A molecular dynamics study on the Mie-Grüneisen equation-of-state and high strain-rate behavior of equiatomic CoCrFeMnNi
Not Available
36 MATERIALS SCIENCE↗
SEARCH · Engineering Papers
Results for “Atomistic 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.
Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.
Data efficiency and extrapolation trends in neural network interatomic potentials
Abstract Recently, key architectural advances have been proposed for neural network interatomic potentials (NNIPs), such as incorporating message-passing networks, equivariance, or many-body expansion terms. Although modern NNIP models exhibit small differences in test accuracy, this metric is still considered the main target when developing new NNIP architectures. In this work, we show how architectural and optimization choices influence the generalization of NNIPs, revealing trends in molecular dynamics (MD) stability, data efficiency, and loss landscapes. Using the 3BPA dataset, we uncover trends in NNIP errors and robustness to noise, showing these metrics are insufficient to predict MD stability in the high-accuracy regime. With a large-scale study on NequIP, MACE, and their optimizers, we show that our metric of loss entropy predicts out-of-distribution error and data efficiency despite being computed only on the training set. This work provides a deep learning justification for probing extrapolation and can inform the development of next-generation NNIPs.
36 MATERIALS SCIENCE↗
Topological energy barrier for skyrmion lattice formation in MnSi
We report the direct measurement of the topological skyrmion energy barrier through a hysteresis of the skyrmion lattice in the chiral magnet MnSi. Measurements were made using small-angle neutron scattering with a custom-built resistive coil to allow for high-precision minor hysteresis loops. The experimental data were analyzed using an adapted Preisach model to quantify the energy barrier for skyrmion formation and corroborated by the minimum-energy path analysis based on atomistic spin simulations. Here, we reveal that the skyrmion lattice in MnSi forms from the conical phase progressively in small domains, each of which consisting of hundreds of skyrmions, and with an activation barrier of several eV.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Triple junction solute segregation in Al-based polycrystals
Solute segregation is a crucial means of stabilizing nanostructured alloys, and at very small grain sizes, this requires consideration of triple junctions (TJs), which attain a meaningful volume fraction and thus become relevant for bulk material behavior. Here, in this study, the solute segregation spectra for grain boundary (GB) and TJ sites are calculated for a large number of dilute Al-based binary systems with available interatomic potentials. A defect-identifying algorithm is applied to quantify the average GB thickness and classify the intergranular site spectra into GB and junction subspectra. The algorithm is also applied to a hybrid electronic-level database for GB segregation of various solutes in Al, yielding polycrystalline TJ solute segregation spectra from first principles. The results suggest that TJ segregation is alloy or interatomic potential dependent and can exhibit either boundary or junction preference. With these spectra as inputs, the spectral GB segregation model gives quantitative predictions of segregation as a function of grain size, temperature, and total solute concentration, suitable for alloy screening and design.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
OpenFerro v0.1.0
OpenFerro is a Python package for on-lattice atomistic dynamics simulation of ferroic materials. OpenFerro is based on JAX, a high-performance linear algebra package supporting auto-differentiation and GPU acceleration. OpenFerro is designed to minimize the effort required to build on-lattice Hamiltonian models, and to perform molecular dynamics (MD) and Landau-Lifshitz-Gilbert simulations. Unlike existing codes, OpenFerro provides a unified interface to model different types of local order parameters.
Xie, Pinchen [Lawrence Berkeley National Laborator↗
Thermodynamics of grain-boundary phases
The past decade has seen a significant increase in research efforts aimed at understanding the thermodynamics of low-dimensional phases existing in many materials systems, ranging from two-dimensional materials to core regions of extended defects in crystalline solids. We review the current status of theoretical, computational, and experimental research on the “defect phases,” focusing on grain boundaries (GBs) in elemental and multicomponent polycrystalline materials. After reviewing the generalized concept of a phase of any dimensionality, we discuss recent progress in atomistic computer simulations of GB phase transformations and phase coexistences, including the observation of one-dimensional defects separating GB phases (defects in defects). Computational predictions compare well with experimental observations of multiple GB phases and segregation-induced phase transformations. An intriguing open question of GB thermodynamics is whether the GB free energy can be driven to a zero value by increasing solute segregation. We review recent efforts to understand this ultimate thermodynamic stabilization of GB phases and the possible polycrystalline microstructures that may arise. An outlook for future research in the field is discussed.
