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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Molecular dynamics simulation of vacancy and void effects on strain-induced martensitic transformations in Fe-50 at.% Ni model concentrated solid solution alloy

Strain-induced martensitic transformations can improve the strength and ductility of some face centered cubic (FCC) metals and alloys. Irradiation-induced defects such as vacancies, dislocation loops, and voids activate martensitic transformations over a wider range of mechanical loading conditions than in pristine material. Furthermore, the mechanisms underlying irradiation-enabled martensite transformations remain unclear. In this work, we use molecular dynamics simulations to study the effect of vacancies and voids on strain-induced martensitic transformations in a model concentrated solid solution alloy Fe-50 at.% Ni. It has been found that single vacancies have no resolvable effect on the transformation because they reduce the stacking fault energy by a relatively insignificant margin and do so only if the vacancy is located on the stacking fault plane. Voids, however, activate the martensite transformation through shear strain accumulation around the void due to dislocation pileup. The larger the void, the more pronounced this effect.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Molecular dynamics simulations of energy accommodation between gases and polymers for ultra-low thermal conductivity insulation

Determining the energy accommodation between gases and solids is essential to developing porous thermal insulation materials with ultra-low effective thermal conductivity that reduce energy use, greenhouse gas emissions, and fossil fuel consumption. The energy accommodation coefficients of most gases, however, have been rarely studied, especially with respect to solids that have relatively high thermal resistivity, e.g., polymers. Here, by using all-atom nonequilibrium molecular dynamics simulations, we reveal the accommodation coefficients of He, Ar, N 2 , and O 2 with polymers, mainly polystyrene. We find that their values are around 0.51, 0.72, 0.79, and 0.90, respectively, suggesting a critical reexamination of the commonly used theoretical maximum value of 1. We have also conducted experiments and validated the value for air, which is about 0.81. Such a change in accommodation coefficients can lead to a reduction of about 70%, 50%, 35%, and 20% in the thermal conductivity of He, Ar, N 2 , and O 2 gases in nano pores (below 100 nm) or at low pressures (below 1 millibar). With these new accommodation coefficients, we find that in a 10 nm pore with ambient pressure at 300 K, the gas thermal conductivity of He, Ar, N 2 , and O 2 in porous polystyrene can be as low as 9.7 × 10 –4 , 3.4 × 10 –4 , 7.3 × 10 –4 , and 8.5 × 10 –4 W·m –1 ·K –1 , respectively, which are two to three orders of magnitude lower than their bulk values, promising higher thermal resistivity of insulation materials. This work reveals the fundamental energy exchange between gases and polymers, providing important guidance for designing high-performance thermal insulation materials for various applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Sticking Coefficients of Fusion Reactor Impurities from Molecular Dynamics Simulations for the Design of Cryopumps

A cryopump can be utilized as an impurity removal component of a direct internal recirculation (DIR) system for the fusion fuel cycle. The DIR facilitates a low fuel inventory by continuously pumping unburnt fuel while removing impurities from the fusion exhaust stream. A cryopump can target multiple impurity species by maintaining a temperature lower than the gas triple-point temperature that promotes desublimation. The desublimation/condensation of gases in cryopumps can be characterized by the sticking coefficient, which is defined as the probability for a gas particle to stick to a (cryo-)surface upon collision. The sticking coefficient is one of the important design/operation parameters for cryopumps, and it depends on a variety of surface and gas properties. Here, in this study, molecular dynamics simulations were utilized to estimate the sticking coefficients of typical fusion gas impurity species N 2 , CO 2 , and CH 4 over a Cu surface for a range of gas temperatures and surface coverages. The molecular dynamics study showed that the sticking coefficients for gases decrease with an increase in gas temperature. The presence of a single full monolayer of condensate on the metallic surface showed an adverse effect on the sticking of gases; however the sticking improved with two full monolayers of condensate on the surface. The sticking of gases over the mixed condensate on a surface was more favorable than the condensate of the same species for N 2 and CH 4 , with an exception for CO 2 , which showed a decrease in sticking over the mixed condensate.

cryopump↗
DOE OSTI2021

Advanced analysis of laser-driven pulsed magnetic diffusion based on quantum molecular dynamics simulation

