Enhanced Exploration of Protein Conformational Space through Integration of Ultra-Coarse-Grained Models to Multiscale Workflows
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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
SEARCH · Engineering Papers
Results for “multiscale simulation”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Assessing Two Approaches for Enhancing the Range of Simulated Scales in the E3SMv1 and the Impact on the Character of Hourly US Precipitation
Abstract Improving the representation of precipitation in Earth system models is essential for understanding and projecting water cycle changes across scales. Progress has been hampered by persistent deficiencies in representing precipitation frequency, intensity, and timing in current models. Here, we analyze simulated US precipitation in the low‐resolution (LR) configuration of the Energy Exascale Earth System Model (E3SMv1) and assess the effect of two approaches to enhance the range of explicitly resolved scales: high‐resolution (HR) and multiscale modeling framework (MMF), which incur similar computational expense. Both E3SMv1‐MMF and E3SMv1‐HR capture more intense and less frequent precipitation on hourly and daily timescales relative to E3SMv1‐LR. E3SMv1‐HR improves the intensity over the Eastern and Northwestern US during winter, while E3SMv1‐MMF improves the intensity over the Eastern US and summer diurnal timing over the Central US. These results indicate that both methods may be needed to improve simulations of different storm types, seasons, and regions.
58 GEOSCIENCES↗
Software For Advanced Large-scale Analysis Of Magnetic Confinement For Numerical Design, Engineering & Research (salamander)
As magnetic confinement fusion energy gains traction internationally to enable abundant energy production, designing components for fusion systems is a pressing challenge. During the planned lifetime of a fusion device, components evolve in extreme environments and must withstand large, repeated thermal loads and bombardment by 14 MeV neutrons, plasma ions, and neutral particles (deuterium, tritium, and helium), corrosive conditions, etc. All these physical processes take place simultaneously, interact in intricate ways, and impose important constraints that can affect performance. Experimental data is rare and costly to obtain, making design particularly challenging. Predictive computational frameworks must be an integral part of an accelerated and cost-effective design process by modeling fusion system performance in simulated environments. To better understand component degradation and operational impacts on their performance, the Software for Advanced Large-scale Analysis of MAgnetic confinement for Numerical Design, Engineering & Research (SALAMANDER) is designed as an open-source, fully integrated, multiphysics, multiscale, NQA-1 compliant framework facilitating 3D, high-fidelity fusion system modeling. To that end, SALAMANDER is a MOOSE-based framework, and therefore leverages MOOSE upstream libraries such as PETSc and libMesh to deliver sophisticated finite element, finite volume, and nonlinear solver technology for fusion energy simulations. SALAMANDER couples MOOSE physics module capabilities—such as thermal hydraulics, heat conduction, Navier-Stokes, and thermomechanics—with tritium transport via TMAP8, neutronics via Cardinal, and nascent particle-in-cell capabilities. Direct simulation Monte Carlo methods will be used to address neutral transport near the walls. By coupling all these physics in an integrated application, SALAMANDER will enable high-fidelity modeling of irradiation levels and plasma exposure conditions of plasma facing components and their impact on heat and tritium distributions, as well as the resulting mechanical constraints experienced by the plasma facing components and performance of blanket systems. Furthermore, SALAMANDER will be particularly suited for engineering studies thanks to the stochastic tool module readily available in MOOSE, allowing for extended uncertainty quantification and risk analysis studies. It is also able to use computer-aided design (CAD) meshes to model complex geometries, which is indispensable for fusion systems. SALAMANDER therefore supports design, safety, engineering, and research projects for magnetic confinement fusion systems
Simon, Pierre-Clement [Idaho National Laboratory (↗
Evaluation of present-day extreme precipitation over the United States: an inter-comparison of convection and dynamic permitting configurations of E3SMv1
Abstract Accurate simulation of the present-day characteristics of mean and extreme precipitation at regional scales remains a challenge for Earth system models, which is due in part to deficiencies in model physics such as convective parameterization (CP), and coarse resolution. High horizontal resolution (HR, ∼25 km) and multiscale modeling framework (MMF, i.e. replacing conventional CP with embedded km-scale cloud-resolving models) are two promising directions that could help improve the interaction between subgrid-scale physical processes and large-scale climate. Here, we evaluate simulated extreme precipitation over the United States (US) across three configurations (i.e. low-resolution [LR], HR, and MMF) of the Energy Exascale Earth System Model (E3SMv1) and intercompare them against two gridded observation datasets (climate prediction center daily US precipitation and integrated multi-satellite retrievals for global precipitation measurement). We assess the model’s ability to simulate very heavy seasonal precipitation (illustrated