SEARCH · Engineering Papers

Results for “coarse graining”

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.

SourceResearch connectionFrom yearThrough year

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 37 records · Page 2

All sources NASA NTRS DOE OSTI

DOE OSTI2025

Coarse-grained molecular dynamics simulation of solvent-dependent cellulose nanofiber interactions

Associations between cellulose are important both in biofuel production and in the use of cellulose for biomaterials. Cellulose nanofibers (CNFs) are sustainable, strong, light-weight alternatives to traditional materials in manufacturing, but are challenging to obtain due to irreversible aggregation in solution during preparative fibrillation. Therefore, it is imperative to understand the underlying factors driving aggregation with a view to designing solvents that can effectively compete with interfiber interactions, hence reducing aggregation. Molecular dynamics (MD) simulation at atomic detail can provide useful information on local interactions. However, the length and timescales accessible are too short to fully capture association processes. Here, we provide a method for accessing the longer length and timescales required using coarse-grained (CG) MD simulations with a MARTINI force field to calculate the interaction behavior of CNFs in three selected solvents: NaOH-urea-water, acetone, and neat water. The CG results are consistent with our prior all-atom MD and with previous experimental results. While acetone is found not to be an effective solvent, urea and ionic moieties in NaOH-urea-water not only solvate the fibrils but also improve the confinement of water molecules around them as shown by the solvent residence times and mean-square displacements. Overall, the presence of urea and ions reduces the likelihood of aggregation in multi-CNF systems relative to neat water irrespective of whether the hydrophobic or hydrophilic CNF surfaces are interacting. In conclusion, the CG method shows clear promise for selecting potential high-performance solvents for experimental prioritization in bioenergy and biomaterials research in a relatively fast manner as well as for understanding the aggregation and rheological behavior of CNF-solvent systems.

aggregation↗

DOE OSTI2026

Learning Latent Representations to Bridge Coarse-Grained and Atomistic Resolutions in Polymer Simulations

We present a machine-learning-based framework for learning reduced-order representations of polymer chain conformations across coarse-grained (CG) and united-atom (UA) fidelities. By employing linear singular value decomposition and nonlinear autoencoders, we compress high-dimensional polymer configurations into latent spaces with minimal loss of structural accuracy. Crucially, we demonstrate a near-perfect linear mapping between CG and UA latent spaces, enabling an efficient super-resolution back-mapping procedure that reconstructs high-fidelity UA configurations from CG simulations. While minor structural inaccuracies occur, they are effectively corrected through a brief molecular dynamics relaxation, forming a practical hybrid machine learning−physics scheme. This approach establishes the key structural prerequisites for accelerated polymer dynamics simulations: a compact and accurate latent encoding of polymer chain conformations and a validated multi-fidelity mapping that permits reconstruction of UA structures from CG configurations. The extension of this framework to explicit time evolution within the latent space, enabling dynamics to be propagated at CG fidelity and decoded to UA resolution only when required, represents a natural and well-motivated direction for future work.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Coarse Graining Discrete Element Method Information in Particle-in-Cell Length Scales Using a Machine Learning Approach

This report details the development of a machine learning (ML)-driven framework to coarse-grain inter-particle collision dynamics from high-fidelity Discrete Element Method (DEM) simulations to Particle-in-Cell (PIC) scales for gas-solid systems. Traditional PIC models, while computationally efficient, rely on empirical granular stress formulations that fail to capture the full complexity of collision physics, particularly the heterogeneity in particle dynamics. This study adopts a bottom-up approach, integrating insights from DEM simulations to improve the physical fidelity and interpretability of PIC-scale models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Dissolution of Nb(C,N) and (Ti,V)N in the Coarse-Grained Heat-Affected Zone of Electric Resistance Welded X65 Line Pipe

Nb-rich and Ti/V-rich precipitates were introduced into the X65 linepipe via thermomechanical controlled processing. Their dissolution kinetics were investigated in the coarse-grained heat-affected zone after electric resistance welding. Nb-rich precipitates were found to dissolve completely, whereas Ti/V-rich precipitates were found to dissolve partially, because of slower dissolution kinetics. In conclusion, a complete dissolution of Nb-rich precipitates was associated with significant austenite grain coarsening, which promoted bainite as a quench product, which might have reduced the impact toughness.

microstructure↗

DOE OSTI2026

Structure and Flow-Viscosity of Filled-Polymer-Based 3D Printing Ink: Exploration through Coarse-Grained Molecular Dynamics

