Empirical Potential Molecular Dynamics Research Articles

Anomalous Thermal Transport across the Superionic Transition in Ice

Superionic ices with highly mobile protons within stable oxygen sub-lattices occupy an important proportion of the phase diagram of ice and widely exist in the interior of icy giants and throughout the Universe. Understanding the thermal transport in superionic ice is vital for the thermal evolution of icy planets. However, it is highly challenging due to the extreme thermodynamic conditions and dynamical nature of protons, beyond the capability of the traditional lattice dynamics and empirical potential molecular dynamics approaches. By utilizing the deep potential molecular dynamics approach, we investigate the thermal conductivity of ice-VII and superionic ice-VII″ along the isobar of P = 30 GPa. A non-monotonic trend of thermal conductivity with elevated temperature is observed. Through heat flux decomposition and trajectory-based spectra analysis, we show that the thermally activated proton diffusion in ice-VII and superionic ice-VII″ contribute significantly to heat convection, while the broadening in vibrational energy peaks and significant softening of transverse acoustic branches lead to a reduction in heat conduction. The competition between proton diffusion and phonon scattering results in anomalous thermal transport across the superionic transition in ice. This work unravels the important role of proton diffusion in the thermal transport of high-pressure ice. Our approach provides new insights into modeling the thermal transport and atomistic dynamics in superionic materials.

Insight into Atomic-Scale Adhesion at the C–Cu Interface During the Initial Stage of Nanoindentation

Adhesion is a common phenomenon in nanomachining which affects processing accuracy and repeatability. As material removal approaches the atomic or close-to-atomic scale, quantum mechanics becomes the dominant principle behind the atomic-level interaction. However, atomic-scale effects cannot be properly described by empirical potential function-based molecular dynamics simulations. This study uses a first-principles method to reveal the atomic-scale adhesion between a diamond tip and a copper slab during initial-stage nanoindentation. Using a simplified tip and slab model, adhesion energy, electronic distribution, and density of states are analyzed based on quantum chemistry calculation. Results show that atomic adhesion is primarily due to the covalent bonding interaction between C and Cu atoms, which can induce structural changes to the diamond tip and copper slab. The effects of tip position and angles on adhesion are further studied through a series of simulations. The results show that adhesion between the tip and slab is sensitive to the lattice structure and a variant in angstroms is enough to cause different adhesion and structural changes. The actual determinants of adhesion can only be the atomic and electronic structures at the tip–slab interface. Bond rotation and breakage are observed during simulation and their effects on adhesion are further discussed. To conclude, the first-principles method is important for the analysis of an atomic-scale interaction system, even if only as an aid to describing adhesion at atomic and electronic scales.

On the hydration of DOPE in solution.

The atomic-scale hydration structure around the 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) headgroup in a chloroform/water solution has been investigated using neutron diffraction enhanced by isotopic substitution and NMR, coupled with empirical potential structure refinement and molecular dynamics simulations. The results obtained show the preferential binding sites for water molecules on the DOPE headgroups, with the most predominant interactions being with the ammonium and phosphate groups. Interestingly, the level of hydration, as well as the association of DOPE molecules, varies according to the simulation method used. The results here suggest the presence of a tight water network around these lipid headgroups that could affect the permeability of the membrane for lipid-mediated diffusion.

The stability of graphene-based Möbius strip with vacancy and at high-temperature

The structural and electronic properties of mono-vacancy (MV) defect in graphene-based Möbius strip (GMS) are studied in the framework of density functional theory (DFT) combined with the molecular dynamics (MD) simulations. Two kinds of MV defects are observed: the 59-type MV (a configuration with one pentagon and one nonagon ring) located at the curved areas of Möbius strip, and the 5566-type MV (a configuration with two pentagon and two hexagon rings) with one sp3 hybridized carbon appeared in the twisted areas. The 5566-type MV defect is the most stable configuration at 0 K, while the DFT-MD calculations show that it is unstable at room-temperature and will transform into a 59-type MV. Additionally, the melting behavior of GMSs is investigated through empirical potential MD simulations, and we find that their melting temperatures are about 2750 K, which is lower than that of carbon nanotubes and graphene.