Materials science↗
Multi-Scale Modeling Framework for Mercury Biogeochemistry
Multi-Scale modeling of mercury (Hg) geochemical speciation and reactions has been performed by integrating atomistic quantum chemical calculations with continuum scale speciation models. Major progress has been made in the improvement of quantum chemical models to calculate critical thermodynamic data for Hg complexes in aquatic environments. Rapid and reliable quantum chemical approaches have been developed for calculating acid dissociation constants (pK a ) and stability constants (log K), with calculated mean unsigned errors of 0.5 and 1.5 log units, respectively for ligand molecules and Hg complexes. At the continuum scale, systematic analysis of uncertainty propagation in mercury (Hg) speciation modeling has been conducted and was used to identify environmental conditions under which thermodynamic constant uncertainties are significant and recommended to be accounted for. The integrated framework for multi-scale modeling of mercury geochemistry is open to the research community through the web-based multiscale modeling aqueous speciation resource, AQUA-MER. The improved quantum chemical approaches for thermodynamic constant calculations are accessible through AQUA-MER and can be used to provide the missing constants in the continuum scale speciation calculations. In addition to low molecular mass Hg complex speciation, modeling natural aquatic environments also involve the transport of high molecular weight dissolved organic matter (DOM) in reactive flows simultaneously with equilibrium and kinetic reactions. To this end, atomistic MD simulations were performed to capture the details of aggregation, mechanisms and distribution of functional groups in DOM at the molecular level. The elemental composition and calculated bulk properties of the DOM models are in close agreement with experimental measurements. A travel-time based reactive transport model in the hyporheic zone of stream corridors was established for the multicomponent Hg-DOM-S system and implemented through PFLOTRAN.
54 ENVIRONMENTAL SCIENCES↗
Interfacial Atomistic Mechanisms of Lithium Metal Stripping and Plating in Solid–State Batteries
All-solid-state batteries based on a Li metal anode represent a promising next-generation energy storage system, but are currently limited by low current density and short cycle life. Further research to improve the Li metal anode is impeded by the lack of understanding in its failure mechanisms at lithium–solid interfaces, in particular, the fundamental atomistic processes responsible for interface failure. Here, using large-scale molecular dynamics simulations, the first atomistic modeling study of lithium stripping and plating on a solid electrolyte is performed by explicitly considering key fundamental atomistic processes and interface atomistic structures. In the simulations, the interface failure initiated with the formation of nano-sized pores, and how interface structures, lithium diffusion, adhesion energy, and applied pressure affect interface failure during Li cycling are observed. By systematically varying the parameters of solid-state lithium cells in the simulations, the parameter space of applied pressures and interfacial adhesion energies that inhibit interface failure during cycling are mapped to guide selection of solid-state cells. Furthermore, this study establishes the atomistic modeling for Li stripping and plating, and predicts optimal solid interfaces and new strategies for the future research and development of solid-state Li-metal batteries.
25 ENERGY STORAGE↗
Comparison of water nanodroplet properties on different graphite-based substrates
The molecular structure and dynamics of water differ considerably at various interfaces. We compare the interfacial water structure–property relationship on three different carbon substrates, namely, amorphous carbon, compressed expanded natural graphite, and pure graphite by utilizing atomistic molecular dynamics simulations. The effect of different substrates on the structural and dynamical properties of water can readily be observed. Here, the density distributions parallel and normal to the substrates show oblate droplet structures. The normal to the substrate water distribution shows a strong hydration layer at the interface that does not vary with substrates. However, the disparity in the structure and dynamics on three different substrates shows that the surface morphologies of the substrates are critical for determining nanoscale water properties. Furthermore, it is observed that the formation of an interfacial water layer or the hydration layer is a direct consequence of both water “confinement” at the nanoscale and “attraction” between water molecules and the carbon substrates.
