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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Integrating Ultra-Coarse-Grained Protein Models into Accessible Workflows for Multiscale Molecular Dynamics

To capture protein conformational transitions using molecular dynamics (MD), several simulation resolutions covering different spatial and temporal scales are typically needed. All-atom (AA) simulations provide fine resolution, but are computationally infeasible for large systems over longer durations. Coarse-grained (CG) and ultra-coarse-grained (UCG) models have a lower resolution and computational cost while still being able to conserve essential protein features. Prior work on a Multiscale Machinelearned Modeling Infrastructure (MuMMI) combined both AA and CG simulations to study RAS-RAF protein interactions, leveraging CG models for longer time scales and using AA to investigate unusual conformations in greater detail. However, MuMMI is still resource-intensive, and this study aims to maximize exploration of the protein conformational space while reducing computational cost. In this paper, we build on prior work that integrates UCG models based on heterogeneous elastic network modeling (hENM) into the MuMMI workflow. We demonstrate that UCG models enable accurate sampling of protein conformations, focusing on simulating RAS-RAF protein interactions. Using higher-resolution CG Martini simulation data, we can automatically refine intramolecular interactions in UCG models. We present a scalable Python package that uses fluctuations observed in higher-resolution CG Martini simulations to estimate bond coefficients of the UCG model. We built novel machine learning-based backmapping methods to recover more detailed CG Martini structures from UCG structures, using diffusion models to learn the mapping between scales. Finally, we present UCG-mini-MuMMI, an accessible and less compute-intensive version of MuMMI as a resource for the scientific community. Incorporating UCG models into MD studies is applicable to a broad range of systems and proteins, and our study offers insights into the advantages and limitations of these methods.

Chemical structure↗
DOE OSTI2025

Calibration of RAFM Micromechanical Model for Creep Using Bayesian Optimization for Functional Output

A Bayesian optimization procedure is presented for calibrating a multimechanism micromechanical model for creep to experimental data of F82H steel. Reduced activation ferritic martensitic (RAFM) steels based on Fe(8–9)%Cr are the most promising candidates for some fusion reactor structures. Although there are indications that RAFM steel could be viable for fusion applications at temperatures up to 600°C, the maximum operating temperature will be determined by the creep properties of the structural material and the breeder material compatibility with the structural material. Due to the relative paucity of available creep data on F82H steel compared to other alloys such as Grade 91 steel, micromechanical models are sought for simulating creep based on relevant deformation mechanisms. As a point of departure, this work recalibrates a model form that was previously proposed for Grade 91 steel to match creep curves for F82H steel. Due to the large number of parameters (9) and cost of the nonlinear simulations, an automated approach for tuning the parameters is pursued using a recently developed Bayesian optimization for functional output (BOFO) framework (Huang et al., 2021, “Bayesian optimization of functional output in inverse problems,” Optim. Eng., 22, pp. 2553–2574). Incorporating extensions such as batch sequencing and weighted experimental load cases into BOFO, a reasonably small error between experimental and simulated creep curves at two load levels is achieved in a reasonable number of iterations. In conclusion, validation with an additional creep curve provides confidence in the fitted parameters obtained from the automated calibration procedure to describe the creep behavior of F82H steel.

42 ENGINEERING↗
DOE OSTI2024

Numerical validation of scaling laws for stratified turbulence

Recent theoretical progress using multiscale asymptotic analysis has revealed various possible regimes of stratified turbulence. Notably, buoyancy transport can either be dominated by advection or diffusion, depending on the effective Péclet number of the flow. Two types of asymptotic models have been proposed, which yield measurably different predictions for the characteristic vertical velocity and length scale of the turbulent eddies in both diffusive and non-diffusive regimes. The first, termed a ‘single-scale model’, is designed to describe flow structures having large horizontal and small vertical scales, while the second, termed a ‘multiscale model’, additionally incorporates flow features with small horizontal scales, and reduces to the single-scale model in their absence. By comparing predicted vertical velocity scaling laws with direct numerical simulation data, we show that the multiscale model correctly captures the properties of strongly stratified turbulence within regions dominated by small-scale isotropic motions, whose volume fraction decreases as the stratification increases. Meanwhile its single-scale reduction accurately describes the more orderly, layer-like, quiescent flow outside those regions.