by the difference between the 99th and 90th percentile values) as well as the spatial distributions of several extreme precipitation indices defined by the expert team on climate change detection and indices. Our results show that both the dry (i.e. consecutive dry days (CDD)) and wet (i.e. consecutive wet days, maximum 5 day precipitation, and very wet days) extremes evaluated herein show some improvement as well as degradation with MMF and HR relative to LR. These results vary across seasons and US subregions. For instance, only the very heavy precipitation of winter is improved with MMF and HR. Both configurations alleviate the well-known drizzling bias evident in LR across both winter and summer in many parts of the US, largely due to the overall improvement in intensity and frequency of precipitation. Additionally, our results suggest that while E3SMv1-MMF has higher intensity rates when it does rain, it has too many CDD during the summer, contributing to a low mean precipitation bias.
54 ENVIRONMENTAL SCIENCES↗
Multiscale and Machine Learning Modeling for Process-informed Microstructure Prediction in Additively Manufactured Materials using MALAMUTE
The Advanced Materials and Manufacturing Technologies (AMMT) program under the Department of Energy Office of Nuclear Energy aims to develop and qualify additively manufactured materials for nuclear applications. One key challenge to this is the microstructural variability observed in the additively manufactured products and their impact on the properties and performance of the material in extreme environments. AMMT is using a combination of high-throughput experimental and modeling techniques to accelerate qualification. Conventionally, in-situ and ex-situ characterizations and testing are performed to correlate different aspects of the additive manufacturing process to the final product and its performance. However, adopting a trial-and-error approach to experimentally evaluate the vast range of process parameters required to capture microstructural variability is cost-prohibitive. Modeling and simulation provide a comparatively inexpensive way to understand and correlate the microstructural evolution to the processing conditions. The modeling and simulation work-packages within the AMMT program aims to use physics-based and machine learning models to develop a digital twin for additive manufacturing that can correlate the process conditions to the final product and establish a process-structure-property-performance (PSPP) correlation. The melting and subsequent solidification that occurs during the additive process is a complex phenomenon that requires multiscale multiphysics analysis. This work package focuses on understanding the role of process variabilities on the unique microstructural characteristics of additively manufactured materials. Microstructural features at the subgrain level, such as compositional micro-heterogeneity and dislocation cells, are of particular interest here since they can influence the creep properties and radiation performance. Idaho National Laboratory’s Multiphysics Object-Oriented Simulation Environment (MOOSE), specifically the MOOSE Application Library for Advanced Manufacturing UTilitiEs (MALAMUTE) software, provides an ideal platform for developing the multiphysics multiscale model to explore the intricacies of the microstructural evolution during the AM processes within a single framework. Furthermore, given that such full-fidelity simulations can be computationally intensive, reduced order models are necessary to explore the PSPP space for additively manufactured materials in an efficient, reliable, and cost-effective way. This work focuses on capturing the microstructural variabilities at the subgrain level that are often missing in the part-scale models. In fiscal year 2025, we significantly advanced upon our work in the last fiscal year, in terms of the predictive capabilities of the physics-based and ML models, by adding the capabilities to capture subgrain-level micro-segregation during solidification using phase-field model and to predict the time-dependent dynamics of the AM process through the MOGPAR model. The alloy solidification model in MOOSE incorporates the thermodynamic properties and free energy relevant to 316 stainless steel. The model demonstrates the Cr and Ni segregation that occurs during solidification, including that the rate of solidification. The microstructural evolution model is connected to the process conditions via the surrogate model developed in this work. This enables predictions of the final microstructure in conjunctions with the manufacturing process. This work supports AMMT's rapid qualification goals by laying the foundation for an efficient and cost-effective model establishing the PSPP correlation for AM. The generated microstructures and predicted micro-segregation can be used by other work packages under AMMT to evaluate the properties and environmental response of the material at the mesoscale. Thus, this work helps to identify the key microstructural features at the subgrain level that are significant in property and performance predictions of additively manufactured components. This work will also provide inputs to the large-scale process variability models to reevaluate and validate assumptions and simplifications made in the part-scale models. Furthermore, through active learning this work can help identify the data need from both modeling and experimental sides for development of a robust digital twin for additive manufacturing and accelerate the AMMT's qualification efforts.