42 ENGINEERING↗
Porous Covalent Organic Polymers for Efficient Fluorocarbon‐Based Adsorption Cooling
Abstract Adsorption‐based cooling is an energy‐efficient renewable‐energy technology that can be driven using low‐grade industrial waste heat and/or solar heat. Here, we report the first exploration of fluorocarbon adsorption using porous covalent organic polymers (COPs) for this cooling application. High fluorocarbon R134a equilibrium capacities and unique overall linear‐shaped isotherms are revealed for the materials, namely COP‐2 and COP‐3. The key role of mesoporous defects on this unusual adsorption behavior was demonstrated by molecular simulations based on atomistic defect‐containing models built for both porous COPs. Analysis of simulated R134a adsorption isotherms for various defect‐containing atomistic models of the COPs shows a direct correlation between higher fluorocarbon adsorption capacities and increasing pore volumes induced by defects. Combined with their high porosities, excellent reversibility, fast kinetics, and large operating window, these defect‐containing porous COPs are promising for adsorption‐based cooling applications.
Zheng, Jian↗
Porous Covalent Organic Polymers for efficient Fluorocarbon-based Adsorption Cooling
Adsorption-based cooling is an energy-efficient renewable-energy technology that can be driven using low-grade industrial waste heat and/or solar heat. Here, we report the first exploration of fluorocarbon adsorption using porous covalent organic polymers (COPs) for this cooling application. High fluorocarbon R134a equilibrium capacities and unique overall linear-shaped isotherms are revealed for the materials, namely COP-2 and COP-3. The key role of mesoporous defects on this unusual adsorption behavior was demonstrated by molecular simulations based on atomistic defect-containing models built for both porous COPs. Analysis of simulated R134a adsorption isotherms for various defect-containing atomistic models of the COPs shows a direct correlation between higher fluorocarbon adsorption capacities and increasing pore volumes induced by defects. Combined with their high porosities, excellent reversibility, fast kinetics, and large operating window, these defect-containing porous COPs are promising for adsorption-based cooling applications.
32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
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↗
Dataset_for_Conserved_macromolecular_architecture_of_Poplar_secondary_cell_walls_revealed_by_ssNMR_and_atomistic_modeling
This dataset contains solid-state 13C NMR data and atomistic molecular dynamics simulation files supporting the study of nanoscale secondary cell wall architecture across 13 genetically diverse Populus trichocarpa genotypes grown under uniform greenhouse conditions in 13C-enriched CO2 atmospheres (~89% 13C enrichment).The dataset contains two collections of solid-state 13C NMR data. (1) 200 MHz data (Bruker Avance III HD, 4 mm HX probe, 10 kHz MAS): raw Bruker TopSpin experiment folders and DMFIT-exported ascii spectra for selective and non-selective 1D 13C-13C spin diffusion experiments (3000 ms mixing) used to quantify inter-polymer spatial proximities, and short-mixing (1 ms) reference spectra used for polymeric abundance quantification by spectral deconvolution. (2) 600 MHz data (Bruker Avance III, 1.6 mm PhoenixNMR HXY probe, 30 kHz MAS): raw Bruker TopSpin experiment folders containing 2D CORD, 2D CP-INADEQUATE, and 13C/1H relaxation (T1, T1rho) experiments for all 13 genotypes, with processed Excel workbooks per experiment type. Molecular dynamics simulation code, coordinate files, and analysis scripts (NAMD/CHARMM/Python) for six atomistic cell wall models are included. Summarized ssNMR data are compiled into a single excel file and subjected to statistical analysis. Multivariate analysis code (PCA, Pearson correlation) and summary data are provided as excel worksheets and Jupyter notebooks (Python 3).
