Large Scale Molecular Dynamics Computer Research Articles

Machine learning molecular dynamics simulations toward exploration of high-temperature properties of nuclear fuel materials: case study of thorium dioxide

Predicting materials properties of nuclear fuel compounds is a challenging task in materials science. Their thermodynamical behaviors around and above the operational temperature are essential for the design of nuclear reactors. However, they are not easy to measure, because the target temperature range is too high to perform various standard experiments safely and accurately. Moreover, theoretical methods such as first-principles calculations also suffer from the computational limitations in calculating thermodynamical properties due to their high calculation-costs and complicated electronic structures stemming from f-orbital occupations of valence electrons in actinide elements. Here, we demonstrate, for the first time, machine-learning molecular-dynamics to theoretically explore high-temperature thermodynamical properties of a nuclear fuel material, thorium dioxide. The target compound satisfies first-principles calculation accuracy because f-electron occupation coincidentally diminishes and the scheme meets sampling sufficiency because it works at the computational cost of classical molecular-dynamics levels. We prepare a set of training data using first-principles molecular dynamics with small number of atoms, which cannot directly evaluate thermodynamical properties but captures essential atomistic dynamics at the high temperature range. Then, we construct a machine-learning molecular-dynamics potential and carry out large-scale molecular-dynamics calculations. Consequently, we successfully access two kinds of thermodynamic phase transitions, namely the melting and the anomalous lambda transition induced by large diffusions of oxygen atoms. Furthermore, we quantitatively reproduce various experimental data in the best agreement manner by selecting a density functional scheme known as SCAN. Our results suggest that the present scale-up simulation-scheme using machine-learning techniques opens up a new pathway on theoretical studies of not only nuclear fuel compounds, but also a variety of similar materials that contain both heavy and light elements, like thorium dioxide.

Temperature-dependent kinetic pathways featuring distinctive thermal-activation mechanisms in structural evolution of ice VII

Ice amorphization, low- to high-density amorphous (LDA-HDA) transition, as well as (re)crystallization in ice, under compression have been studied extensively due to their fundamental importance in materials science and polyamorphism. However, the nature of the multiple-step "reverse" transformation from metastable high-pressure ice to the stable crystalline form under reduced pressure is not well understood. Here, we characterize the rate and temperature dependence of the structural evolution from ice VII to ice I recovered at low pressure (∼5 mTorr) using in situ time-resolved X-ray diffraction. Unlike previously reported ice VII (or ice VIII)→LDA→ice I transitions, we reveal three temperature-dependent successive transformations: conversion of ice VII into HDA, followed by HDA-to-LDA transition, and then crystallization of LDA into ice I. Significantly, the temperature-dependent characteristic times indicate distinctive thermal activation mechanisms above and below 110-115 K for both ice VIII-to-HDA and HDA-to-LDA transitions. Large-scale molecular-dynamics calculations show that the structural evolution from HDA to LDA is continuous and involves substantial movements of the water molecules at the nanoscale. The results provide a perspective on the interrelationship of polyamorphism and unravel its underpinning complexities in shaping ice-transition kinetic pathways.

Atomistic simulations of a helium bubble in silicon carbide

Large scale molecular dynamics calculations have been carried out to investigate the properties of nanometric helium bubbles in silicon carbide as a function of helium density and temperature. A dedicated interatomic potential has been developed to describe the interactions between helium and SiC atoms. The simulations revealed that the helium density cannot exceed a certain threshold value, which depends on temperature, because of the plastic deformation of the SiC matrix. Both local amorphization at low temperatures, and nucleation and propagation of dislocations at high temperatures, have been identified as activated plasticity mechanisms. This work also predicts that very high pressure up to 60 GPa could be reached in helium bubbles in silicon carbide.

Nanoprobe diffusion in entangled polymer solutions: Linear vs. unconcatenated ring chains.

We employ large-scale molecular dynamics computer simulations to study the problem of nanoprobe diffusion in entangled solutions of linear polymers and unknotted and unconcatenated circular (ring) polymers. By tuning both the diameter of the nanoprobe and the density of the solution, we show that nanoprobes of diameter smaller than the entanglement distance (tube diameter) of the solution display the same (Rouse-like) behavior in solutions of both polymer architectures. Instead, nanoprobes with larger diameters appear to diffuse markedly faster in solutions of rings than in solutions of linear chains. Finally, by analysing the distribution functions of spatial displacements, we find that nanoprobe motion in rings' solutions shows both Gaussian and ergodic behaviors, in all regimes considered, while, in solutions of linear chains, nanoprobes exceeding the size of the tube diameter show a transition to non-Gaussian and non-ergodic motion. Our results emphasize the role of chain architecture in the motion of nanoprobes dispersed in polymer solutions.