Mechanics↗
NASA NTRS2012

Multiscale Modeling of Structurally-Graded Materials Using Discrete Dislocation Plasticity Models and Continuum Crystal Plasticity Models

A multiscale modeling methodology that combines the predictive capability of discrete dislocation plasticity and the computational efficiency of continuum crystal plasticity is developed. Single crystal configurations of different grain sizes modeled with periodic boundary conditions are analyzed using discrete dislocation plasticity (DD) to obtain grain size-dependent stress-strain predictions. These relationships are mapped into crystal plasticity parameters to develop a multiscale DD/CP model for continuum level simulations. A polycrystal model of a structurally-graded microstructure is developed, analyzed and used as a benchmark for comparison between the multiscale DD/CP model and the DD predictions. The multiscale DD/CP model follows the DD predictions closely up to an initial peak stress and then follows a strain hardening path that is parallel but somewhat offset from the DD predictions. The difference is believed to be from a combination of the strain rate in the DD simulation and the inability of the DD/CP model to represent non-monotonic material response.

Saether, Erik↗
DOE OSTI2020

Active- and transfer-learning applied to microscale-macroscale coupling to simulate viscoelastic flows

Active- and transfer-learning are applied to microscale dynamics of polymer flows for the multiscale discovery of effective constitutive approximations required in viscoelastic flow simulation. The result is macroscopic rheology directly connected to a microstructural model. Micro and macroscale simulations are adaptively coupled by means of Gaussian process regression (GPR) to run the expensive microscale computations only as necessary. This multiscale method is demonstrated with flows of a polymer solution as a model system. At the microscale level dissipative particle dynamics (DPD) is employed to model the fluid as a suspension of bead-spring micro-structures subjected to steady shear flow. The results yield the non-Newtonian viscosity and the first normal stress difference at strain rates as training data used in a GPR model. DPD parameters are calibrated with respect to experimental data for a real polymer solution. Compliance with these data requires adjustment of the DPD model's cutoff radius, which then becomes a function of the second invariant of the strain rate tensor. The FENE-P model is chosen for the macroscale description using the spectral element method (SEM) to simulate channel flow and flow past a circular cylinder. The DPD results at the lowest possible shear strain rate yield an estimate of the zero-shear rate viscosity, which allows the initiation of the macroscale flow by SEM as a Newtonian fluid. The resulting strain-rate field is surveyed to determine additional shear strain rate sampling points for the DPD system. This new information allows an initial fitting of parameters of the constitutive equation followed by new SEM simulations at the macroscale. Additionally, guided by active-learning GPR to select new sampling points, this process continues until convergence is achieved. The effectiveness of this new simulation paradigm for viscoelastic flows is tested with different macroscale operating conditions. The effective closure learned in the channel simulation is then transferred directly to the flow past a circular cylinder at low Reynolds number, where the results show that only two additional DPD simulations are required to achieve a satisfactory constitutive model. With an increase of the Reynolds number, the active-learning scheme automatically detects the inaccuracy of the learned constitutive model, and initiates additional DPD simulations for the extra data needed to once again close the microscale-macroscale coupled system. This new paradigm of active- and transfer-learning for multiscale modeling is readily applicable to other microscale-macroscale coupled simulations of complex fluids and other materials. Furthermore, the coupling between microscale and macroscale solvers can be seamlessly implemented with our open source multiscale universal interface (MUI) library.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Automated Generation of Microkinetics for Heterogeneously Catalyzed Reactions Considering Correlated Uncertainties**

Abstract The study presents an ab‐initio based framework for the automated construction of microkinetic mechanisms considering correlated uncertainties in all energetic parameters and estimation routines. 2000 unique microkinetic models were generated within the uncertainty space of the BEEF‐vdW functional for the oxidation reactions of representative exhaust gas emissions from stoichiometric combustion engines over Pt(111) and compared to experiments through multiscale modeling. The ensemble of simulations stresses the importance of considering uncertainties. Within this set of first‐principles‐based models, it is possible to identify a microkinetic mechanism that agrees with experimental data. This mechanism can be traced back to a single exchange‐correlation functional, and it suggests that Pt(111) could be the active site for the oxidation of light hydrocarbons. The study provides a universal framework for the automated construction of reaction mechanisms with correlated uncertainty quantification, enabling a DFT‐constrained microkinetic model optimization for other heterogeneously catalyzed systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Editors’ Choice—Perspective—Challenges in Moving to Multiscale Battery Models: Where Electrochemistry Meets and Demands More from Math

There has been significant recent interest in studying multiscale characteristics of current and next-generation batteries, including lithium-metal and lithium-sulfur batteries. Advances in computing power make researchers believe that the detailed multiscale models can be efficiently simulated to arrive at the insights for the degradation and performance loss; however, this is not true and special attention needs to be paid to local singularities, boundary layers, moving boundaries, etc. This article presents 2D examples that illustrate the importance of grid convergence studies, provides well-defined detailed models to test the efficiency of numerical schemes, and discusses the associated simulation challenges.