09 BIOMASS FUELS↗
Large-scale atomistic model construction of subbituminous and bituminous coals for solvent extraction simulations with reactive molecular dynamics
Large-scale atomistic models for complex polycyclic aromatic hydrocarbon systems help understand the chemical properties and behaviors of complex feedstocks such as coal or petroleum. However, the development and utilization of large-scale models remain limited due to the difficulty in achieving the varied structural characteristics necessary to capture stochastic nature of these feedstocks. Here we demonstrate a systematic workflow to construct stochastic molecular systems from a broad analytical suite: high-resolution transmission electron microscopy (HRTEM), carbon-13 nuclear magnetic resonance spectroscopy ( 13 C NMR), laser desorption ionization mass spectroscopy (LDI-MS), and elemental analysis. We present a model construction and analysis utility of a new Python-based module. We selected one subbituminous and three high-volatile bituminous coals to construct large-scale models (~40,000 atoms). The constructed models were utilized to examine the affinity for solvent extraction (naphthalene or tetralin) and the effect of structural properties (e.g., aromatic cluster size, functional groups, and cross-linking) in reactive molecular dynamics simulations. Complex chemical reactions were monitored with bond order transitions, intermediates formation, and mass distributions. Reactive molecular dynamics simulations suggest a plausible chemical extraction process and products for the complex fossil feedstocks. The results indicated that radical formations with bond breaking of bridging oxygens and carbons were required at high temperatures to facilitate hydrogeneration and extraction of gas molecules from radical-free molecules. We observed that aliphatic chains of tetralin were easily decomposed and combined with radicals to form small size of molecules with aryl bonding, mainly increasing molecules in the 500–1000 Da, while naphthalene had little impact on chemical extraction process.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Accuracy, transferability, and computational efficiency of interatomic potentials for simulations of carbon under extreme conditions
Large-scale atomistic molecular dynamics (MD) simulations provide an exceptional opportunity to advance the fundamental understanding of carbon under extreme conditions of high pressures and temperatures. However, the fidelity of these simulations depends heavily on the accuracy of classical interatomic potentials governing the dynamics of many-atom systems. Here, this study critically assesses several popular empirical potentials for carbon, as well as machine learning interatomic potentials (MLIPs), in their ability to simulate a range of physical properties at high pressures and temperatures, including the diamond equation of state, its melting line, shock Hugoniot, uniaxial compressions, and the structure of liquid carbon. Empirical potentials fail to accurately predict the behavior of carbon under high pressure–temperature conditions. In contrast, MLIPs demonstrate quantum accuracy, with Spectral Neighbor Analysis Potential (SNAP) and atomic cluster expansion (ACE) being the most accurate in reproducing the density functional theory results. ACE displays remarkable transferability despite not being specifically trained for extreme conditions. Furthermore, ACE and SNAP exhibit superior computational performance on graphics processing unit-based systems in billion atom MD simulations, with SNAP emerging as the fastest. In addition to offering practical guidance in selecting an interatomic potential with a fine balance of accuracy, transferability, and computational efficiency, this work also highlights transformative opportunities for groundbreaking scientific discoveries facilitated by quantum-accurate MD simulations with MLIPs on emerging exascale supercomputers.
36 MATERIALS SCIENCE↗
Effects of Al:Si and (Al+Na):Si Ratios on the Properties of the International Simple Glass, Part II: Structure
High-alumina containing high-level waste (HLW) will be vitrified at the Waste Treatment Plant at the Hanford Site. The resulting glasses, high in alumina, will have distinct composition-structure-property (C-S-P) relationships compared to previously studied HLW glasses. These C-S-P relationships determine the processability and product durability of glasses and therefore must be understood. The main purpose of this study is to understand the detailed structural changes caused by Al:Si and (Al+Na):Si substitutions in a simplified nuclear waste model glass (ISG, International Simple Glass) by combining experimental structural characterizations and molecular dynamics (MD) simulations. The structures of these two series of glasses were characterized by neutron total scattering and 27Al, 23Na, 29Si, and 11B solid-state nuclear magnetic resonance (NMR) spectroscopy. Additionally, MD simulations were used to generate atomistic structural models of the borosilicate glasses and simulation results were validated by the experimental structural data. Short-range (e.g., bond distance, coordination number, etc.) and medium-range (e.g., oxygen speciation, network connectivity, polyhedral linkages) structural features of the borosilicate glasses were systematically investigated as a function of the degree of substitution. The results show that bond distance and coordination number of the cation-oxygen pairs are relatively insensitive to Al:Si and (Al+Na):Si substitutions with the exception of the B-O pair. Additionally, the Al:Si substitution results in an increase of tri-bridging oxygen species, while (Al+Na):Si substitution creates non-bridging oxygen species. Charge compensator preferences were found for Si-[NBO] (Na+), [3]B-[NBO] (Na+), [4]B (mostly Ca2+), [4]Al (nearly equally split Na+ and Ca2+), and [6]Zr (mostly Ca2+). The network former-BO-network former linkages preferences were also tabulated; Si-O-Al and Al-O-Al were preferred at the expense of lower Si-O-[3]B and [3]B-O-[3]B linkages. These results provide insights on the structural origins of property changes such as glass transition temperature caused by the substitutions, providing a basis for future improvements of theoretical and computer simulation models.
