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At least 73 records · Page 4

Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations

To gain molecular and mechanistic insights into initiation of the RAS-RAF signaling cascade, we developed and used a combination of multiscale simulation and experimental approaches. The influence and impact of the membrane on RAS and RAF proteins is a factor we are just beginning to understand and appreciate in more detail. Molecular simulation is an ideal methodology to further study this complicated relationship between the membrane and associated proteins. Our previous work using Multiscale Machine-learned Modeling Infrastructure investigated different lipid compositions solely around the KRAS4b protein and the interplay between protein behavior and these membrane environments. Multiscale Machine-learned Modeling Infrastructure uses machine learning to couple adjacent simulation scales and has been efficiently scaled across some of the world’s largest high-performance computers. Recently, we have expanded this multiresolution framework to include the all-atom simulation scale and to incorporate the RAF RBDCRD domains. Here, we present the overall analysis results from this new simulation campaign comprising a mixture of RAS and RAF RBDCRD proteins. Approximately 35,000 coarse-grained and 10,000 all-atom molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations that were generated from a micron-scale continuum simulation containing hundreds of copies of the proteins. Our studies suggest that orientations of the RAS-RBDCRD complex on the membrane occupy distinct configurational states, and the spatial patterns of lipid arrangements around these different protein states are unique to each state. The extent and size of lipid “fingerprints” imposed on the membrane by the RAS-RBDCRD protein complex are significantly larger than observed for just the RAS protein on its own. These protein complexes strongly associate, but we do not observe statistically significant preferred protein-protein orientations. These observations indicate that spatial colocalization of RAS-RBDCRD proteins in the same vicinity may be assisted by specific membrane environments, acting to increase the probability of signaling complex formation.

Carpenter, Timothy S. [Lawrence Livermore National↗

Documentation, assessment, and improvements of fission gas modeling capabilities in BISON

Fission gas behavior critically affects nuclear fuel performance, influencing thermal conductivity, microstructure, swelling, and fuel-cladding interactions. The Simple Integrated Fission Gas Release and Swelling (Sifgrs) model, implemented within the BISON fuel performance code, provides advanced capabilities for modeling these phenomena. This manuscript reviews and assesses Sifgrs’ modular structure and submodels describing intragranular, intergranular, and release mechanisms. The modular implementation enables rapid improvements as our understanding advances and new fuel forms emerge. After an overview of capabilities, we present a comprehensive validation suite, comparing predictions to experimental data from tests under normal and transient conditions, including reproduction of the Vitanza curve. Results demonstrate Sifgrs’ accuracy, robustness, and applicability. Current limitations and ongoing efforts are discussed, including mechanistic, multiscale modeling, uncertainty quantification, and validation within the Nuclear Energy Advanced Modeling and Simulation (NEAMS) program, supporting the safe and efficient use of nuclear fuels.

BISON↗

Materials Informatics at NASA GRC: Machine Learning Surrogate Modeling, Data Management, and Integrated Toolsets for Establishing/Maintaining the Digital Thread

Integrated Computational Materials Engineering (ICME) has recently received widespread attention due to its promises in reducing dependence on physical testing for engineering design by relying on simulation, reducing both time and cost to market for various applications. ICME however requires validated multiscale material models, which heavily depend on available test data with full material and test pedigree, including material processing, test and measurement equipment, raw data collection, and analysis methodology and results that is findable and usable, along with integrated, efficient toolsets for effectively passing information across various length and time scales across such models. At the NASA Glenn Research Center under the Transformational Tools and Technologies Project, significant recent efforts have been directed towards establishing the required cyberinfrastructure to enable optimized ICME processes and the design of “fit-for-purpose” materials to achieve the goals outlined in the NASA Vision 2040 report. Such efforts include development of multiscale physics-based material models, which can be used to train highly efficient surrogate machine learning models, development of best practices and infrastructure for effective, traceable materials information management, and development of toolsets that integrate with physics-based codes, machine learning models, and an information management system to enable high throughput of materials data collection and analysis, establishment of digital twins and the digital thread, and automation of the ICME design process for material optimization.