Shah, Krishna (ORCID:0000000278026361)↗
DOE OSTI2026

Establishment of a Vertically Integrated Domestic Manufacturing Process for Production of Substrates Needed for Manufacture of Gas Diffusion Layers

In this project, AvCarb, LLC evaluated the baseline performance metrics of commercial carbon veils and their corresponding Gas Diffusion Layers (GDLs) with the goal of establishing an optimized, vertically integrated production system for wet-laid nonwoven substrates used in gas diffusion media for electrochemical energy storage and conversion devices. Mechanical testing and microstructural characterization were conducted and used to develop a multiscale computational model capable of simulating and predicting the performance of GDLs in fuel cells. Although the project successfully generated foundational transport and modeling data, it was terminated prior to identifying the critical GDL design parameters necessary for full optimization. The program aimed to improve carbon veil fabrication through enhanced fiber dispersion, fiber-fiber adhesion control, and improved web formation, enabling the production of high-quality, uniform substrates. Simulations were intended to guide mixing and solution delivery system design and process conditions, followed by production-scale trials to evaluate fiber dispersion, web uniformity, and mechanical robustness. At full deployment, the proposed production line would have been capable of producing approximately 650,000 m² of carbon veil annually. This capability remains strategically important, as the United States currently lacks a domestic source of wet-laid nonwoven carbon substrates that satisfy the stringent quality requirements for fuel-cell GDLs and electrolyzers representing an ongoing supply-chain vulnerability. Beyond supply-chain benefits, the project established a robust benchmarking dataset for existing commercial carbon veils while advancing next-generation material concepts targeting improved performance and manufacturing consistency.

Olson, Cynthia Lemay↗
DOE OSTI2025

IM3 Projected U.S. Western Interconnection Grid Stress Dataset

This dataset provides projected grid stress and reliability results (including all model inputs and outputs from GO WEST and TEP) for Integrated Multisector, Multiscale Modeling (IM3) Phase 2 simulations across eight different scenarios for the U.S. Western Interconnection through 2055. The scenarios include combinations of two Shared Socioeconomic Pathways (SSP3 and SSP5) with four high-resolution climate projections specific to the United States from a set of Thermodynamic Global Warming (TGW) simulations. These climate projections include "hotter" and "cooler" variants for two Representative Concentration Pathways (RCP4.5 and RCP8.5). The resulting eight simulations are: rcp45cooler_ssp3 rcp45cooler_ssp5 rcp45hotter_ssp3 rcp45hotter_ssp5 rcp85cooler_ssp3 rcp85cooler_ssp5 rcp85hotter_ssp3 rcp85hotter_ssp5 GO WEST is an open-source power grid modeling framework for the U.S. Western Interconnection, which allows users to tailor the model depending on their research study and science questions. It covers 28 balancing authorities (BAs) and 12 states in U.S. Western Interconnection. GO WEST allows users to select different number of nodes and come up with a simplified network by utilizing 10,000 nodal topology of the U.S. Western Interconnection (ACTIVSg10k). Users can select different number of nodes, mathematical formulations (linear programming vs. mixed-integer linear programming), transmission line limit scaling factors, and hurdle rate scaling factors. GO WEST offers a unit commitment and economic dispatch (UC/ED) module to simulate grid operations on an hourly scale. In this sense, users can calibrate and validate their model versions by comparing model outputs to historical datasets. TEP is an open-source transmission capacity expansion model, built on the GO WEST framework. It utilizes linear programming to optimize transmission capacity addition investment on existing lines within the GO WEST framework. The TEP model only increases the thermal capacity of existing transmission lines and does not add new lines to the system, which leaves the topology preserved. In order to use TEP model, users need to create scenarios with the GO WEST framework. Please refer to README file for a detailed description of the dataset including individual files and references.

Capacity Expansion Model↗
NASA NTRS2005

Prediction of Mechanical Properties of Polymers With Various Force Fields

The effect of force field type on the predicted elastic properties of a polyimide is examined using a multiscale modeling technique. Molecular Dynamics simulations are used to predict the atomic structure and elastic properties of the polymer by subjecting a representative volume element of the material to bulk and shear finite deformations. The elastic properties of the polyimide are determined using three force fields: AMBER, OPLS-AA, and MM3. The predicted values of Young s modulus and shear modulus of the polyimide are compared with experimental values. The results indicate that the mechanical properties of the polyimide predicted with the OPLS-AA force field most closely matched those from experiment. The results also indicate that while the complexity of the force field does not have a significant effect on the accuracy of predicted properties, small differences in the force constants and the functional form of individual terms in the force fields determine the accuracy of the force field in predicting the elastic properties of the polyimide.

