Modeling Graphene Growth in a Carbon Liquid and the Dynamical Matrix for Phonon Transport Using Molecular Dynamics
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Vattikuti, Venkata Hasith↗
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Results for “Molecular dynamics”
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Molecular dynamics simulation of zirconium tungstate amorphization and the amorphous-crystalline interface
Classical molecular dynamics (MD) simulations were performed to provide a conceptual understanding of the amorphous-crystalline interface for a candidate negative thermal expansion (NTE) material, ZrW 2 O 8 . Simulations of pressure-induced amorphization at 300 K indicate that an amorphous phase forms at pressures of 10 GPa and greater, and this phase persists when the pressure is subsequently decreased to 1 bar. However, the crystalline phase is recovered when the slightly distorted 5 GPa phase is relaxed to 1 bar. Simulations were also performed on a two-phase model consisting of the high-pressure amorphous phase in direct contact with the crystalline phase. Upon equilibration at 300 K and 1 bar, the crystalline phase remains unchanged beyond a thin layer of disrupted structure at the crystalline-amorphous interface. In conclusion, the differences in local atomic structure at the interface are quantified from the simulation trajectories.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Investigation of the thermal conductivity of molten LiF-NaF-KF with experiments, theory, and equilibrium molecular dynamics
Molten salts are being proposed for numerous advanced energy applications, including advanced nuclear reactors, concentrating solar power plants, thermal energy storage, and fusion reactors. Accurate knowledge of the thermophysical properties of molten salts directly impact the performance of these energy systems and are essential for design and safety analyses. Thermal conductivity data for fluoride molten salts and mixtures are especially lacking. In this work, experimental measurements of thermal conductivity using the steady-state variable gap technique were performed on eutectic LiF-NaF-KF from 834 to 1195 K. The experiment accounts for radiative, convective, and conductive heat losses. In addition, theoretical and molecular dynamics models are used, from 750 K up to 1300 K, to estimate the thermal conductivity for comparison with the experimental results. The results of experiments show a weak negative deviation of thermal conductivity with temperature, unlike previous experimental results in the literature. The measured thermal conductivity magnitudes agree with the theoretical and molecular dynamics predictions, aside from the data above 1100 K, where heat losses and radiative errors are the most significant, having a 16% maximum deviation from theory. These experimental results provide new thermal conductivity data for the LiF-NaF-KF system and further validation of the predictive models. The theoretical model was used to map the composition and temperature dependent thermal conductivity of LiF-NaF-KF and the mapping’s deviation from a linear additivity estimation of thermal conductivity. Additionally, this mapping showed the highest deviations from linearity for KF-LiF rich mixtures and increasing deviation with temperature. Notably, the deviation from linearity near the LiF-NaF-KF eutectic composition was around 25%.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Nanomechanics of Carbon and CxByNz Nanotubes: Via a Quantum Molecular Dynamics Method
Nanomechanics of single-wall C, BN and BC$_3$ and B doped C nanotubes under axial compression and tension are investigated through a generalized tight-binding molecular dynamics (GTBMD) and {\it ab-initio} electronic structure methods. The dynamic strength of BN, BC$_3$ and B doped C nanotubes for small axial strain are comparable to each other. The main difference is in the critical strain at which structural collapse occurs. For example, even a shallow doping with B lowers the value of critical strain for C nanotubes. The critical strain for BN nanotube is found to be more than that for the similar C nanotube. Once the structural collapse starts to occur we find that carbon nanotubes irreversibly go into plastic deformation regime via the formation of tetrahedral (four-fold coordinated) bonds at the location of sharp pinches or kinks. This finding is considerably different from the classical MD (molecular dynamics) simulation results known so far. The energetics and electronic densities of states of the collapsed structures, investigated with {\it ab-initio) methods, will also be discussed.
Srivastava, Deepak↗
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↗
Molecular Dynamics Simulations of a Liquid Metal Wetting Zirconia Suboxides
Molecular dynamics simulations were performed of a liquid metal (Ag) interacting with various zirconia suboxides to calculate the work of adhesion between the liquid metal and the suboxides. These simulations were then used to assess the impact of oxygen content on wetting. The results of this work show a wetting transition as oxygen content is reduced.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Molecular Dynamics Study of Creep Deformation in Nickel-based Superalloy
The present study employs molecular dynamics simulations of Ni-based superalloy to investigate the creep behavior under uniaxial compression test. Dislocation dynamics is analyzed for the nickel-based single crystal superalloy with the presence of void and with varying the distribution of gamma-prime phase The results show that multiple-void systems are more prone to yield than single-void systems and single-void systems are more prone to yield than the system withoutvoid. From the simulations, it has been determined that the creep mechanism in Ni/Ni3Al is subject to change on the applied stress depending on the distribution of gamma-prime phases change. Dislocation behavior is also observed in addition to the time evolution of dislocation nucleation and growth to quantify the propensity and mechanism of creep in nickel-based single crystal superalloy. The studies confirmed that dislocation length prior to plastic deformation decreased as the number of voids increased. In addition, the deformation behavior for finegrained nickel-based polycrystalline superalloy upon grain size variation is also investigated. Our findings show that both the movement mechanisms of the grains and grain boundaries and the relationship between grain size and yield strength are highly affected by the grain size of the materials. All the databases have then been classified to accurately predict the target class vi machine learning using the data mining tool WEKA.