36 - MATERIALS SCIENCE↗
Multiscale and multidimensional modeling of particle acceleration and transport in solar flares
Multi-messenger, multi-viewpoint, and time-resolved observations of solar flares are now providing unprecedented constraints on particle acceleration sites, energy conversion, and energy transport. The interpretation of current observations, including microwave imaging spectroscopy from EOVSA, hard x-ray (HXR) imaging from Solar Orbiter/STIX, gamma-ray diagnostics from Fermi, and in situ measurements from Parker Solar Probe and Solar Orbiter, collectively demands modeling frameworks that go beyond traditional spatially unresolved, one-zone models or single-mechanism descriptions. This review surveys multiscale and multidimensional modeling approaches, including kinetic, magnetohydrodynamic (MHD), and macroscopic particle models, that are being developed to meet the need. Kinetic simulations reveal that three-dimensional (3D) effects, including field-line chaos and self-generated turbulence, are essential for sustained power-law particle acceleration. MHD simulations now capture flux-rope eruptions, plasmoid-unstable current sheets, and turbulent flare regions in realistic magnetic topologies. Macroscopic models coupling MHD with energetic-particle models produce spatially resolved electron distributions and synthetic HXR and microwave emissions for direct comparison with observations. Despite these advances, outstanding challenges remain in bridging kinetic and global scales, improving MHD simulations and macroscopic particle models, and achieving quantitative model-observation closure.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Investigating the Unique Ability of Trichodesmium To Fix Carbon and Nitrogen Simultaneously Using MiMoSA
The open ocean is an extremely competitive environment, partially due to the dearth of nutrients. Trichodesmium erythraeum, a marine diazotrophic cyanobacterium, is a keystone species in the ocean due to its ability to fix nitrogen and leak 30 to 50% into the surrounding environment, providing a valuable source of a necessary macronutrient to other species. While there are other diazotrophic cyanobacteria that play an important role in the marine nitrogen cycle, Trichodesmium is unique in its ability to fix both carbon and nitrogen simultaneously during the day without the use of specialized cells called heterocysts to protect nitrogenase from oxygen. Here, we use the advanced modeling framework called multiscale multiobjective systems analysis (MiMoSA) to investigate how Trichodesmium erythraeum can reduce dimolecular nitrogen to ammonium in the presence of oxygen. Our simulations indicate that nitrogenase inhibition is best modeled as Michealis-Menten competitive inhibition and that cells along the filament maintain microaerobia using high flux through Mehler reactions in order to protect nitrogenase from oxygen. We also examined the effect of location on metabolic flux and found that cells at the end of filaments operate in distinctly different metabolic modes than internal cells despite both operating in a photoautotrophic mode. These results give us important insight into how this species is able to operate photosynthesis and nitrogen fixation simultaneously, giving it a distinct advantage over other diazotrophic cyanobacteria because they can harvest light directly to fuel the energy demand of nitrogen fixation.