Odegard, Gregory M.↗
DOE OSTI2025

Influence of simple terrain on the spatial variability of a low-level jet and wind farm performance in the AWAKEN field campaign

In wind energy research, scientific challenges are often associated with complex terrain sites, where orography, vegetation, and buildings disrupt flow uniformity. However, even sites characterized as simple terrain can exhibit significant spatial variability in wind speed, particularly during stable boundary layers (SBLs) and low-level jets (LLJs). This study investigates these terrain interactions using both simulations and observations from the American WAKe ExperimeNt (AWAKEN). We employ a multiscale Weather Research and Forecasting (WRF) model simulation, integrating mesoscale forcing in the coarse domains and representing three rows of turbines from the King Plains wind farm as generalized actuator disks (GAD) in the large-eddy simulation (LES) domains. During a nocturnal LLJ event on 3 April 2023, the downstream, wake-affected turbine rows outperformed the upstream, unwaked row by 25 %–51 %. This counterintuitive result arises from terrain-induced streamwise variations in hub-height wind speed of approximately 4 m s −1 over 5 km – equivalent to ∼50 % of the upstream reference speed. This enhancement outweighs the wake-induced reduction in mean wind speed (∼12 %) and global blockage effects reported in the literature (∼1 %–3.4 %). The multiscale simulations capture the intra-farm spatial variability in power performance observed in SCADA data. Terrain-induced vertical displacement of the LLJ, coupled with large wind shear below the jet maximum, drives the substantial streamwise acceleration within the wind farm. These findings underscore the importance of accounting for spatial variability related to terrain, even in simple landscapes, particularly during LLJ conditions. Incorporating such effects into reduced-order modeling frameworks for wind farm design and control could significantly enhance their effectiveness.

17 WIND ENERGY↗
DOE OSTI2022

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↗
NASA NTRS2007

Improvements in the Scalability of the NASA Goddard Multiscale Modeling Framework for Hurricane Climate Studies

Improving our understanding of hurricane inter-annual variability and the impact of climate change (e.g., doubling CO2 and/or global warming) on hurricanes brings both scientific and computational challenges to researchers. As hurricane dynamics involves multiscale interactions among synoptic-scale flows, mesoscale vortices, and small-scale cloud motions, an ideal numerical model suitable for hurricane studies should demonstrate its capabilities in simulating these interactions. The newly-developed multiscale modeling framework (MMF, Tao et al., 2007) and the substantial computing power by the NASA Columbia supercomputer show promise in pursuing the related studies, as the MMF inherits the advantages of two NASA state-of-the-art modeling components: the GEOS4/fvGCM and 2D GCEs. This article focuses on the computational issues and proposes a revised methodology to improve the MMF's performance and scalability. It is shown that this prototype implementation enables 12-fold performance improvements with 364 CPUs, thereby making it more feasible to study hurricane climate.

Shen, Bo-Wen↗
DOE OSTI2023

Assessing turbulence and mixing parameterizations in the gray-zone of multiscale simulations over mountainous terrain during the METEX21 field experiment

Multiscale numerical weather prediction models transition from mesoscale, where turbulence is fully parameterized, to microscale, where the majority of highly energetic scales of turbulence are resolved. The turbulence gray-zone is situated between these two regimes and multiscale models must downscale through these resolutions. Here, we compare three multiscale simulations which vary by the parameterization used for turbulence and mixing within the gray-zone. The three parameterizations analyzed are the Mellor-Yamada Nakanishi and Niino (MYNN) Level 2.5 planetary boundary layer scheme, the TKE-1.5 large eddy simulation (LES) closure scheme, and a recently developed three-dimensional planetary boundary layer scheme based on the Mellor-Yamada model. The simulation domain includes complex (i.e., mountainous) terrain in Nevada that was instrumented with meteorological towers, profiling and scanning lidars, a tethered balloon, and a surface flux tower. Simulations are compared to each other and to observations, with assessment of model skill at predicting wind speed, wind direction and TKE, and qualitative evaluations of transport and dispersion of smoke from controlled releases. This analysis demonstrates that microscale predictions of transport and dispersion can be significantly influenced by the choice of turbulence and mixing parameterization in the terra incognita , particularly over regions of complex terrain and with strong local forcing. This influence may not be apparent in the analysis of model skill, and motivates future field campaigns involving controlled tracer releases and corresponding modeling studies of the turbulence gray-zone.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