Lu, Xiaonan↗
Predicting Small Molecule Transfer Free Energies by Combining Molecular Dynamics Simulations and Deep Learning
Accurately predicting small molecule partitioning and hydrophobicity is critical in the drug discovery process. There are many heterogeneous chemical environments within a cell and entire human body. For example, drugs must be able to cross the hydrophobic cellular membrane to reach their intracellular targets, and hydrophobicity is an important driving force for drug–protein binding. Atomistic molecular dynamics (MD) simulations are routinely used to calculate free energies of small molecules binding to proteins, crossing lipid membranes, and solvation but are computationally expensive. Machine learning (ML) and empirical methods are also used throughout drug discovery but rely on experimental data, limiting the domain of applicability. We present atomistic MD simulations calculating 15,000 small molecule free energies of transfer from water to cyclohexane. This large data set is used to train ML models that predict the free energies of transfer. We show that a spatial graph neural network model achieves the highest accuracy, followed closely by a 3D-convolutional neural network, and shallow learning based on the chemical fingerprint is significantly less accurate. A mean absolute error of ~4 kJ/mol compared to the MD calculations was achieved for our best ML model. We also show that including data from the MD simulation improves the predictions, tests the transferability of each model to a diverse set of molecules, and show multitask learning improves the predictions. This work provides insight into the hydrophobicity of small molecules and ML cheminformatics modeling, and our data set will be useful for designing and testing future ML cheminformatics methods.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Effect of a micro-scale dislocation pileup on the atomic-scale multi-variant phase transformation and twinning
In this paper, we perform concurrent atomistic–continuum (CAC) simulations to assess the contribution of the internal stress induced by the microscale dislocation pileup at an atomically structured interface to the atomic-scale phase transformations (PTs), reverse PTs, and twinning. The main novelty of this work is to unify the atomistic description of the interface and the coarse-grained (CG) description of the lagging dislocations away from the interface within one single framework. Our major findings are: (a) the interface dynamically responds to a pileup by forming steps/ledges, the height of which is proportional to the number of dislocations arriving at the interface; (b) the pileup-induced internal stress concentration profile follows neither the classical Eshelby model nor the super-dislocation model alone, but a combination of them; (c) when the pre-sheared sample is compressed, a direct square-to-hexagonal PT occurs ahead of the pileup tip and eventually grows into a wedge shape. The two variants of the hexagonal phases form a twin with respect to each other; (d) upon a further increase of the loading, part of the newly formed hexagonal phase transforms back to the square phase. The square product phase resulting from this reverse PT forms a twin with respect to the initial square phase. All phase boundaries (PBs) and twin boundaries (TBs) are stationary and correspond to zero thermodynamic Eshelby driving forces; and (e) the microscale dislocation pileup-induced internal shear stress and the structural change at the atomic-scale interface reduces the stress required for initiating a PT by a factor of 5.5, comparing with that in the sample containing no dislocations. This work is the first characterization of the behavior of PTs/twinning resulting from the reaction between a microscale dislocation slip and an atomically structured interface. In conclusion, the gained knowledge will advance our understanding of how the multi-phase material behaves in many complex physical processes, such as the synthesis of multi-phase high-entropy alloys or superhard ceramics under high-pressure torsion, deep mantle earthquakes in geophysics, and so on, which all involve dislocation slip, PTs, twinning, and their interactions across from the atomistic to the microscale and beyond.
36 MATERIALS SCIENCE↗