Magnetic diffusion plays an important role in inertial confinement fusion with strong magnetic fields. In this paper, we improve a previous analysis of the generation and diffusion of the magnetic field [Morita et al., Phys. Plasmas 25, 094505 (2018)]. For the generation process, we calculate the temporal evolution of the coil current using a self-consistent circuit model. The results show that the peak of the calculated magnetic field is delayed by 1.2 ns compared with that of the incident laser pulse. For the diffusion process, we evaluate the electrical conductivity of warm dense gold over a wide temperature range (300 K–100 eV) by combining the Kubo–Greenwood formula based on a quantum molecular dynamics simulation with the modified Spitzer model. Our simulation shows that the maximum magnetic field (530 T) that penetrates the cone is delayed by 2.5 ns compared with the laser peak. This result is consistent with experiments [Sakata et al., Nat. Commun. 9, 3937 (2018)] that showed that applying a strong magnetic field improved the heating efficiency of fusion fuel.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2020

Statistically averaged molecular dynamics simulations of hydrogen diffusion in magnesium and magnesium hydrides

Magnesium has a different crystal structure from its dihydride with hydrogenation leading to a phase transition from the hexagonal closely packed Mg into a tetragonal α-MgH 2 rutile type structure. Such materials exhibit complex hydrogen uptake and release kinetics because hydrogen diffusivities significantly change when the crystal structure changes. To provide a foundational understanding of (de)hydrogenation kinetics that is applicable to all stages of the reaction, we performed statistically averaged molecular dynamics simulations to derive hydrogen diffusivities as a function of temperature and hydrogen content for both magnesium and magnesium hydride. Furthermore, our studies confirm that hydrogen diffusivities in magnesium hydride are much lower than in magnesium, in agreement with experimental data. Additionally, we observe that in either magnesium or magnesium hydride, higher hydrogen compositions result in reduced diffusivities. The latter was not revealed by prior experiments, which were conducted at fixed hydrogen composition. Finally, we discover a non-Arrhenius behavior in magnesium hydride. The physical origin of this behavior is also discussed.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Effect of Zwitterionic Additives on Solvation and Transport of Sodium and Potassium Cations in (Ethylene Oxide)10: A Molecular Dynamics Simulation Study

Sodium- (Na + ) and potassium- (K + ) ion batteries are cost-effective alternatives to lithium-ion (Li + ) batteries due to the abundant sodium and potassium resources. Solid polymer electrolytes (SPEs) are essential for safer and more efficient Na + and K + batteries because they often exhibit low ionic conductivity at room temperature. While zwitterionic (ZW) materials enhance Li+ battery conductivity, their potential for Na + and K + transport in batteries remains unexplored. In this study, we investigated the effect of three ZW molecules (ChoPO4, i.e., 2-methacryloyloxyethyl phosphorylcholine, ImSO3, i.e., sulfobetaine ethylimidazole, and ImCO2, i.e., carboxybetaine ethylimidazole) on the dissociation of Na + and K + coordination with ethylene oxide (EO) chains in EO-based electrolytes through molecular dynamics simulations. Our results showed that ChoPO4 possessed the highest cation–EO10 dissociation ability, while ImSO3 exhibited the lowest. Such dissociation ability correlated with the cation–ZW molecule coordination strength: ChoPO4 and ImSO3 showed the strongest and the weakest coordination with cations. However, the cation–ZW molecule coordination could slow the cationic diffusion. The competition of these effects resulted in accelerating or decelerating cationic diffusion. Our simulated results showed that ImCO2 enhanced Na + diffusion by 20%, while ChoPO4 and ImSO3 led to a 10% reduction. For K + , ChoPO4 reduced its diffusion by 40%, while ImCO2 and ImSO3 caused a similar decrease of 15%. These findings suggest that the ZW structure and the cationic size play an important role in the ionic dissociation effect of ZW materials.

25 ENERGY STORAGE↗
DOE OSTI2022

On the equivalence of nonequilibrium and equilibrium measurements of slip in molecular dynamics simulations

Here, we show that nonequilibrium and equilibrium measurements of slip are consistent, provided the hydrodynamic wall location associated with the equilibrium measurement is properly taken into account. The latter is a strong function of the fluid state and wall-fluid interaction and cannot be neglected as it typically has been. Our results are based on an alternative approach for calculating the hydrodynamic wall location which alleviates most of the difficulties associated with its calculation via a Green-Kubo integral that appear to have contributed to its neglect. Extensive molecular dynamics simulations are used to validate our approach including a model for calculating the slip length that does not involve a Green-Kubo integral.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Investigating the time dependence of neutron-proton equilibration using molecular dynamics simulations