The addition of nanofiller particles to a polymer matrix has long been known to enhance or modify the composite’s mechanical and rheological properties. However, quantitatively capturing such changes with molecular level simulations remains computationally challenging. Toward that goal, we performed coarse-grained molecular dynamics of a nanocomposite system at a fixed (25 vol %) filler loading under nonspecific, weak polymer–filler interactions representative of a broad class of technologically important materials. We report several interesting results, including: (1) the equilibrium chain-configuration remains Gaussian-like as in an unfilled melt; (2) smaller filler particles display a stronger tendency to cluster; (3) larger fillers act as plasticizers by reducing the entanglement density and accelerating the chain mobility; and (4) fillers enhance the tensile response modulus, with the effect being stronger for larger particles. We also simulate cluster breakup, yielding, and elongational flow under an applied time-linear tensile strain and study the flow viscosity as a function of filler-size and chain-length.

Materials science↗

DOE OSTI2025

Attention-based functional-group coarse-graining: a deep learning framework for molecular prediction and design

Machine learning (ML) offers considerable promise for the design of new molecules and materials. In real-world applications, the design problem is often domain-specific, and suffers from insufficient data, particularly labeled data, for ML training. In this study, we report a data-efficient, deep-learning framework for molecular discovery that integrates a coarse-grained functional-group representation with a self-attention mechanism to capture intricate chemical interactions. Our approach exploits group-contribution concepts to create a graph-based intermediate representation of molecules, serving as a low-dimensional embedding that substantially reduces the data demands typically required for training. Using a self-attention mechanism to learn the subtle but highly relevant chemical context of functional groups, the method proposed here consistently outperforms existing approaches for predictions of multiple thermophysical properties. In a case study focused on adhesive polymer monomers, we train on a limited dataset comprising only 6,000 unlabeled and 600 labeled monomers. The resulting chemistry prediction model achieves over 92% accuracy in forecasting properties directly from SMILES strings, exceeding the performance of current state-of-the-art techniques. Furthermore, the latent molecular embedding is invertible, enabling the design pipeline to automatically generate new monomers from the learned chemical subspace. We illustrate this functionality by targeting several properties, including high and low glass transition temperatures (Tg), and demonstrate that our model can identify new candidates with values that surpass those in the training set. The ease with which the proposed framework navigates both chemical diversity and data scarcity offers a promising route to accelerate and broaden the search for functional materials.

Han, Ming [Univ. of Chicago, IL (United States)]↗

DOE OSTI2026

Coarse-Grained Simulations of Polyrotaxane Hydrogels under Quiescent and Shear Conditions

Cyclodextrin-based polyrotaxanes (PR) form hydrogels in water through cyclodextrin (CD) aggregation and crystallization. These networks can break under shear flows, making them versatile platforms for extrusion-based 3D printing. To optimize the material properties of 3D-printed PR gels, a microscopic understanding of the structural evolution during 3D printing is necessary. Here, we employ coarse-grained (CG) simulations to reveal the PR assembly process at the molecular level. Our simulations reproduce the experimental crystal morphologies of PR at varying concentrations and chain lengths under quiescent conditions. Using nonequilibrium simulations, we show shear flow ruptures crystalline domain connectivity in PR gels and stacks the lamellae in the gradient direction, allowing the materials to flow during 3D printing. After the cessation of flow, the anisotropic crystal alignment and absence of available dangling PR diminish the intercrystal connectivity. The printed materials are therefore mechanically weaker than the pristine hydrogels, in agreement with experimental results. Nonetheless, by relating the microscopic structural evolution with viscoelastic properties of PR gels and solutions, we elucidate how flow conditions and sample composition affect the 3D printing performance of PR hydrogels.

Smith, Cameron D. [Dartmouth College, Hanover, NH ↗

DOE OSTI2025

Coarse-Grained Modeling Elucidates Differential Metabolism of Saccharomyces cerevisiae under Varied Nutrient Limitations

Microorganisms such as Saccharomyces cerevisiae have a native ability to adapt their metabolism to varying nutrient conditions. Understanding their responses to nutrient limitations is critical for decoding cellular physiology and designing strategies for metabolic engineering. While the influence of carbon availability on yeast metabolism has been extensively studied, the role of nitrogen availability remains relatively underexplored. In this study, we utilized a coarse-grained kinetic model to systematically analyze and compare the effects of carbon and nitrogen limitations on yeast metabolism. Our model successfully revealed the differential metabolic characteristics of S. cerevisiae under carbon- and nitrogen-limited chemostat conditions. It also highlighted the significance of protein activity regulation at varying carbon-to-nitrogen ratios, and elucidated distinct strategies employed to maintain ATP homeostasis. Furthermore, this study provides a computational tool for investigating yeast physiology under nutrient limitations and offers quantitative and mechanistic insights into yeast metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Microstructure, Transport, and Mechanics of Compacted Clay Simulated at the 0.1 μm Scale (1400 Smectite Clay Particles) Using a Coarse-Grained Model with Explicit Counterions