Dynamical processes of low-energy carbon ion collision with the graphene supported by diamond

The dynamical processes of a low-energy carbon ion collision with the graphene sheet supported by diamond at three impact positions are studied by using empirical potential molecular dynamics simulations. The energy transformation and the structural evolution have been studied. Five types of processes are observed: adsorption, hybridization, defects formation in diamond, atom emission and transmission. We find that the irradiation damage is closely related to the incident energy and impact position. In our simulations, as the projectile collides at a graphene atom, it transfers most of its energy to the primary knock-on atom, and defects are created in graphene. When the projectile moves perpendicular towards the center of a C-C bond in the graphene sheet, the energy transferred from the projectile to the atoms associated with the bond increases firstly and then decreases with the increasing incident energy, and the graphene sheet remains two-dimensional crystal structure after collision when the incident energy is larger than 360 eV. While the impact location is the center of a hexagonal ring on the graphene sheet, the energy transferred from the projectile to the atoms of the target ring is very small regardless of how large is the incident energy, and the graphene sheet is able to keep perfect crystal structure when the incident energy is larger than 34 eV.

Origins of the high temperature increase of the thermal conductivity of transition metal carbides from atomistic simulations

To understand the unexpected increase of the thermal conductivity of transition metal carbides at high temperatures, we calculate, with atomistic simulations, the thermal conductivity of zirconium carbide (ZrC). To account for the common substoichiometry of this material, various numbers of carbon vacancies are considered. The vibrational part of the conductivity is calculated by empirical potential molecular dynamics while the electronic part is calculated from density functional theory electronic structure with the Kubo–Greenwood formula on selected atomic configurations generated by the same empirical potential. We find that the vibrational part of the conductivity is negligible at temperatures higher than 1500 K. The increase of thermal conductivity with temperature is quantitatively reproduced in the calculations. It appears for all compositions and proves to rely entirely on its electronic component. Three phenomena are found responsible for the rise of the thermal conductivity with temperature: the semi-metallic shape of the electronic density of states, the additional electrical resistivity induced by carbon vacancies and the rise of the density of states with either temperature or the concentration of vacancies.

Classical molecular dynamics investigation of microstructure evolution and grain boundary diffusion in nano-polycrystalline UO2

The High Burnup Structure (HBS) observed at pellet periphery in conventional Light Water Reactor nuclear fuels and around spots presenting high plutonium content in mixed (U, Pu) oxide fuel – MOX fuel – consists of a restructuration of the original grains into smaller ones. The process is often postulated to occur because of the accumulation of irradiation damage and the retention of fission products in the matrix. The computing power nowadays available enables for simulating larger systems at the atomic scale up to the point that nano-polycrystalline material can now be investigated by empirical potential molecular dynamics. Simulations of nano-polycrystalline UO2 structures have been carried out at various temperatures to investigate atom mobility close to grain boundaries. The variation of Arrhénius parameters for the diffusion coefficient of oxygen, uranium and xenon as a function of the distance from a grain boundary was studied, leading to the distinction of three zones: the grain boundary layers (up to 1nm depth) presenting enhanced diffusion, an intermediate zone (1 to roughly 2nm depth) with intermediate diffusion values and the bulk of the grains. The following Arrhénius relations for grain boundary diffusion were derived:Oxygendiffusion:DO(T)=5.4×10-4exp[(0.74eV)/(kBT)]cm2/sUraniumdiffusion:DU(T)=1.7×10-6exp[(0.50eV)/(kBT)]cm2/sXenondiffusion:DXe(T)=1.4×10-5exp[(0.50eV)/(kBT)]cm2/swhere kB stands for Boltzmann’s constant and T for temperature. Besides, changes in the microstructure could be “observed” over the 1ns duration of the simulations, such as the formation of small gas clusters.

Sampling the energy landscape of Pt13 with metadynamics

The potential energy surface of a metallic nanoparticle formed by 13 atoms of platinum is efficiently explored using metadynamics in combination with empirical potential molecular dynamics. The scenario obtained is wider and more complex of what was previously reported: more than thirty independent energy basins are found, corresponding to different local minima of Pt. It is demonstrated that in almost all the cases these motifs are local minima even at ab-initio level, hence proving the effectiveness of the method to sample the energy landscape. A classification of the minima in structural families is proposed, and a discussion regarding the shape and the connections between energy basins is reported.