creep, nickel-based superalloy, molecular dynamics↗
Exploring non-adiabaticity to CO reduction reaction through ab initio molecular dynamics simulation
Non-adiabatic chemical reaction refers to the electronic excitation during reactions. This effect cannot be modeled by the ground-state Born-Oppenheimer molecular dynamics (BO-MD), where the electronic structure is at the ground state for every step of ions' movement. Although the non-adiabatic effect has been explored extensively in gas phase reactions, its role in electrochemical reactions, such as water splitting and CO 2 reduction, in electrolyte has been rarely explored. On the other hand, electrochemical reactions usually involve electron transport; thus, a non-adiabatic process can naturally play a significant role. In this work, using one-step CO 2 reduction as an example, we investigated the role of the non-adiabatic effect in the reaction. The reaction barriers were computed by adiabatic BO-MD and non-adiabatic real-time time dependent density functional theory (rt-TDDFT). We found that by including the non-adiabatic effect, rt-TDDFT could increase the reaction barrier up to 6% compared to the BO-MD calculated barrier when the solvent model is used to represent water. Simulations were carried out using explicit water molecules around the reaction site under different overpotentials, and similar non-adiabatic effects were found.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Stress Distribution During Deformation of Polycrystalline Aluminum by Molecular-Dynamics and Finite-Element Modeling
In this paper, a multiscale modelling strategy is used to study the effect of grain-boundary sliding on stress localization in a polycrystalline microstructure with an uneven distribution of grain size. The development of the molecular dynamics (MD) analysis used to interrogate idealized grain microstructures with various types of grain boundaries and the multiscale modelling strategies for modelling large systems of grains is discussed. Both molecular-dynamics and finite-element (FE) simulations for idealized polycrystalline models of identical geometry are presented with the purpose of demonstrating the effectiveness of the adapted finite-element method using cohesive zone models to reproduce grain-boundary sliding and its effect on the stress distribution in a polycrystalline metal. The yield properties of the grain-boundary interface, used in the FE simulations, are extracted from a MD simulation on a bicrystal. The models allow for the study of the load transfer between adjacent grains of very different size through grain-boundary sliding during deformation. A large-scale FE simulation of 100 grains of a typical microstructure is then presented to reveal that the stress distribution due to grain-boundary sliding during uniform tensile strain can lead to stress localization of two to three times the background stress, thus suggesting a significant effect on the failure properties of the metal.
Yamakov, V.↗
Molecular dynamics of the early stages of high-temperature corrosion
In this work, we performed molecular dynamics simulations of the high-temperature oxidation of metal alloys composed of Al, Cr, and Fe and compared their behavior with that of pure Fe. The metal alloy elements (Al and Cr) segregated to the surface during oxidation, producing a lower stress gradient at the metal/environment interface compared to pure Fe. We have found that the lowered stress gradients produced in the alloy material appear to play a key role in the development of corrosion. Interfaces with lower stress gradients have reduced rates of H 2 O adsorption, especially for the ferritic (bcc) alloys. The diffusivity of oxygen and hydrogen drops more rapidly for the interfaces with reduced stress gradients. The stress gradient is also diminished when the gas pressure is increased, indicating that the Fe-Cr-Al alloy system is more resistant to oxidation than pure Fe at higher pressures. Therefore, we conclude that the lower stress gradients at the alloy/environment interface reduce the stress concentration and can slow down the rate of the initial oxide scale growth. We also compared bcc and fcc alloys with pure Fe based on our three evaluation criteria (peak stress, stress gradient, and summation of stress in the oxide scale). We found that the alloys have lower values under the three criteria compared to pure Fe. The bcc alloy has the best score under a water rich environment and the fcc alloy is proven to be better for peak stress and summation of stress in the oxide scale under an oxygen rich environment. For surface segregation to occur, we find that a minimum content of Al or Cr in the near-surface region must be achieved. We also learned that the role of Al is more important than that of Cr in terms of corrosion resistant behavior at relatively higher temperatures for the Fe-Cr-Al ternary alloys.