Large-scale molecular dynamics modeling of boron-doped amorphous SiCO ceramics.

At high temperature, silicon oxycarbide (SiCO) exhibits excellent mechanical properties and thermal stability. The incorporation of boron in SiCO results in improved performance in creep temperatures. In this work, large-scale molecular dynamics calculations were applied to obtain amorphous SiCO structures containing boron. Phase separation of C-C, B-C and Si-O was achieved for three compositions, and silicon-centered mixed-bond tetrahedrons were reproduced successfully. As the boron content increases, the boron atoms tend to form B-C and B-Si bonds in the voids, which stretches the free carbon network in some instances, causing a increase in C-C distance. Young's modulus remains stable at high temperature for the high-carbon case, which indicates that the free carbon network plays a critical role in the structural and thermal stability of SiBCO. Graphical Abstract Three major typical structures in the cooling down process for silicon boron oxycarbide (Si5BC2O8). Bonds: red Si-O, blue Si-C, black C-C, green B-C, purple Si-B.

Electron-phonon interaction within classical molecular dynamics

We present a model for nonadiabatic classical molecular dynamics simulations that captures with high accuracy the wave-vector $q$ dependence of the phonon lifetimes, in agreement with quantum mechanics calculations. It is based on a local view of the $e$-ph interaction where individual atom dynamics couples to electrons via a damping term that is obtained as the low-velocity limit of the stopping power of a moving ion in a host. The model is parameter free, as its components are derived from ab initio-type calculations, is readily extended to the case of alloys, and is adequate for large-scale molecular dynamics computer simulations. We also show how this model removes some oversimplifications of the traditional ionic damped dynamics commonly used to describe situations beyond the Born-Oppenheimer approximation.

Prediction of Giant Thermoelectric Efficiency in Crystals with Interlaced Nanostructure.

We present a theoretical study of the thermoelectric efficiency of "interlaced crystals", recently discovered in hexagonal-CuInS2 nanoparticles. Interlaced crystals are I-III-VI2 or II-IV-V2 tetrahedrally bonded compounds. They have a perfect Bravais lattice in which the two cations have an infinite set of possible ordering patterns within the cation sublattice. The material comprises nanoscale interlaced domains and phases with corresponding boundaries. Here we employ density functional theory and large-scale molecular dynamics calculations based on model classical potentials to demonstrate that the phase and domain boundaries are effective phonon scatterers and greatly suppress thermal conductivity. However, the absence of both structural defects and strain in the interlaced material results in a minimal effect on electronic properties. We predict an increase of thermal resistivity of up to 2 orders of magnitude, which makes interlaced crystals an exceptional candidate for thermoelectric applications.

Molecular Dynamics Simulations of Energetic Ar Cluster Bombardment of Ag(111)

Large-scale molecular dynamics computer simulations are used to investigate the dynamics of material ejection during high-energy Arn cluster bombardment of Ag(111) at normal incidence. The silver sample containing 7 million atoms is bombarded with Arn projectiles (n = 45−30000) with kinetic energy spanning from a few keV up to 1 MeV. Such a wide range of projectile parameters allows probing processes taking place during low-density collision cascade as well as during high-density events characteristic of micrometeorite bombardment in space. The material modi cations and total sputtering yield of ejected particles are investigated. While at low-energy impacts, ejection of individual silver atoms is the main emission channel, the ejection of large clusters from the corona of the created crater dominates for the high-energy impacts.

Molecular dynamics simulations of the Ca2+-pump: a structural analysis

We report large scale molecular dynamics computer simulations, ∼100 ns, of the ion pump Ca(2+)-ATPase immersed in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayer. The structure simulated here, E1, one of the several conformations resolved using X-ray diffraction techniques, hosts two Ca(2+)-ions in the hydrophobic domain. Our results indicate that protonated residues lead to stronger ion-residue interactions, supporting previous conclusions regarding the sensitivity of the Ca(2+) behaviour to the protonated state of the amino acid binding sites. We also investigate how the protein perturbs the bilayer structure. We show that the POPC bilayer is ∼12% thinner than the pure bilayer, near the protein surface. This perturbation decays exponentially with the distance from the protein with a characteristic decay length of 0.8 nm. We find that the projected area per lipid also decreases near the protein. Using an analytical model we show that this change in the area is only apparent and it can be explained by considering the local curvature of the membrane. Our results indicate that the real area per lipid near the protein is not significantly modified with respect to the pure bilayer result. Further our results indicate that the local deformation of the membrane around the protein might be compatible with the enhanced protein activity observed in experiments over a narrow range of membrane thicknesses.