Neutron-proton equilibration has previously been studied experimentally in dynamically deformed nuclei in heavy ion collisions [Phys. Rev. Lett. 118, 062501 (2017); Phys. Rev. C 95, 044604 (2017)] using the NIMROD detector array at the Cyclotron Institute at Texas A&M University. Results indicated the composition of the two heaviest fragments originating from the excited projectile-like fragment evolved exponential with respect to their orientation angle to be more similar. Constrained Molecular Dynamics and Antisymmetrized Molecular Dynamics simulations were performed for different formulations of the density dependence of the asymmetry energy term of the nuclear equation of state. The simulations are compared to experimental results, which indicate a better agreement with a softer interaction in the nuclear equation of state.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2021

Prediction of Bi 2 Te 3 -Sb 2 Te 3 Interfacial Conductance and Superlattice Thermal Conductivity Using Molecular Dynamics Simulations

Bismuth telluride (Bi 2 Te 3 ) and its alloys with antimony telluride (Sb 2 Te 3 ) have long been considered to be the best room-temperature bulk thermoelectric (TE) materials. In recent decades, proof-of-concept demonstrations on Bi 2 Te 3 -Sb 2 Te 3 nanostructures have shown high TE performance due to reduction in lattice thermal conductivities. Particularly, ultra-low thermal conductivities have been observed in Bi 2 Te 3 -Sb 2 Te 3 1D superlattices, leading to thermoelectric figures of merit (ZT) as high as 2.4. In contrast, very few computational studies have been performed to provide insight into the phonon transport across these nanostructures. In this work, we use non-equilibrium molecular dynamics simulations with previously developed force fields to simulate thermal transport across Bi 2 Te 3 -Sb 2 Te 3 interfaces and superlattices. We first calculate the thermal conductance associated with a Bi 2 Te 3 -Sb 2 Te 3 interface across a temperature range of 200–400 K. Furthermore, the values are also compared with thermal conductances calculated by a modified Landauer transport formalism using phonon transmission coefficients obtained from the diffuse mismatch model. Our results show that inelastic scattering processes contribute to an increase in interfacial thermal conductance at higher temperatures. Finally, we calculate the thermal conductivities of Bi 2 Te 3 -Sb 2 Te 3 superlattices with varying period lengths from 2 to 18 nm. A minimum thermal conductivity of 0.27 W/mK is observed at a period length of 4 nm, which is attributed to the competition between incoherent and coherent phonon transport regimes. In comparison with previous experimental measurements in the literature, our results show good agreement with respect to the range of thermal conductivity values and the period length corresponding to the minimum superlattice thermal conductivity.

42 ENGINEERING↗
DOE OSTI2023

Fluid-phase helium: Shock-compression experiments, quantum molecular dynamics simulations, and development of an equation of state

Helium (He) plays a critical role in numerous areas ranging from the study of celestial objects like brown dwarfs and gas giants to modern-day technologies like nuclear energy and rocket propulsion. For many of these applications, it is essential to have a reliable equation of state (EOS) for He that yields an accurate representation of its thermodynamic behavior. To help constrain and develop such EOS models, we have performed a series of shock-compression experiments on cryogenic liquid He to pressures exceeding 100 GPa using a magnetically accelerated flyer plate on Sandia National Laboratories' Z-machine. We have also performed quantum molecular dynamics simulations that are consistent with our shock measurements. None of the previously available EOSs agree with our experimental and simulation results, motivating the development of a fluid-phase He EOS that we present in this study. Here, we show that our EOS yields good agreement with published data that span temperatures and pressures encountered across a diverse array of applications.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Structural water in amorphous carbonate minerals: ab initio molecular dynamics simulations of X-ray pair distribution experiments