components for the MuMMI software release

The Department of Energy and the National Cancer Institute have developed new software for conducting multi-scale simulations of complex systems. This software, called the Multiscale Machine-Learned Modeling Infrastructure (MuMMI), couples simulations on three spatial scales to study slow, large-scale reorganizations of biomolecular systems with the speed of continuum and coarse-grained models while revealing selected interactions at full atomic precision. In these simulations, coarse-to-fine model conversions are used to spawn relevant fine-scale simulations along chosen order parameters, and fine-to-coarse feedback is used to iteratively improve the accuracy and multi-scale consistency of coarse-scale and continuum simulations. The complete MuMMI framework will be reviewed and released as open-source software by Lawrence Livermore National Laboratory. This review covers a subset of the MuMMI components that were developed exclusively at the Los Alamos National Laboratory.

Neale, Christopher↗
DOE OSTI2022

Woven ceramic matrix composite surrogate model based on physics-informed recurrent neural network

A recurrent neural network (RNN) based surrogate model is developed to emulate the nonlinear constitutive behavior of woven ceramic matrix composites (CMCs) driven by matrix damage at multiple length scales. Physics-informed constraints are introduced into the surrogate model through regularization to ground the prediction in physics and improve its predictive capabilities. Training data is generated using the multiscale generalized method of cells (MSGMC) approach coupled with a matrix damage model. This coupling permits simulating the nonlinear behavior of woven CMCs based on constituent response at the micro-, meso-, and macroscales. The multiscale repeating unit cell is loaded under non-monotonic conditions including multiple load / unload cycles and tension / compression. The fiber volume fraction as well as the intra- and intertow void volume fractions are also varied in the generation of training data. Therefore, the RNN-based surrogate model is tasked with predicting, as a function of variable input strain sequence and fiber and void volume fractions, the resulting stress versus strain response while satisfying physical constraints such as positive semi-definiteness of the tangent stiffness matrix and linear elastic unloading. Further, the trained surrogate model effectively matches the stress versus strain response and successfully predicts the tangent modulus throughout the loading regime. Neural network based surrogate models can offer efficient alternatives to running computationally intensive multiscale material models to simulate the nonlinear response of large structural models. Therefore the presented work provides evidence towards the feasibility of developing, training, and running such models for CMCs with complex architectures, nonlinear multiaxial material response, and under non-monotonic loading conditions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Understanding and Strategies for Controlled Interfacial Phenomena in Lithium-Ion Batteries and Beyond

Electrolyte chemistry and properties and electrode structure and chemical properties particularly at the interfaces are crucial for the development of advanced battery components. This project focused on elucidating the roles of the electrolyte and electrode on the formation and evolution of the SEI layer and cell electrochemical performance on silicon and on Li metal anodes. For Si nano/microstructures we evaluated lithiation, volume changes, reactivity, and chemo-mechanical transformations as functions of nanoparticle size, shape, presence of coatings, electrolyte composition, electron leakage to the electrolyte, and cycling. For Li metal anodes we provided detailed analyses of the electrode and electrolyte effects on interfacial reactivity and as a function of microstructural evolution and underlying stochasticity as dendrites nucleate and grow. We thoroughly investigated and simulated how the chemistry of the various components of the electrolyte and the electrode architecture may affect the electrochemical reactions as well as cell degradation. A multiscale modeling approach was utilized, where atomistic simulations informed about the microscopic behavior of the system, and intermediate time and length scales were investigated with mesoscopic models. Results were also tested against selected experiments from our collaborators. The combined theoretical-experimental strategy saves costs by utilizing predictions from computational analyses to guide experimentation.

25 ENERGY STORAGE↗
DOE OSTI2021

Multiscale Modeling of Cr 2 O 3 -doped UO 2 Creep and Fracture

The pursuit of UO 2 fuel with various dopants (e.g., Cr 2 O 3 , Al 2 O 3 ) for improved accident tolerance due to larger grain sizes and suspected reductions in fission gas release and creep requires advanced modeling and simulation tools. These tools enable rapid multiscale development and understanding of material behavior in regimes where experimental measurements may be lacking. This work builds upon previous multiscale modeling efforts for fission gas behavior of Cr 2 O 3 -doped UO 2 to begin looking at the effects of dopants on mechanical properties with a particular focus on creep and fracture. The results indicate that dislocation climb is the most dominate creep mechanism at almost all temperatures with sensitivity analyses further providing evidence in support of that claim. Limited experimental data from the Advanced Fuels Campaign (AFC) program in the U. S. Department of Energy on tensile strength of Cr 2 O 3 -doped UO 2 indicates that fracture may be less severe in doped specimens. The results on creep and fracture are preliminary given the large uncertainty associated with the models.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