Machine Learning↗

Commutative Algebra Modeling in Materials Science – A Case Study on Metal–Organic Frameworks (MOFs)

Metal-organic frameworks (MOFs) are a class of important crystalline and highly porous materials whose hierarchical geometry and chemistry hinder interpretable predictions in materials properties. Commutative algebra is a branch of abstract algebra that has been rarely applied in data and material sciences. We introduce the first ever commutative algebra modeling and prediction in materials science. Specifically, category-specific commutative algebra (CSCA) is proposed as a new framework for MOF representation and learning. It integrates element-based categorization with multiscale algebraic invariants to encode both local coordination motifs and global network organization of MOFs. These algebraically consistent, chemically aware representations enable compact, interpretable, and data efficient modeling of MOF properties such as Henry’s constants and uptake capacities for common gases. Compared to traditional geometric and graph-based approaches, CSCA achieves comparable or superior predictive accuracy while substantially improving interpretability and stability across data sets. By aligning commutative algebra with the chemical hierarchy, the CSCA establishes a rigorous and generalizable paradigm for understanding structure and property relationships in porous materials and provides a nonlinear algebra-based framework for data-driven material discovery.

Khaemba, Caleb S.↗

Multiscale design of nonlinear materials using a Eulerian shape optimization scheme

Motivated by recent advances in manufacturing, the design of materials is the focal point of interest in the material research community. One of the critical challenges in this field is finding optimal material microstructure for a desired macroscopic response. This work presents a computational method for the mesoscale-level design of particulate composites for an optimal macroscale-level response. The method relies on a custom shape optimization scheme to find the extrema of a nonlinear cost function subject to a set of constraints. Three key “modules” constitute the method: multiscale modeling, sensitivity analysis, and optimization. Multiscale modeling relies on a classical homogenization method and a nonlinear NURBS-based generalized finite element scheme to efficiently and accurately compute the structural response of particulate composites using a nonconformal discretization. A three-parameter isotropic damage law is used to model microstructure-level failure. An analytical sensitivity method is developed to compute the derivatives of the cost/constraint functions with respect to the design variables that control the microstructure's geometry. The derivation uncovers subtle but essential new terms contributing to the sensitivity of finite element shape functions and their spatial derivatives. Several structural problems are solved to demonstrate the applicability, performance, and accuracy of the method for the design of particulate composites with a desired macroscopic nonlinear stress-strain response.

42 ENGINEERING↗

High-Temperature Air Stability of Electrodeposited Copper Cobalt Oxide and Copper Manganese Oxide Absorber Coatings for Concentrating Solar Power

The solar absorptance of a thermal receiver surface significantly affects the photothermal conversion efficiency of concentrating solar power (CSP) plants. The stability of solar receivers and coatings applied to improve solar absorptance at high temperatures is critical for efficient and long-term operation. This study analyzes the high-temperature air stability of multiscale fractal textured electrodeposited copper manganese oxide and copper cobalt oxide solar receiver coatings over a range of temperatures. The study also investigates the effect of high temperature on phase stability, chemical and morphological evolution, and the optical properties of the two solar absorber materials. A computational model is developed to determine the absorptance of the textured absorbers and is shown to match the experimental measurements closely over a range of heat treatment temperatures from 450 °C to 850 °C and durations up to 100 h. Degradation curves and coating stability maps are developed from the study. Copper manganese oxide and copper cobalt oxide coatings exhibit good thermal stability up to ~815 °C and 630 °C, respectively, with minimal changes in their optical and structural properties with thermal efficiency greater than 90%. Furthermore, the study offers valuable insights into the high-temperature annealing effects on the optical and structural properties of multiscale copper alloyed coatings fabricated by electrodeposition and presents a means of designing the optimal temperature range for maximizing absorber efficiency in practical applications.

14 SOLAR ENERGY↗

Predicting Fiber Failure of Plain Weave Fabric with Recursive Multiscale Micromechanics