09 BIOMASS FUELS↗
A multiresolution adaptive wavelet method for nonlinear partial differential equations
We report the multiscale complexity of modern problems in computational science and engineering can prohibit the use of traditional numerical methods in multi-dimensional simulations. Therefore, novel algorithms are required in these situations to solve partial differential equations (PDEs) with features evolving on a wide range of spatial and temporal scales. To meet these challenges, we present a multiresolution wavelet algorithm to solve PDEs with significant data compression and explicit error control. We discretize in space by projecting fields and spatial derivative operators onto wavelet basis functions. We provide error estimates for the wavelet representation of fields and their derivatives. Then, our estimates are used to construct a sparse multiresolution discretization which guarantees the prescribed accuracy. Additionally, we embed a predictor-corrector procedure within the temporal integration to dynamically adapt the computational grid and maintain the accuracy of the solution of the PDE as it evolves. We present examples to highlight the accuracy and adaptivity of our approach.
97 MATHEMATICS AND COMPUTING↗
Modeling-Based Assessment of Deep Seismic Potential Induced by Geologic Carbon Storage
Induced seismicity is an inherent risk associated with geologic carbon storage (GCS) in deep rock formations that could contain undetected faults prone to failure. Modeling-based risk assessment has been implemented to quantify the potential of injection-induced seismicity, but typically simplified multiscale geologic features or neglected multiphysics coupled mechanisms because of the uncertainty in field data and computational cost of field-scale simulations, which may limit the reliable prediction of seismic hazard caused by industrial-scale CO 2 storage. The degree of lateral continuity of the stratigraphic interbedding below the reservoir and depth-dependent fault permeability can enhance or inhibit pore-pressure diffusion and corresponding poroelastic stressing along a basement fault. In conclusion, this study presents a rigorous modeling scheme with optimal geological and operational parameters needed to be considered in seismic monitoring and mitigation strategies for safe GCS.
58 GEOSCIENCES↗
Changes in Tropical Clouds and Atmospheric Circulation Associated with Rapid Adjustment Induced by Increased Atmospheric CO2 – A Multiscale Modeling Framework Study
The radiative heating increase due to increased CO2 concentration is the primary source for the rapid adjustment of atmospheric circulation and clouds. In this study, we investigate the rapid adjustment resulting from doubling of CO2 and its physical mechanism using a multiscale modeling framework (MMF). The MMF includes an advanced higher-order turbulence closure in its cloud-resolving model component and simulates realistic shallow and deep cloud climatology and boundary layer turbulence. The rapid adjustment over the tropics is characterized by 1) reduced ascent and descent strengths over the ocean, 2) increased lower tropospheric stability (LTS) over the subsidence region, 3) shoaling of planetary boundary layers over the ocean, 4) increased deep convection over lands and shift of cloud coverage from the ocean to lands, and 5) reduced sensible (SH) and latent heat (LH) fluxes over the oceanic deep convective regions. Unlike conventional general circulation models and another MMF, a reduction in the global-mean shortwave cloud radiative cooling is not simulated, due to the increase in low clouds at lower altitudes over the ocean, resulting from reduced cloud-top entrainment due to strengthened inversion. Changes in regional circulation play a key role in cloud changes and shift of cloud coverage to lands. Weaker energy transport resulting from water vapor and cloud CO2 masking effects reduces the upward motion and convective clouds in the oceanic regions. The ocean-land transports are linked to the partitioning of surface SH and LH fluxes that increases humidity over lands and enhances deep convection over the tropical lands.
Xu, Kuan-Man↗
Magnetic reconnection for low-density inflow conditions
Like in all environments, magnetic reconnection in the Earth’s magnetotail and its efficacy depend on plasma conditions in the inflow region. The Earth’s magnetotail is a particularly interesting environment to study this dependency, because plasma densities in the inflow region can vary widely. Under conditions of strong magnetospheric convection, high density plasma from ionospheric or solar wind origin can impact reconnection significantly, whereas at other times, particle density in the inflow region can be extremely low. The present study is motivated by recent observations by the Magnetospheric Multiscale Mission, which indicate an unusually large level of plasma turbulence when the plasma inflow density is very low. In this simulation-based study, we aim to shed light on the question, whether low density in the inflow region intrinsically leads to enhanced turbulence, or whether density variations are essential to create significant deviations from the usual, more laminar, picture of reconnection. Finally, we will comment on the implications of extremely low inflow density on the reconnection process.