Transport properties and equation of state of 1-bar eutectic melt in the system CaAl2Si2O8-CaMgSi2O6 by molecular dynamics simulation

Empirical potential molecular dynamics (EPMD) simulations of 1-bar eutectic composition liquid in the system CaAl2Si2O8-CaMgSi2O6 have been conducted using the interatomic pair-potential of Matsui (1998). Simulations using ~10000 atoms over a wide range of conditions (ρ: 2200–5000 kg/m3; T : 1600–5500 K; P : 0–170 GPa) were used to derive an equation of state, determine self-diffusivities for all atoms, calculate melt viscosity, and investigate melt structures by coordination statistics. EOS results compare well to laboratory shock wave data up to ~25 GPa, diverging at higher pressure. Based on simulations of the end-member compositions of the join using the same potential, non-ideality in the volume of mixing at pressures below 10 GPa disappears at higher pressures. Ideal volume mixing at elevated pressure is consistent with inferences from laboratory shock wave studies of liquids in this system. The non-ideal volume of mixing at low pressure is directly correlated to structural differences between the end-member liquids and the mixing of cation-anion coordination polyhedra of differing volume. Self-diffusivities show reasonable agreement with laboratory values, with activation energies and activation volumes in the range 90–100 kJ/mol and 1–3 cm3/mol, respectively. Shear viscosities at 3500 K span from 1.8 × 10−3 Pa·s at low P to ~4.4 × 10−3 Pa·s at ~14 GPa.

Molecular Dynamics Study of Grain Boundary Diffusion of Fission Gas in Uranium Dioxide

Among the various products originating from fission events, the noble gas elements Xe and, in a lesser extent, Kr present important fission yields. The accumulated gas inventory in its various states (e.g. atomically dissolved, precipitated in cavities or released from the fuel) has a strong impact on the performance of LWR fuel and is presently one of the limiting factors for fuel burnup extension. A more fundamental understanding of fission gas behaviour at the atomic scale would enable to improve the modelling of the various mechanisms ultimately leading to fission gas release and to refine conservative safety margins. Lots of efforts have already been undertaken using atomistic computer simulations, ab initio calculations and Empirical Potential Molecular Dynamics (EP-MD) techniques, that relate to the bulk behaviour. This article will discuss EP-MD investigations in nanosized polycrystalline UO2, constructed from Voronoi cells in a 3-D periodic environment. This study has focused on Xe diffusion at and close to grain boundaries.

Structure, thermodynamic and transport properties of liquid MgSiO 3: Comparison of molecular models and laboratory results

Liquid MgSiO 3 is a model for the Earth’s magma ocean and of remnant melt present near the core–mantle boundary. Here, models for molten MgSiO 3 are computed employing empirical potential molecular dynamics (EPMD) and results are compared to published results including two EPMD studies and three first-principles molecular dynamics (FPMD) models and to laboratory data. The EPMD results derived from the Oganov (OG) potential come closest to the density of MgSiO 3 liquid at the 1-bar melting point inferred from the melting curve. At higher P, EPMD densities calculated from the OG potential and FPMD broadly match shock wave studies, with the OG potential yielding the better comparison. Matsui (M) potential results deviate from other studies above ∼50 GPa. Overall, results based on the OG potential compare best to experimental densities over the P–T range of the mantle. Isothermally, upon increasing P the mean coordination numbers ( CN ¯ ) of oxygen around Si and Mg monotonically increase with pressure. Tetrahedral Si and octahedral Si monotonically increase and decrease, respectively, whereas pentahedral Si maximizes at 10–20 GPa. Tetrahedral Mg decreases monotonically as P increases whereas pentahedral, octahedral and higher coordination polyhedra each show similar behavior first increasing and then decreasing after attaining a maximum; the P of the maximum for each polyhedra type migrates to higher P as the CN increases. Free oxygen and oxygen with one nearest neighbor of either Si or Mg decreases whereas Si or Mg with two or three nearest oxygens (i.e., tricluster oxygen) increases with increasing P isothermally. The increase of tricluster oxygen is consistent with spectroscopy on MgSiO 3 glass quenched from 2000 K and 0–40 GPa and high-energy X-ray studies constraining the coordination of O around Mg and around Si at 2300 K and 1 bar. Coordination statistics from FPMD studies for O around Si and Si around O are in agreement with the EPMD results based on the M and OG potentials. Mg self-diffusivity is greater than O and Si self-diffusivities for both the M and OG potentials. All D values monotonically decrease with increasing pressure isothermally and all atoms are more diffusive in the M liquid compared to the OG liquid except at T > ∼5000 K and P > 100 GPa. Previously published EPMD diffusivities fall between values given by the M and OG potentials, at least up to 45 GPa. The M liquid is generally less viscous than the OG liquid except at P > ∼80 GPa. Activation energy and volume are around 96 kJ/mol and 1.5 cm 3/mol, respectively. The FPMD viscosity results at 120 GPa and 4000 and 4500 K are essentially identical to the values from the M and OG potentials. FPMD viscosity results are similar to the OG results for P < 60 GPa; at higher P, the FPMD viscosities are higher. At 4000 K and 100 GPa the shear viscosity of liquid MgSiO 3 is ∼0.1 Pa s. More extensive laboratory results are required to better define the thermodynamic, transport and structural properties of MgSiO 3 liquids and for comparison with computational studies.