36 MATERIALS SCIENCE↗
Exploring far-from-equilibrium ultrafast polarization control in ferroelectric oxides with excited-state neural network quantum molecular dynamics
Ferroelectric materials exhibit a rich range of complex polar topologies, but their study under far-from-equilibrium optical excitation has been largely unexplored because of the difficulty in modeling the multiple spatiotemporal scales involved quantum-mechanically. To study optical excitation at spatiotemporal scales where these topologies emerge, we have performed multiscale excited-state neural network quantum molecular dynamics simulations that integrate quantum-mechanical description of electronic excitation and billion-atom machine learning molecular dynamics to describe ultrafast polarization control in an archetypal ferroelectric oxide, lead titanate. Far-from-equilibrium quantum simulations reveal a marked photo-induced change in the electronic energy landscape and resulting cross-over from ferroelectric to octahedral tilting topological dynamics within picoseconds. The coupling and frustration of these dynamics, in turn, create topological defects in the form of polar strings. The demonstrated nexus of multiscale quantum simulation and machine learning will boost not only the emerging field of ferroelectric topotronics but also broader optoelectronic applications.
36 MATERIALS SCIENCE↗
Path integral molecular dynamics: A high-fidelity approach to quantum dynamics of electrons
We investigate electron transport in the uniform electron gas using ring-polymer molecular dynamics (RPMD). Working in the weakly coupled, non-degenerate regime, we use RPMD to probe how the onset of quantum diffraction effects at high temperature reshapes electron–electron collisions and leads to a classical-to-quantum crossover in macroscopic transport properties. Static thermodynamics obtained with RPMD are consistent with the weak-coupling equation of state, confirming correct quantum Boltzmann sampling. Real-time transport extracted from mean square displacements exhibits the expected ballistic-to-diffusive transition and a systematic reduction of the electronic self-diffusivity as quantum effects strengthen, due to quantum diffraction modifying electron–electron collisions. Direct ring-polymer scattering simulations reveal diffractive “softening” of binary deflections, providing a micro-to-macro link between collision physics and diffusion. The present study establishes RPMD as a quantitative, trajectory-based tool for electron transport across the classical–quantum crossover and furnishes benchmarks for improving Coulomb-log interpolation models. We outline extensions to multi-component plasmas and a path to incorporate Fermi–Dirac statistics within path-integral dynamics.
Electronic transport↗
Molecular dynamics and quasidynamics simulations of the annealing of bulk and near-surface interstitials formed in molecular-beam epitaxial Si due to low-energy particle bombardment during deposition
The relaxation, diffusion, and annihilation of split and hexagonal interstitials resulting from 10 eV Si irradiation of (2x1)-terminated Si(100) are investigated. Molecular dynamics and quasidynamics simulations, utilizing the Tersoff many-body potential are used in the investigation. The interstitials are created in layers two through six, and stable atomic configurations and total potential energies are derived as a function of site symmetry and layer depth. The interstitial Si atoms are allowed to diffuse, and the total potential energy changes are calculated. Lattice configurations along each path, as well as the starting configurations, are relaxed, and minimum energy diffusion paths are derived. The results show that the minimum energy paths are toward the surface and generally involved tetrahedral sites. The calculated interstitial migration activation energies are always less than 1.4 eV and are much lower in the near-surface region than in the bulk.
Kitabatake, M.↗
An Investigation into the Approximations Used in Wave Packet Molecular Dynamics for the Study of Warm Dense Matter
Wave packet molecular dynamics (WPMD) has recently received a lot of attention as a computationally fast tool with which to study dynamical processes in warm dense matter beyond the Born–Oppenheimer approximation. These techniques, typically, employ many approximations to achieve computational efficiency while implementing semi-empirical scaling parameters to retain accuracy. We investigated three of the main approximations ubiquitous to WPMD: a restricted basis set, approximations to exchange, and the lack of correlation. We examined each of these approximations in regard to atomic and molecular hydrogen in addition to a dense hydrogen plasma. We found that the biggest improvement to WPMD comes from combining a two-Gaussian basis with a semi-empirical correction based on the valence-bond wave function. A single parameter scales this correction to match experimental pressures of dense hydrogen. Ultimately, we found that semi-empirical scaling parameters are necessary to correct for the main approximations in WPMD. However, reducing the scaling parameters for more ab-initio terms gives more accurate results and displays the underlying physics more readily.