Improved hydrocarbon potentials for sputtering studies

We refit the REBO hydrocarbon potentials by reparameterizing the bond lengths and energies of hydrocarbons with recent data, using systematic addition of the parameters of all hydrocarbons CxDy with x equal or less than four. In addition we also refit the short-distance potentials to reproduce a repulsive ZBL term. To test the improved potential, we performed large scale molecular dynamics calculations of amorphous deuterated carbon bombarded by deuterium, and compare our results with data obtained using the REBO potential as well as with recent experiments.

Molecular dynamics prediction of thermal conductivity of GaN films and wires at realistic length scales

Recent molecular dynamics simulation methods have enabled thermal conductivity of bulk materials to be estimated. In these simulations, periodic boundary conditions are used to extend the system dimensions to the thermodynamic limit. Such a strategy cannot be used for nanostructures with finite dimensions which are typically much larger than it is possible to simulate directly. To bridge the length scales between the simulated and the actual nanostructures, we perform large-scale molecular dynamics calculations of thermal conductivities at different system dimensions to examine a recently developed conductivity vs. dimension scaling theory for both film and wire configurations. We demonstrate that by an appropriate application of the scaling law, reliable interpolations can be used to accurately predict thermal conductivity of films and wires as a function of film thickness or wire radius at realistic length scales from molecular dynamics simulations. We apply this method to predict thermal conductivities for GaN wurtzite nanostructures.

Network Topology and the Fragility of Tetrahedral Glass-Forming Liquids

Network-forming liquids comprising tetrahedral motifs are investigated by large-scale molecular dynamics computer simulations within the framework of an ionic interaction model. The network topology is controlled by varying the anion polarizability, which governs the intertetrahedral bond angle, for different system densities. A coupling is found between the growth in magnitude and range of extended range oscillations and the appearance of ordering on an intermediate length scale. The interrelation between the system fragility and the structural arrangements on these two different length scales shows the trends that are observed for glass-forming systems. In particular, the fragility increases with number of edge-sharing motifs.

Computational challenges of large-scale, long-time, first-principles molecular dynamics

Plane wave density functional calculations have traditionally been able to use the largest available supercomputing resources. We analyze the scalability of modern projector-augmented wave implementations to identify the challenges in performing molecular dynamics calculations of large systems containing many thousands of electrons. Benchmark calculations on the Cray XT4 demonstrate that global linear-algebra operations are the primary reason for limited parallel scalability. Plane-wave related operations can be made sufficiently scalable. Improving parallel linear-algebra performance is an essential step to reaching longer timescales in future large-scale molecular dynamics calculations.

A molecular dynamics study of free energy of micelle formation for sodium dodecyl sulfate in water and its size distribution

Free energy of micelle formation has been evaluated for spherical sodium dodecyl sulfate (SDS) in water by a thermodynamic integration method combined with a series of large-scale molecular dynamics calculations following the chemical species model. In particular, free energy change delta mu(n+1)0 with respect to the addition of one surfactant molecule to the spherical micelle of size n was obtained as a function of n. The free energy profile showed a minimum followed by a maximum, which corresponds to a peak in the size distribution. The calculated peak size n = 57 near its critical micelle concentration is in good agreement with the experimental averaged aggregation number n = 55-75 of the SDS micelle. The distribution showed a rather sharp peak, indicating that the size is almost a monodisperse one. The size is likely to be insensitive to the total concentration of the surfactant.

Atomic scale modelling of the primary damage state of irradiated fcc and bcc nanocrystalline metals

Large scale molecular dynamics computer simulations of the irradiation of nanocrystalline fcc Ni and bcc Fe show differences in defect production, with different vacancy cluster structures forming during displacement cascades. Differences in defect production also exist in comparison to their single crystal counterparts. The primary damage state after irradiation is discussed in terms of defect production as a consequence of the grain boundaries present and of the crystalline structure in order to describe the effect of these microstructural parameters.

Structure and transport properties of amorphous aluminium silicates: Computer simulation studies

The structure and transport properties of SiO 2–Al 2O 3 melts containing 13 mol% and 47 mol% Al 2O 3 are investigated by means of large scale molecular dynamics computer simulations. The interactions between the atoms are modelled by a pair potential which is a modified version of the one proposed by Kramer et al. [Kramer, G.J., de Man, A.J.M., van Santen, R.A., 1991. Zeolites versus aluminosilicate clusters: the validity of a local description. J. Am. Chem. Soc. 64, 6435–6441]. Fully equilibrated melts in the temperature range 6000 K ≥ T > 2000 K are considered as well as glass configurations that were obtained by a rapid quench from the lowest melt temperatures. Each system is simulated at two different densities in order to study the effect of pressure on structural and dynamic properties. We find that the Al atoms are, like the Si atoms, mainly four-fold coordinated by oxygen. However, the packing of the AlO 4 tetrahedra is very different from that of the SiO 4 tetrahedra, which is reflected by the presence of triclusters (O atoms surrounded by three cations) and edge-sharing AlO 4 tetrahedra. On larger length scales, a micro-segregation occurs, resulting in an Al-rich network percolating through the Si–O network. This is reflected in a prepeak of concentration–concentration structure factors around 0.5 Å − 1 (both in the system with 47 mol% and 13 mol% Al 2O 3!). We also address the interplay between structure and mass transport. To this end, the behavior of the selfdiffusion constants for the different compositions and densities is studied.