Atomistic study of the thermodynamic equilibrium of nano-sized helium cavities in βSiC

The estimation of the number of inert gas atoms contained at equilibrium in microscale bubbles in a solid usually relies on a well-known formula equilibrating the internal pressure of He to the surface energy of the bubble. This approach evidences a strong variation with temperature of He content for a given bubble. At the opposite, at the Angstrom scale, ab initio calculations for He contained in vacancy assemblies neglect temperature effects. In this work, empirical potential molecular dynamics simulations are used to study, in the case of helium inserted in cubic silicon carbide, the variation of the He content of sub-nanoscale cavities with temperature. To do so free energy for He atoms inserted in cavities made of a few vacancies (up to 29) are calculated. One then evidences the existence of a sub-surface segregation in interstitial sites close to the surface of the cavity. The variation of the He content with temperature is observed to be negligible at the nanoscale, thus validating the ab initio approach.

Atomistic simulation of point defects behavior in ceria

The cerium and oxygen threshold displacement energies and the Frenkel pair recombination in CeO 2 have been investigated with empirical potential molecular dynamics simulations. The oxygen and cerium threshold displacement energies have been evaluated to be 27 and 56 eV, respectively, in agreement with experimental results. The short-range cerium and oxygen Frenkel pair recombination processes are found to be strongly dependent on the local topology and the pathways. The oxygen Frenkel pair recombinations are either spontaneous or thermally activated unlike the standard recombination usually defined in rate equations. The lifetime of Frenkel pair recombination is in general found to be much shorter than the characteristic time for single defect diffusion.

Molecular dynamics simulation of point defect accumulation in MgAl2O4

The kinetics of phase transformation under irradiation of magnesium aluminate spinel MgAl2O4 has been investigated by means of continuous Frenkel pair introduction in the framework of empirical potential molecular dynamics simulations. Phase transformation to defective rock-salt structure was observed with a cation displacement dose rate of 5×108dpc/s (dpc: displacements per cation) at temperatures ranging from 30 to 2200K. The critical dose for the phase transformation is in the range of 0.5–2.5dpc, and it is prolonged with increasing temperature. No amorphization was realized in the simulations at 30K up to a dose of 68dpc with an accelerated displacement dose rate of 5×109dpc/s.

Insights into the Structure and Dynamics of a Room-Temperature Ionic Liquid: Ab Initio Molecular Dynamics Simulation Studies of 1-n-Butyl-3-methylimidazolium Hexafluorophosphate ([bmim][PF6]) and the [bmim][PF6]−CO2 Mixture

Ab initio molecular dynamics (AIMD) studies have been carried out on liquid 1-n-butyl-3-methylimidazolium hexafluorophosphate ([bmim][PF6]) and its mixture with CO2 using the Car-Parrinello molecular dynamics (CPMD) method. Results from AIMD and empirical potential molecular dynamics (MD) have been compared and were found to differ in some respects. With a strong resemblance to the crystal, the AIMD simulated neat liquid exhibits many cation-anion hydrogen bonds, a feature that is almost absent in the MD results. The anions were observed to be strongly polarized in the condensed phase. The addition of CO2 increased the probability of this hydrogen bond formation. CO2 molecules in the vicinity of the ions of [bmim][PF6] exhibit larger deviations from linearity in their instantaneous configurations. The polar environment of the liquid induces a dipole moment in CO2, lifting the degeneracy of its bending mode. The calculated splitting in the vibrational mode compares well with infrared spectroscopic data. The solvation of CO2 in [bmim][PF6] is primarily facilitated by the anion, as seen from the radial and spatial distribution functions. CO2 molecules were found to be aligned tangential to the PF6 spheres with their most probable location being the octahedral voids of the anion. The structural data obtained from AIMD simulations can serve as a benchmark to refine interaction potentials for this important room-temperature ionic liquid.