heliophysics↗
NeuroSEM: A hybrid framework for simulating multiphysics problems by coupling PINNs and spectral elements
Multiphysics problems that are characterized by complex interactions among fluid dynamics, heat transfer, structural mechanics, and electromagnetics, are inherently challenging due to their coupled nature. While experimental data on certain state variables may be available, integrating these data with numerical solvers remains a significant challenge. Physics-informed neural networks (PINNs) have shown promising results in various engineering disciplines, particularly in handling noisy data and solving inverse problems in partial differential equations (PDEs). However, their effectiveness in forecasting nonlinear phenomena in multiphysics regimes, particularly involving turbulence, is yet to be fully established. Here, this study introduces NeuroSEM, a hybrid framework integrating PINNs with the highfidelity Spectral Element Method (SEM) solver, Nektar++. NeuroSEM leverages the strengths of both PINNs and SEM, providing robust solutions for multiphysics problems. PINNs are trained to assimilate data and model physical phenomena in specific subdomains, which are then integrated into the Nektar++ solver. We demonstrate the efficiency and accuracy of NeuroSEM for thermal convection in cavity flow and flow past a cylinder. The framework effectively handles data assimilation by addressing those subdomains and state variables where the data is available. We applied NeuroSEM to the Rayleigh-B´enard convection system, including cases with missing thermal boundary conditions and noisy datasets. Finally, we applied the proposed NeuroSEM framework to real particle image velocimetry (PIV) data to capture flow patterns characterized by horseshoe vortical structures. Our results indicate that NeuroSEM accurately models the physical phenomena and assimilates the data within the specified subdomains. The framework’s plug-and-play nature facilitates its extension to other multiphysics or multiscale problems. Furthermore, NeuroSEM is optimized for efficient execution on emerging integrated GPU-CPU architectures. This hybrid approach enhances the accuracy and efficiency of simulations, making it a powerful tool for tackling complex engineering challenges in various scientific domains.
42 ENGINEERING↗
Multiscale analysis in solids with unseparated scales: fine-scale recovery, error estimation, and coarse-scale adaptivity
There are several engineering applications in which the assumptions of homogenization and scale separation may be violated, in particular, for metallic structures constructed through additive manufacturing. Instead of resorting to direct numerical simulation of the macroscale system with an embedded fine scale, an alternative approach is to use an approximate macroscale constitutive model, but then estimate the model-form error using a posteriori error estimation techniques and subsequently adapt the macroscale model to reduce the error for a given boundary value problem and quantity of interest. Here, we investigate this approach to multiscale analysis in solids with unseparated scales using the example of an additively manufactured metallic structure consisting of a polycrystalline microstructure that is neither periodic nor statistically homogeneous. As a first step to the general nonlinear case, we focus here on linear elasticity in which each grain within the polycrystal is linear elastic but anisotropic.
42 ENGINEERING↗
Dendrite Growth Morphology Modeling in Liquid and Solid Electrolytes
The main goal of this project is to develop a multi-scale modeling approach that connects micron-scale phase-field models and atomic-scale density functional theory (DFT)-based simulations via parameter- and relationship-passing in order to predict Li-metal dendrite morphology evolution, in both liquid and solid electrolytes. The key hypothesis of the DFT-informed phase-field multiscale modeling approach is that it can capture the electrochemical-mechanical driving forces and incorporate the roles of nano-meter-thin solid electrolyte interphase (SEI) in liquid electrolytes as well as of the microstructures of micro-meter-thick solid electrolytes (SEs) for all-solid-state batteries. In this project, we have formulated and implemented phase-field models to incorporate the electrochemical driving forces in liquid electrolytes and then incorporate mechanical driving forces to simulate dendrite growth in solid electrolytes with resolved microstructures. We have implemented two treatments for the SEI: an explicit model to include the microstructure of the SE or SEI in the phase field model and an implicit model to simulate the impact of nano-meter thick SEI in liquid electrolytes by varying the electrode/electrolyte interfacial properties. The key interfacial properties, including the electronic and ionic transport properties, the charge transfer reaction kinetics, and mechanical properties, were computed by DFT-based calculations. At the DFT-based model, one key advancement is to directly predict the charge transfer reaction kinetics at a complex Li/SEI/electrolyte interface by linking DFT with density functional tight binding (DFTB) calculations. As the main accomplishments, we have demonstrated two successful predictions in both solid electrolyte and liquid electrolyte based on this multiscale approach. The predicted intergranular Li dendrite growth in LLZO revealed the importance of trapped electrons at internal interfaces in the microstructure of LLZO. The predicted electroplating morphology of mossy Li and faceted Mg agreed well with experiments. The insights provided by the multiscale model and the model enabled electrolyte and SEI design will accelerate the development of Li-metal electrode for high energy density batteries, that meet DOE’s target on cell density (>350 Wh/kg) and cost below $100/kWhuse for EV applications.