Spontaneity in the patellamide biosynthetic pathway

Post-translationally modified ribosomal peptides are unusual natural products and many have potent biological activity. The biosynthetic processes involved in their formation have been delineated for some, but the patellamides represent a unique group of these metabolites with a combination of a macrocycle, small heterocycles and d-stereocentres. The genes encoding for the patellamides show very low homology to known biosynthetic genes and there appear to be no explicit genes for the macrocyclisation and epimerisation steps. Using a combination of literature data and large-scale molecular dynamics calculations with explicit solvent, we propose that the macrocyclisation and epimerisation steps are spontaneous and interdependent and a feature of the structure of the linear peptide. Our study suggests the steps in the biosynthetic route are heterocyclisation, macrocyclisation, followed by epimerisation and finally dehydrogenation. This study is presented as testable hypothesis based on literature and theoretical data to be verified by future detailed experimental investigations.

Structure and diffusion in amorphous aluminum silicate: a molecular dynamics computer simulation.

The amorphous aluminum silicate (Al2O3)2(SiO2) [AS2] is investigated by means of large scale molecular dynamics computer simulations. We consider fully equilibrated melts in the temperature range 6100 K> or =T> or =2300 K as well as glass configurations that were obtained from cooling runs from T=2300 to 300 K with a cooling rate of about 10(12) K/s. Already at temperatures as high as 4000 K, most of the Al and Si atoms are fourfold coordinated by oxygen atoms. Thus, the structure of AS2 is that of a disordered tetrahedral network. The packing of AlO4 tetrahedra is very different from that of SiO4 tetrahedra in that Al is involved with a relatively high probability in small-membered rings and in triclusters in which an O atom is surrounded by four cations. We find as typical configurations two-membered rings with two Al atoms in which the shared O atoms form a tricluster. On larger length scales, the system shows a microphase separation in which the Al-rich network structure percolates through the SiO2 network. The latter structure gives rise to a prepeak in the static structure factor at a wave number q=0.5 A(-1). A comparison of experimental x-ray data with the results from the simulation shows good agreement for the structure function. The diffusion dynamics in AS2 is found to be much faster than in SiO2. We show that the self-diffusion constants for O and Al are very similar and that they are by a factor of 2-3 larger than the one for Si.

Stacking fault tetrahedra formation in the neighbourhood of grain boundaries

Large scale molecular dynamics computer simulations are performed to study the role of the grain boundary (GB) during the cascade evolution in irradiated nanocrystalline Ni. At all primary knock-on atom (PKA) energies in cascades near GBs, the damage produced after cooling down is vacancy dominated. Truncated stacking fault tetrahedra (TSFTs) are easily formed at 10 keV and higher PKA energies. At the higher energies a complex partial dislocation network forms, consisting of TSFTs. The GB acts as an interstitial sink without undergoing major structural changes.

Static and dynamic properties of a viscous silica melt

We present the results of a large scale molecular dynamics computer simulation in which we investigated the static and dynamic properties of a silica melt in the temperature range in which the viscosity of the system changes from ${O(10}^{\ensuremath{-}2})$ P to ${O(10}^{2})$ P. We show that even at temperatures as high as 4000 K the structure of this system is very similar to the random tetrahedral network found in silica at lower temperatures. The temperature dependence of the concentration of the defects in this network shows an Arrhenius law. From the partial structure factors we calculate the neutron scattering function and find that it agrees very well with experimental neutron scattering data. At low temperatures the temperature dependence of the diffusion constants D shows an Arrhenius law with activation energies which are in very good agreement with the experimental values. With increasing temperature we find that this dependence shows a crossover to one which can be described well by a power law, $D\ensuremath{\propto}(T\ensuremath{-}{T}_{c}{)}^{\ensuremath{\gamma}}$. The critical temperature ${T}_{c}$ is 3330 K and the exponent $\ensuremath{\gamma}$ is close to 2.1. Since we find a similar crossover in the viscosity, we have evidence that the relaxation dynamics of the system changes from a flowlike motion of the particles, as described by the ideal version of mode-coupling theory, to a hoppinglike motion. We show that such a change of the transport mechanism is also observed in the product of the diffusion constant and the lifetime of a Si-O bond or the space and time dependence of the van Hove correlation functions.