic stopping. Our approach uses TDDFT to compute the electronic stopping from first principles in several directions and then machine learning to interpolate to other directions at a cost of 10 million times fewer core-hours. We demonstrate the combined approach in a study of proton irradiation in aluminum and employ it to predict how the depth of maximum energy deposition, the “Bragg Peak,” varies depending on the incident angle—a quantity otherwise inaccessible to modelers and far outside the scales of quantum mechanical simulations. The lack of any experimental information requirement makes our method applicable to most materials, and its speed makes it a prime candidate for enabling quantum-to-continuum models of radiation damage. The prospect of reusing valuable TDDFT data for training the model makes our approach appealing for applications in the age of materials data science.

36 MATERIALS SCIENCE↗

Tandem bulk oxygen diffusion and surface reactions in reducible metal oxides control redox cycle dynamics

The interplay between bulk oxygen diffusion and surface reactions in reducible metal oxides is key in heterogeneous catalysts, but direct measurements of oxygen mobility, transient kinetics, and in situ spectroscopies have been lacking. Here, we reveal complex dynamic behavior of ceria-zirconia by H 2 using transient kinetics via mass spectrometry and in situ Raman and near-ambient pressure x-ray photoelectron spectroscopies. Molecular dynamics simulations with a machine learning potential delineate competitive oxygen diffusion mechanisms, with an optimal mobility at intermediate reductions. We expose a compensation between vacancy availability and lattice distortion at intermediate to high reductions and Frenkel defects at low reductions, underscoring a potential deficiency of 16 O/ 18 O exchange experiments in deducing oxygen mobility. Vacancies in proximity require electron localization on Ce atoms further away. The continuous replenishment of surface oxygen results in a varying reduction rate, with H 2 dissociation being the rate-limiting step. Multiscale transient simulations, consistent with experiments, indicate catalysts of potentially spatially varying oxidation states. The approach is broadly applicable to reducible oxide materials.

36 MATERIALS SCIENCE↗

Active learning of a crystal plasticity flow rule from discrete dislocation dynamics simulations

Continuum-scale material deformation models, such as crystal plasticity (CP), can significantly enhance their predictive accuracy by incorporating input from lower-scale (i.e. mesoscale) models. The procedure to generate and extract the relevant information is however typically complex and ad hoc, involving decision and intervention by domain experts, leading to long development times. In this study, we develop a principled approach for calibration of continuum-scale models using lower scale information by representing a CP flow rule as a Gaussian process model. This representation allows for efficient parameter space exploration, guided by the uncertainty embedded in the model through a process known as Bayesian optimization (BO). We demonstrate a semi-autonomous BO loop which instantiates discrete dislocation dynamics simulations whose initial conditions are automatically chosen to optimize the uncertainty of a model CP flow rule. Our self-guided computational pipeline efficiently generated a dataset and corresponding model whose error, uncertainty, and physical feature sensitivities were validated with comparison to an independent dataset four times larger, demonstrating a valuable and efficient active learning implementation readily transferable to similar material systems.

36 MATERIALS SCIENCE↗

Streaming Data in HPC Workflows Using ADIOS

The “IO Wall” problem, in which the gap between computation rate and data access rate grows continuously, poses significant problems to scientific workflows which have traditionally relied upon using the filesystem for intermediate storage between workflow stages. One way to avoid this problem in scientific workflows is to stream data directly from producers to consumers and avoiding storage entirely. However, the manner in which this is accomplished is key to both performance and usability. This paper presents the Sustainable Staging Transport, an approach which allows direct streaming between traditional file writers and readers with few application changes. SST is an ADIOS “engine”, accessible via standard ADIOS APIs, and because ADIOS allows engines to be chosen at run-time, many existing file-oriented ADIOS workflows can utilize SST for direct application-to-application communication without any source code changes. This paper describes the design of SST and presents performance results from various applications that use SST, for feeding model training with simulation data with substantially higher bandwidth than the theoretical limits of Frontier’s file system, for strong coupling of separately developed applications for multiphysics multiscale simulation, or for in situ analysis and visualization of data to complete all data processing shortly after the simulation finishes.

Podhorszki, Norbert [ORNL] (ORCID:000000019647542X↗

Multiscale modeling of packed-bed microwave reactors and estimation of intrinsic materials' permittivity

Modeling of packed-bed microwave reactors relies on an accurate representation of particle size, shape, and distribution within the bed, as well as the particles' dielectric properties. The measured permittivity of microwave susceptors (powders or structured materials) depends on the geometric features of the particles and the porosity of the bed, as well as the specific form factor of a structured material. These are effective properties and cannot be used to analyze other reactor configurations unless the geometric effects are removed. Therefore, we introduce a methodology for extracting the intrinsic particle permittivity from experimentally measured effective permittivity by combining cavity-based measurements with multiscale simulations and machine learning. Further, we develop the first multiscale model of packed-bed microwave reactors that incorporate particle effects (geometric features, random packing, and particle contact). This approach bridges macroscopic observables with mesoscopic physics, enabling analysis of local hotspots, arcing, and contact effects that control reactor performance. Using polymer-based spherical activated carbon (PBSAC) and silicon carbide (SiC) as examples, we demonstrate that the inferred particle permittivity is consistent with independent experimental heating profiles we collect from microwave reactors without adjustable parameters. Finally, this methodology establishes a foundation for predictive, multiscale design of microwave packed-bed reactors that explicitly accounts for particle-scale effects, enabling the estimation of intrinsic permittivity for the first time.

97 MATHEMATICS AND COMPUTING↗

VOTCA: multiscale frameworks for quantum and classical simulations in soft matter

Many physical phenomena in liquids and soft matter are multiscale by nature and can involve processes with quantum and classical degrees of freedom occurring over a vast range of length- and timescales. Examples range from structure formation processes of complex polymers or even polymer blends (Svaneborg & Everaers, 2023) on the classical side to charge and energy transport and conversion processes (Lee et al., 2019) involving explicit electronic and, therefore, quantum information. The Versatile Object-oriented Toolkit for Coarse-graining Applications (VOTCA) provides multiscale frameworks built on a comprehensive set of methods for the development of classical coarse-grained potentials (VOTCA-CSG) as well as state-of-the art excited state electronic structure methods based on density-functional and many-body Green’s function theories, coupled in mixed quantum-classical models and used in kinetic network models (VOTCA-XTP).

97 MATHEMATICS AND COMPUTING↗