Recent advances in the development of machine learning (ML) algorithms have enabled the creation of predictive models that can improve decision making, decrease computational cost, and improve efficiency in a variety of fields. As an organization begins to develop and implement such models, the data used in the training, validation, and testing of machine learning models, the model parameters, and the use cases or limitations of the models must be properly stored to ensure models are both fully traceable and used correctly. In the context of predicting material behavior, advances in computationally intense, physics-based, modeling of material behavior at various length scales, and the emergence of Integrated Computational Materials Engineering (ICME) have driven the need for developing data-driven surrogate models of the physics-based simulation tools using machine learning (ML) techniques. Surrogate model development allows for accurate material behavior prediction at a fraction of the cost of its physics-based counterpart, allowing for multiscale simulations of real-world applications, further enabling the ability to design fit-for-purpose materials for a reasonable computational investment. However, training such models requires extensive data, and thus effective data management is necessary to reach the full potential that ML can offer to material design and ICME. This paper proposes a generalized, robust schema that allows organizations to store both real (experimental) and virtual (simulation) data used to train machine learning models and the defining model parameters and architectures. The developed schema allows for various types of data inputs and outputs, including single point values, time-series data, and images that can be used in for various types of machine learning models while following outlined best practices for effective data management. An effective schema for machine learning data and models can help prevent the recreation of virtual/real training data and surrogate models, can help reduce the time to create new models similar to existing ones by offering a starting point in the hyperparameter determination stages, minimize resources devoted to verification and validation (V&V) and certification of models, and ensure that data and surrogate models are not misused due to full traceability of both the data and ML model. It also allows organizations access to models that have already been developed, such that they can be used in the design of new materials, enabling the overall goals of ICME.

Failure↗

An adaptive, data-driven multiscale approach for dense granular flows

The accuracy of coarse-grained continuum models of dense granular flows is limited by the lack of high-fidelity closure models for granular rheology. One approach to addressing this issue, referred to as the hierarchical multiscale method, is to use a high-fidelity fine-grained model to compute the closure terms needed by the coarse-grained model. The difficulty with this approach is that the overall model can become computationally intractable due to the high computational cost of the high-fidelity model. In this work, we describe a multiscale modeling approach for dense granular flows that utilizes neural networks trained using high-fidelity discrete element method (DEM) simulations to approximate the constitutive granular rheology for a continuum incompressible flow model. Our approach leverages an ensemble of neural networks to estimate predictive uncertainty that allows us to determine whether the rheology at a given point is accurately represented by the neural network model. Additional DEM simulations are only performed when needed, minimizing the number of additional DEM simulations required when updating the rheology. This adaptive coupling significantly reduces the overall computational cost of the approach while controlling the error. In addition, the neural networks are customized to learn regularized rheological behavior to ensure well-posedness of the continuum solution. We first validate the approach using two-dimensional steady-state and decelerating inclined flows. We then demonstrate the efficiency of our approach by modeling three-dimensional sub-aerial granular column collapse for varying initial column aspect ratios, where our multiscale method compares well with the computationally expensive computational fluid dynamics (CFD)-DEM simulation.

Dense granular flows↗

Theoretical and numerical studies of inverse source problem for the linear parabolic equation with sparse boundary measurements

We consider the inverse source problem in the parabolic equation, where the unknown source possesses the semi-discrete formulation. Theoretically, we prove that the flux data from any nonempty open subset of the boundary can uniquely determine the semi-discrete source. This means the observed area can be extremely small, and that is the reason we call it sparse boundary data. For the numerical reconstruction, we formulate the problem from the Bayesian sequential prediction perspective and conduct the numerical examples which estimate the space-time-dependent source state by state. To better demonstrate the method’s performance, we solve two common multiscale problems from two models with a long source sequence. The numerical results illustrate that the inversion is accurate and efficient.

97 MATHEMATICS AND COMPUTING↗

A New Concurrent Multiscale Methodology for Coupling Molecular Dynamics and Finite Element Analyses

The coupling of molecular dynamics (MD) simulations with finite element methods (FEM) yields computationally efficient models that link fundamental material processes at the atomistic level with continuum field responses at higher length scales. The theoretical challenge involves developing a seamless connection along an interface between two inherently different simulation frameworks. Various specialized methods have been developed to solve particular classes of problems. Many of these methods link the kinematics of individual MD atoms with FEM nodes at their common interface, necessarily requiring that the finite element mesh be refined to atomic resolution. Some of these coupling approaches also require simulations to be carried out at 0 K and restrict modeling to two-dimensional material domains due to difficulties in simulating full three-dimensional material processes. In the present work, a new approach to MD-FEM coupling is developed based on a restatement of the standard boundary value problem used to define a coupled domain. The method replaces a direct linkage of individual MD atoms and finite element (FE) nodes with a statistical averaging of atomistic displacements in local atomic volumes associated with each FE node in an interface region. The FEM and MD computational systems are effectively independent and communicate only through an iterative update of their boundary conditions. With the use of statistical averages of the atomistic quantities to couple the two computational schemes, the developed approach is referred to as an embedded statistical coupling method (ESCM). ESCM provides an enhanced coupling methodology that is inherently applicable to three-dimensional domains, avoids discretization of the continuum model to atomic scale resolution, and permits finite temperature states to be applied.