Water is known to play a controlling role in directing mineralization pathways and stabilizing metastable amorphous intermediates in hydrous carbonate mineral MCO 3 ·nH 2 O systems, where M 2+ is a divalent metal cation. Despite this recognition, the nature of the controls on crystallization is poorly understood, largely owing to the difficulty in characterizing the dynamically disordered structures of amorphous intermediates at the atomic scale. Here, we present a series of atomistic models, derived from ab initio molecular dynamics simulation, across a range of experimentally relevant cations (M = Ca, Mg, Sr) and hydration levels (0 ≤ n ≤ 2). Theoretical simulations of the dependence of the X-ray pair distribution function on the hydration level n show good agreement with available experimental data and thus provide further evidence for a lack of significant nanoscale structure in amorphous carbonates. Upon dehydration, the metal coordination number does not change significantly, but the relative extent of water dissociation increases, indicating that a thermodynamic driving force exists for water dissociation to accompany dehydration. Mg strongly favors monodentate conformation of carbonate ligands and shows a marked preference to exchange monodentate carbonate O for water O upon hydration, whereas Ca and Sr exchange mono- and bidentate carbonate ligands with comparable frequency. Finally, water forms an extensive hydrogen bond network among both water and carbonate groups that exhibits frequent proton transfers for all three cations considered suggesting that proton mobility is likely predominantly due to water dissociation and proton transfer reactions rather than molecular water diffusion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Microscale mechanical property variations of Al-substituted LLZO: insights from compression testing and molecular dynamics simulations

Ceramic solid electrolytes based on LLZO (Li 7 La 3 Zr 2 O 12 ) are promising candidates for all-solid-state batteries due to their high ionic conductivity and good apparent stability vs. lithium metal, however they are prone to mechanical failure. Lithium metal intrusions, alongside cell stack pressure, transition polycrystalline solid electrolyte grains into a compressed state that promotes crack propagation and fracture. Here this work examines the mechanical response of Al-substituted LLZO to compressive forces by measuring ultimate strength under pillar compression with a flat punch tip. Failure modes characterized by in situ scanning electron microscopy show diverse splitting patterns arising from internal porosity, grain boundaries, and slip planes. Large correlated variations in compressive strength (0.93–2.63 GPa) and Young's modulus (72.1–150.97 GPa) are observed across microscale regions of the solid electrolyte. Molecular dynamics simulations of LLZO with different porosities describe the variation of compressive strength and Young's modulus, and enable a microscale porosity model to be fit accounting for Young's modulus reduction across the solid electrolyte. Overall, the results indicate the importance of microscale mechanical testing of ceramic solid electrolytes to identify preferential sites for mechanical degradation and Li intrusion, and ensure the robust design of all-solid-state lithium metal batteries.

25 ENERGY STORAGE↗
DOE OSTI2025

Understanding Viscoelasticity of an Entangled Silicone Copolymer via Coarse-Grained Molecular Dynamics Simulations

Entangled dynamics is important for understanding rheological properties of long-chain polymers. For entangled homopolymers, the classic tube-reptation model and its refinements have been successfully applied to quantify properties like diffusion coefficient and zero-rate viscosity. However, the application of such models to copolymers has been limited despite scientific and industrial importance. Here, we study the entangled melt dynamics of poly(dimethyl-co-diphenyl)siloxane random copolymer for a range of mean-composition-ratio ϕ of the diphenyl component via long-term molecular dynamics simulation with a recently developed coarse-grained model. We found that the segmental relaxation is heterogeneous at the monomeric level because of compositional fluctuations. However, at the chain-entanglement level and higher length scales, the viscoelastic response is homogeneous with compositional dependence only through the overall diphenyl fraction ϕ. The relaxation modulus of the entangled copolymer melt conforms to the Likhtman–McLeish model, and the viscosity predicted using our current coarse-grained parameters is in good quantitative agreement with experimental data.

Copolymers↗
DOE OSTI2022

Polariton relaxation under vibrational strong coupling: Comparing cavity molecular dynamics simulations against Fermi’s golden rule rate

Under vibrational strong coupling (VSC), the formation of molecular polaritons may significantly modify the photo-induced or thermal properties of molecules. In an effort to understand these intriguing modifications, both experimental and theoretical studies have focused on the ultrafast dynamics of vibrational polaritons. Here, following our recent work [Li et al., J. Chem. Phys. 154, 094124 (2021)], we systematically study the mechanism of polariton relaxation for liquid CO 2 under a weak external pumping. Classical cavity molecular dynamics (CavMD) simulations confirm that polariton relaxation results from the combined effects of (i) cavity loss through the photonic component and (ii) dephasing of the bright-mode component to vibrational dark modes as mediated by intermolecular interactions. The latter polaritonic dephasing rate is proportional to the product of the weight of the bright mode in the polariton wave function and the spectral overlap between the polariton and dark modes. Both these factors are sensitive to parameters such as the Rabi splitting and cavity mode detuning. Compared to a Fermi’s golden rule calculation based on a tight-binding harmonic model, CavMD yields a similar parameter dependence for the upper polariton relaxation lifetime but sometimes a modest disagreement for the lower polariton. We suggest that this disagreement results from polariton-enhanced molecular nonlinear absorption due to molecular anharmonicity, which is not included in our analytical model. Finally, we also summarize recent progress on probing nonreactive VSC dynamics with CavMD.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Primary defect production from molecular dynamics simulations of high-energy displacement cascades in NbMoTaW alloys