Angermeier, William A. (ORCID:0000000177161564)↗
Periodic boundary conditions for arbitrary deformations in molecular dynamics simulations
A generalization of the Lees-Edwards periodic boundary conditions (gLE-PBC) for molecular dynamics (MD) simulations is developed to allow for arbitrary deformations to be applied to the domain. The gLE-PBC domain remains a rectangular cuboid regardless of the applied deformation in contrast with the Lagrangian-rhomboid periodic boundary conditions (LR-PBC) where the domain deforms according to the applied deformation. Furthermore, the kinematics of gLE-PBC are validated against pure shear. The gLE-PBC method for interacting systems is then validated against the LR-PBC method and analytical solutions for a solid under isotropic compression, one-dimensional shearing, three-dimensional extension and shearing and for a liquid under Couette flow. Bulk physical properties extracted from the gLE-PBC simulations agree well with values calculated from equilibrium MD simulations. Three dimensional shearing and a deformation with a full velocity gradient matrix are also simulated, showing the range of problems gLE-PBC can explore.
74 ATOMIC AND MOLECULAR PHYSICS↗
REACTER: A Heuristic Method for Reactive Molecular Dynamics
REACTER (www.reacter.org) is a heuristic protocol that enables the simulation of complex reactions using atomistic molecular dynamics (MD) with a fixed-valence force field. Incorporating reactions into classical MD with this approach allows modeling of reactive systems over greatly-increased time scales, enabling systems to be modeled with MD that would not otherwise be feasible. One or more competing multi-step reactions or series of reactions can be invoked simultaneously. Special treatment can be applied to neighboring atoms to relax high energy configurations while the simulation progresses. The original version of REACTER, which was implemented in the open-source LAMMPS simulation package as fix bond/react, was only available for serial simulations. This work describes the expansion of fix bond/react for use in parallel simulations, as well as the addition of various new options, including deletion of reaction by-products, reversible reactions, and custom reaction constraints. These new capabilities are demonstrated through large-scale simulations (200,000+ atoms) of the polymerization of polystyrene and nylon 6,6. The morphologies of both polymers are analyzed after reaching >99% extent of polymerization. Finally, the newly-added reversible reactions feature is demonstrated by rupturing these highly-entangled systems under uniaxial strain by defining a chain scission reaction.
polymer simulations, molecular dynamics↗
Infrared spectral signatures of interfacial water at TiO 2 –electrolyte interfaces from deep potential molecular dynamics
Vibrational spectroscopy is a powerful tool for probing water at oxide–electrolyte interfaces, but its molecular interpretation can be challenging. Here, we employ deep potential long-range molecular dynamics simulations with layer-resolved spectral analysis to investigate the microscopic origins of the infrared (IR) response of water at the interface with anatase TiO 2 (101), a prototypical oxide surface. The calculated interfacial spectra exhibit characteristic modifications compared to bulk water IR spectra, including enhanced intensities, a red shifted and broadened stretching band, and a higher-frequency shoulder, in qualitative agreement with experiments. Spectral decomposition shows that these signatures originate mainly from the first interfacial water layer, dominated by surface-bound H 2 O at Ti 5C sites, with secondary contributions from the second layer. A moderate salt concentration (0.4 M NaCl) leaves both the interfacial structure and the spectra essentially unchanged, while tuning the pH strongly modulates the spectral intensity. We establish a scaling relation linking the spectral intensity to the surface water dissociation fraction and the dipole moment, both governed by interfacial electric fields. These findings provide a microscopic framework for interpreting IR spectra of oxide–electrolyte interfaces.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Ab Initio Molecular Dynamics Study of Pd Nucleation on a γ-Al 2 O 3 Surface
We perform ab initio molecular dynamics (AIMD) free energy simulations to investigate the stability and dynamics of dispersed Pd atoms and subnanometer clusters on γ-Al 2 O 3 . We consider nucleation for varying Pd loadings on dry γ-Al 2 O 3 (100), dry γ-Al 2 O 3 (110) and wet γ-Al 2 O 3 (110) and examine temperature, entropy and water coverage effects on the stability and dynamics of Pd clusters. At low Pd loading (1.07 Pd atoms/nm 2 on the (100) and 0.75 Pd/nm 2 on the (110)), association of the Pd atoms is thermodynamically unfavorable on the dry surfaces and almost thermoneutral on the wet (110) owing to water blocking of the AlIII defect sites. In agreement with past studies, the Pd atoms are quite mobile but the diffusion free energy barriers do not increase with the water coverage, as previously suggested, but rather remain similar in magnitude owing to translational entropy at finite temperatures. At these Pd loadings, oxidized Pd(II) atoms on the wet (110) surface are dispersed and immobile. At higher Pd loading (1.12 and 1.5 Pd atoms/nm 2 ) on the (110) surface, Pd 3 and Pd 4 clusters are thermodynamically very stable and form fast. At the 1.12 Pd atoms/nm 2 loading, the formation of the Pd 3 cluster is two orders of magnitude slower when the surface is hydroxylated as the system becomes somewhat trapped before the dinuclear cluster Pd 2 collides with a Pd atom.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