Yamakov, Vesselin↗

Modeling Materials: Design for Planetary Entry, Electric Aircraft, and Beyond

NASA missions push the limits of what is possible. The development of high-performance materials must keep pace with the agency's demanding, cutting-edge applications. Researchers at NASA's Ames Research Center are performing multiscale computational modeling to accelerate development times and further the design of next-generation aerospace materials. Multiscale modeling combines several computationally intensive techniques ranging from the atomic level to the macroscale, passing output from one level as input to the next level. These methods are applicable to a wide variety of materials systems. For example: (a) Ultra-high-temperature ceramics for hypersonic aircraft-we utilized the full range of multiscale modeling to characterize thermal protection materials for faster, safer air- and spacecraft, (b) Planetary entry heat shields for space vehicles-we computed thermal and mechanical properties of ablative composites by combining several methods, from atomistic simulations to macroscale computations, (c) Advanced batteries for electric aircraft-we performed large-scale molecular dynamics simulations of advanced electrolytes for ultra-high-energy capacity batteries to enable long-distance electric aircraft service; and (d) Shape-memory alloys for high-efficiency aircraft-we used high-fidelity electronic structure calculations to determine phase diagrams in shape-memory transformations. Advances in high-performance computing have been critical to the development of multiscale materials modeling. We used nearly one million processor hours on NASA's Pleiades supercomputer to characterize electrolytes with a fidelity that would be otherwise impossible. For this and other projects, Pleiades enables us to push the physics and accuracy of our calculations to new levels.

Supercomputing↗

E3SM: Improved Climate Prediction with Exascale Capability

The Energy Exascale Earth System Model (E3SM) project is an ongoing, state-of-the-science earth system modeling, simulation, and prediction effort that optimizes Department of Energy (DOE) computing resources to meet the science needs of the nation and the agency’s mission objectives. Climate simulation has become a proven tool for identifying and quantifying the impacts of climate change, but even greater accuracy is required at all levels to improve forecast precision. Understanding the impact of climate change on global and regional water cycles is one of the highest priorities and most difficult challenges in climate change prediction. As part of a subproject of DOE’s Exascale Computing Project, a multidisciplinary team including geophysical and computational scientists developed a multiscale modeling framework (MMF) to refine cloud representation in E3SM climate simulation on GPU accelerated supercomputers, making higher resolution, more computationally efficient predictions possible.

54 ENVIRONMENTAL SCIENCES↗

An Algorithm for Characterization of Fiber Aggregation in Composite Microstructures

Composite structures are susceptible to localized flaws, or variability, that drive global failure. To capture this variance, a multiscale model needs to be introduced that not only accurately represents the statistical nature of the composite microstructure but is also efficient. At the microscale, fiber aggregation creates local stress concentrations, where failure is likely to occur sooner than expected. A method of rapid microstructure generation, in conjunction with cluster characterization, is examined to develop accurate reproductions of 2D composite cross-sections. Parameterization of shape and size of fiber clusters is used to characterize representative volume elements. The discrete element method is used to generate pseudo-microstructures. The clustering parameters from the pseudo- and actual microstructure arrangements (obtained from micrographs) can be compared to determine the validity of the representative volume element generated with the discrete element method. Results show a promising approach to evaluating randomness of fiber distributions and how to accurately recreate microstructures for strength analysis.