25 ENERGY STORAGE↗
Multiscale modeling for high burnup structure formation and associated pulverization
This report summarizes the lower length scale modeling work performed in the fiscal year 2023 under the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program to capture the microstrutural evolution and associated pulverization criteria in the high burnup regions. This year, the resolution mechanisms within the cluster dynamics code has been updated and it influence on the bubble growth in HBS regions at the mesoscale is studied. To improve the accuracy of phase-field models of fission gas bubble growth, a new Helmholtz free energy for high-density Xe gas is derived from a virial equation of state. Two previously used strategies for representing net vacancy production in phase-field models of fission gas bubble growth are compared with each other and with analytical models of bubble growth. The vacancy source only model is found to be more convenient to parameterize realistically compared with the vacancy source+sink model. Furthermore, the phase-field-fracture simulation have been performed using MD- informed failure stress values and realistic HBS structure obtained from the phase-field simulations. We also present the uncertainty bands on prediction of the critical stress to account for the effect of the lower length scale variabilities on the failure criteria at the mesoscale. It is observed that pulverization may occur in partially restructured regions with restructuring fraction as low as 17%. In light of this, an update to the BISON’s pulverization criteria is recommended.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Molecular Dynamics Simulation of Complex Reactivity with the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) Software Package
Simulating chemically reactive phenomena such as proton transport on nanosecond to microsecond and beyond time scales is a challenging task. Ab initio methods are unable to currently access these time scales routinely, and traditional molecular dynamics methods feature fixed bonding arrangements that cannot account for changes in the system’s bonding topology. The Multiscale Reactive Molecular Dynamics (MS-RMD) method, as implemented in the Rapid Approach for Proton Transport and Other Reactions (RAPTOR) software package for the LAMMPS molecular dynamics code, offers a method to routinely sample longer time scale reactive simulation data with statistical precision. RAPTOR may also be interfaced with enhanced sampling methods to drive simulations toward the analysis of reactive rare events, and a number of collective variables (CVs) have been developed to facilitate this. Key advances to this methodology, including GPU acceleration efforts and novel CVs to model water wire formation are reviewed, along with recent applications of the method which demonstrate its versatility and robustness.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
A neural master equation framework for multiscale modeling of molecular processes: application to atomic-scale plasma processes
Plasma-surface interactions (PSI) play a crucial role in microelectronics fabrication; however, their multiscale nature and array of complex, often unknown interactions make computational modeling of PSIs extremely difficult. To this end, we propose a general neural master equation (NME) framework that uses master equations to describe the dynamics of a molecular process, wherein neural networks learned from atomistic simulations represent unknown transitions between different system states. By leveraging the physics-based structure of master equations and data-driven state transitions, the NME framework promotes generalizability and physics interpretability, and can bridge disparate length and time scales. The framework is demonstrated for multiscale modeling of Si atomic layer etching and reactive ion etching, where the learned NME-based surface kinetic models exhibit good predictive and extrapolative capabilities for predicting experimentally relevant observables as a function of process parameters. The NME-based surface kinetic models obey physical constraints, which are violated in models based on neural ordinary differential equations. The proposed NME framework for multiscale modeling of molecular processes can pave the way for the discovery of new chemistries and materials in atomic-scale plasma processes.
Chemical engineering↗