In this work, we report on large-scale molecular-dynamics (MD) simulations of displacement cascades in equiatomic NbMoTaW alloys at PKA energies ranging from 0.15 to 150 keV. We find defect production to be strongly dependent on recoil energy, scaling sublinearly up to 10 keV, and linearly thereafter. We find the sublinear regime to be defined by low values of surviving Frenkel pairs, typically found as isolated point defects or small defect clusters, while at higher recoil energies dense cascades become more frequent, leading to splitting into subcascades and the production of relatively large prismatic-dislocation loops with ⟨111⟩ and ⟨001⟩ Burgers vectors. These loops immobilize large fractions of defects, leading to a rapid growth of the number of surviving defects in the linear regime. We also anneal post-cascade defect configurations using object-kinetic Monte Carlo (OKMC) simulations to account for intracascade recombination on time scales not accessible to MD simulations. Cascade annealing is strongly temperature dependent, with the OKMC simulations only showing significant recovery at 1000 K but not below. Our results are in general agreement with existing published data for refractory concentrated alloys.

Zhou, Xinran [Lawrence Berkeley National Laborator↗
DOE OSTI2020

Molecular Dynamics Simulation of Atomic Interactions in the Vancomycin Binding Site

Vancomycin is a glycopeptide antibiotic produced by Amycolaptopsis orientalis used to treat serious infections by Grampositive pathogens including methicillin-resistant Staphylococcus aureus. Vancomycin inhibits cell wall biosynthesis by targeting lipid II, which is the membrane-bound peptidoglycan precursor. The heptapeptide aglycon structure of vancomycin binds to the D-Ala-D-Ala of the pentapeptide stem structure in lipid II. The third residue of vancomycin aglycon is asparagine, which is not directly involved in the dipeptide binding. Nonetheless, asparagine plays a crucial role in substrate recognition, as the vancomycin analogue with asparagine substituted by aspartic acid (V D ) shows a reduction in antibacterial activities. To characterize the function of asparagine, binding of vancomycin and its aspartic-acid-substituted analogue V D to L-Lys-D-Ala-D-Ala and L-Lys-D-Ala-D-Lac was investigated using molecular dynamic simulations. Binding interactions were analyzed using root-mean-square deviation (RMSD), two-dimensional (2D) contour plots, hydrogen bond analysis, and free energy calculations of the complexes. The analysis shows that the aspartate substitution introduced a negative charge to the binding cleft of V D , which altered the aglycon conformation that minimized the repulsive lone pair interaction in the binding of a depsipeptide. Our findings provide new insight for the development of novel glycopeptide antibiotics against the emerging vancomycin-resistant pathogens by chemical modification at the third residue in vancomycin to improve its binding affinity to the D-Ala-D-Lac-terminated peptidoglycan in lipid II found in vancomycin-resistant enterococci and vancomycinresistant S. aureus.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations

Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Development of a machine-learning-based ionic-force correction model for quantum molecular dynamic simulations of warm dense matter

In this work Δ learning is used to map orbital-free density functional theory (OF-DFT) ionic forces to the corresponding Kohn-Sham (KS) DFT ionic forces. The development of the approximate force difference in terms of the ion positions is constructed and serves as a stand in for the ground truth force difference. Descriptor vectors for ion configurations are constructed using all distance between ions in conjunction with an indexing based on a nearest neighbor ranking. It is demonstrated that such a scheme of descriptors can uniquely describe an ionic configuration up to a rotation and reflection when no ambiguity in the nearest neighbor ranking exists. How to handle the case when an ambiguity exists in the nearest neighbor ranking is discussed. As a proof of principle, the model is trained and tested on warm dense hydrogen at temperatures between 1 and 15 eV. Once tested, the model was used to perform molecular dynamic simulations of warm dense hydrogen. Furthermore, the resulting energies and pressures are within 1% and 2% of their respective target KS values.

36 MATERIALS SCIENCE↗