Carbon fiber↗

Three‐Dimensional Permeability Inversion Using Convolutional Neural Networks and Positron Emission Tomography

Abstract Quantification of heterogeneous multiscale permeability in geologic porous media is key for understanding and predicting flow and transport processes in the subsurface. Recent utilization of in situ imaging, specifically positron emission tomography (PET), enables the measurement of three‐dimensional (3‐D) time‐lapse radiotracer solute transport in geologic media. However, accurate and computationally efficient characterization of the permeability distribution that controls the solute transport process remains challenging. Leveraging the relationship between local permeability variation and solute advection behavior, an encoder‐decoder based convolutional neural network (CNN) is implemented as a permeability inversion scheme using a single PET scan of a radiotracer pulse injection experiment as input. The CNN can accurately capture the 3‐D spatial correlation between the permeability and the radiotracer solute arrival time difference maps in geologic cores. We first test the inversion accuracy using synthetic test datasets and then test the accuracy on a suite of experimental PET imaging datasets acquired on four different geologic cores. The network‐predicted permeability maps from the geologic cores are used to parameterize forward numerical models that are directly compared with the experimental PET imaging data. The results indicate that a single trained network can generate robust 3‐D permeability inversion maps in seconds. Numerical models parameterized with these permeability maps closely capture the experimentally observed solute arrival time behavior. This work provides an unprecedented approach for efficiently characterizing multiscale permeability heterogeneity in complex geologic samples.

54 ENVIRONMENTAL SCIENCES↗

Parallel transport dynamics for mixed quantum states with applications to time-dependent density functional theory

Direct simulation of the von Neumann dynamics for a general (pure or mixed) quantum state can often be expensive. One prominent example is the real-time time-dependent density functional theory (rt-TDDFT), a widely used framework for the first principle description of many-electron dynamics in chemical and materials systems. Practical rt-TDDFT calculations often avoid the direct simulation of the von Neumann equation, and solve instead a set of Schrödinger equations, of which the dynamics is equivalent to that of the von Neumann equation. However, the time step size employed by the Schrödinger dynamics is often much smaller. Here, in order to improve the time step size and the overall efficiency of the simulation, we generalize a recent work of the parallel transport (PT) dynamics for simulating pure states [An, Lin, Multiscale Model. Simul. 18, 612, 2020] to general quantum states. The PT dynamics provides the optimal gauge choice, and can employ a time step size comparable to that of the von Neumann dynamics. Going beyond the linear and near adiabatic regime in previous studies, we find that the error of the PT dynamics can be bounded by certain commutators between Hamiltonians, density matrices, and their derived quantities. Such a commutator structure is not present in the Schrödinger dynamics. We demonstrate that the parallel transport-implicit midpoint (PT-IM) method is a suitable method for simulating the PT dynamics, especially when the spectral radius of the Hamiltonian is large. The commutator structure of the error bound, and numerical results for model rt-TDDFT calculations in both linear and nonlinear regimes, confirm the advantage of the PT dynamics.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Cooperative Research and Development Agreement among National Energy Technology Laboratory, Advanced Manufacturing LLC, and Connecticut Center for Advanced Technology [Abstract]

The National Energy Technology Laboratory (NETL), Advanced Manufacturing LLC (AMLLC) and Connecticut Center for Advanced Technology (CCAT) will collaborate to develop and manufacture cost-effective, oxide dispersion-strengthened, NiCrFeCo-rich high entropy alloys that are superior to Nickel-based superalloys (e.g. IN740) for repair or replacement service in extreme environments. The new alloys can result in higher efficiency and reduced cost of advanced power systems such as advanced ultra-supercritical (AUSC) boilers and gas turbines. High throughput, multiscale computational modeling will be performed to accelerate alloy discovery by interrogating the intrinsic properties of the alloys including thermodynamic, kinetic, and mechanical properties. Validation and evaluation will be performed, including additive manufacturing, microstructure characterization, and mechanical properties tests.

36 MATERIALS SCIENCE↗

Emerging multiscale insights on microbial carbon use efficiency in the land carbon cycle

Microbial carbon use efficiency (CUE) affects the fate and storage of carbon in terrestrial ecosystems, but its global importance remains uncertain. Accurately modeling and predicting CUE on a global scale is challenging due to inconsistencies in measurement techniques and the complex interactions of climatic, edaphic, and biological factors across scales. The link between microbial CUE and soil organic carbon relies on the stabilization of microbial necromass within soil aggregates or its association with minerals, necessitating an integration of microbial and stabilization processes in modeling approaches. In this perspective, we propose a comprehensive framework that integrates diverse data sources, ranging from genomic information to traditional soil carbon assessments, to refine carbon cycle models by incorporating variations in CUE, thereby enhancing our understanding of the microbial contribution to carbon cycling.

54 ENVIRONMENTAL SCIENCES↗