Spontaneous cationic Frenkel pair recombinations in lanthanum pyrozirconate (La2Zr2O7)

Spontaneous cationic Frenkel pair recombinations in lanthanum zirconate (La2Zr2O7) pyrochlore are studied with empirical potential molecular dynamics. A complex behavior is observed depending on the distance between the vacancy and the interstitial and on the nature of the cations lying in between them. While interstitials of the first shell near a vacancy readily recombine, interstitials of the second shell never do. The third shell interstitials recombine in half the configurations, i.e. when the intermediate cation is lanthanum, leading to antisites when a zirconium defect pair is considered. The behavior is globally the same in the corresponding disordered fluorite structure, but we observed that in this structure, the number of spontaneous recombinations increases with temperature.

Potential Energy Surfaces of an Adenine−Thymine Base Pair and Its Methylated Analogue in the Presence of One and Two Water Molecules: Molecular Mechanics and Correlated Ab Initio Study

Potential energy surfaces of monohydrated and dihydrated adenine-thymine and 9-methyladenine-1-methylthymine base pairs were examined by the molecular dynamics/quenching technique using the Cornell et al. force field (J. Am. Chem. Soc. 1995, 117, 5179). Long runs of molecular dynamics/quenching calculations allowed us to evaluate the free energy surface. The most stable and populated structures found were fully reoptimized at the correlated ab initio level employing the resolution of identity Møller-Plesset method. A systematic study of the base pairs' microhydration using both the empirical and the high-level correlated ab initio approaches is presented for the first time. We show that the occurrence of water molecules and their gradually increasing number as well as the methylation of the bases favor stacked structures over the planar hydrogen-bonded ones. These results based on the correlated ab initio calculations are in the excellent agreement with data obtained from our previous empirical potential molecular dynamics study (Kabelác et al. Chem.-Eur. J. 2001, 7, 2067).

Neutral self-defects in a silica model: A first-principles study

We present a statistical study of silicon and oxygen neutral defects in a silica glass model. This work is performed following two complementary approaches: first-principles calculations and empirical potential molecular dynamics. We show that the defect formation energies and structures are distributed and that the energy distributions are correlated with the local stress before the defect formation. Combining defect energies calculated from first principles and local stresses from empirical potential calculations in undefected silica, we are able to predict the formation energy distributions in larger systems, the size of which precludes the use of ab initio methods. Using the resulting prediction we will show that the cell size used in our modeling contains all the formation energy fluctuations needed to describe a real glass.

An atomistic-based continuum theory for carbon nanotubes: analysis of fracture nucleation

Carbon nanotubes (CNTs) display unique properties and have many potential applications. Prior theoretical studies on CNTs are based on atomistic models such as empirical potential molecular dynamics (MD), tight-binding methods, or first-principles calculations. Here we develop an atomistic-based continuum theory for CNTs. The interatomic potential is directly incorporated into the continuum analysis through constitutive models. Such an approach involves no additional parameter fitting beyond those introduced in the interatomic potential. The atomistic-based continuum theory is then applied to study fracture nucleation in CNTs by modelling it as a bifurcation problem. The results agree well with the MD simulations.

Dynamic Properties of Disordered Phases of Carbon Studied by an Empirical Potential: Stringent Tests toward Hybrid Approach with the Density-Functional Theory

The dynamic properties of the liquid and the amorphous carbon are studied by empirical-potential molecular-dynamics (MD) simulations as well as ab initio MD methods based on the density-functional theory. As the empirical potential, the environment-dependent interatomic potential (EDIP) proposed recently by Marks is used. Detailed investigations on the density–density time correlation function, known as van Hove correlation functions, are given. It is shown that the EDIP is extremely transferable in the sense that the dynamic properties, as well as the static properties, of the disordered phases of carbon are well reproduced using the EDIP. It is also shown that the EDIP is usable for the hybrid ab initio /empirical-potential MD simulation, by applying the hybrid method to a graphite sheet (graphen) for investigating the dynamic properties such as the heat transfer.