Clay-rich geomaterials play a critical role in many subsurface systems. The macroscale properties of these materials (low permeability, high ionic conductivity, high swelling pressure, etc.) are sensitive to molecular-level adsorption and hydration interactions at clay−water interfaces. Efforts to develop multiscale simulation approaches to predict these properties reveal a scale gap between atomistic simulations (typically limited to systems smaller than 10 nm) and continuum-scale models (which use computational grid elements with dimensions ≳ 10 μm). In this study, we present a coarse-grained (CG) framework that partly bridges this gap by simulating compacted smectite clay assemblages with dimensions of 0.1 μm containing 1,400 clay particles across a range of dry densities (1,050 to 1,850 kg·m −3 ) and Na/Ca counterion compositions (Na fraction ranging from 0.2 to 1). The simulated systems, along with their reconstructed binary three-dimensional pore networks, are used to evaluate the microstructure, pore size distribution, tortuosity, ion diffusivity, and swelling pressure of compacted smectite clay. Results show that our approach captures important features of the mesoscale heterogeneity of compacted clays, including tactoid formation, hierarchical porosity, and anisotropic pore networks. Results also reveal how compaction and counterion composition govern emergent behaviors, including dominant pore sizes, directional transport, and electrochemical response. This work highlights the potential of CG simulations to bridge molecular and continuum scales and to advance geotechnical and environmental applications involving clay-rich materials as well as related nanoporous media such as geopolymers and calcium-silicate-hydrate. However, the results also suggest that accurate prediction of certain microstructural and mechanical properties (e.g., swelling pressure) may require even larger-scale systems on the order of 1 μm.

02 PETROLEUM↗

DOE OSTI2024

A coarse-grained model of clay colloidal aggregation and consolidation with explicit representation of the electrical double layer

The aggregation of clay minerals in liquid water exemplifies colloidal self-assembly in nature. These negatively charged aluminosilicate platelets interact through multiple mechanisms with different sensitivities to particle shape, surface charge, aqueous chemistry, and interparticle distance and exhibit complex aggregation structures. Experiments have difficulty resolving the associated colloidal assemblages at the scale of individual particles. Conversely, all-atom molecular dynamics (MD) simulations provide detailed insight on clay colloidal interaction mechanisms, but they are limited to systems containing a few particles. We develop a new coarse-grained (CG) model capable of representing assemblages of hundreds of clay particles with accuracy approaching that of MD simulations, at a fraction of the computational cost. Our CG model is parameterized based on MD simulations of a pair of smectite clay particles in liquid water. A distinctive feature of our model is that it explicitly represents the electrical double layer (EDL), i.e., the cloud of charge-compensating cations that surrounds the clay particles. Our model captures the simultaneous importance of long-range colloidal interactions (i.e., interactions consistent with simplified analytical models, already included in extant clay CG models) and short-range interactions such as ion correlation and surface and ion hydration effects. The resulting simulations correctly predict, at low solid-water ratios, the existence of ordered arrangements of parallel particles separated by water films with a thickness up to ~10 nm and, at high solid-water ratios, the coexistence of crystalline and osmotic swelling states, in agreement with experimental observations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Development of a coarse-grained molecular dynamics model for poly(dimethyl- co -diphenyl)siloxane

Polydimethylsiloxane is an important polymeric material with a wide range of applications. However, environmental effects like low temperature can induce crystallization in this material with resulting changes in its structural and dynamic properties. The incorporation of phenyl-siloxane components, e.g., as in a poly(dimethyl-co-diphenyl)siloxane random copolymer, is known to suppress such crystallization. Molecular dynamics (MD) simulations can be a powerful tool to understand such effects in atomistic detail. Unfortunately, all-atomistic molecular dynamics (AAMD) is limited in both spatial dimensions and simulation times it can probe. Here, to overcome such constraints and to extend to more useful length- and time-scales, we systematically develop a coarse-grained molecular dynamics (CGMD) model for the poly(dimethyl-co-diphenyl)siloxane system with bonded and non-bonded interactions determined from all-atomistic simulations by the iterative Boltzmann inversion (IBI) method. Additionally, we propose a lever rule that can be useful to generate non-bonded potentials for such systems without reference to the all-atomistic ground truth. Our model captures the structural and dynamic properties of the copolymer material with quantitative accuracy and is useful to study long-time dynamics of highly-entangled systems, sequence-dependent properties, phase behaviour, etc.

36 MATERIALS SCIENCE↗

DOE OSTI2025