Classical Molecular Dynamics Method Research Articles

Investigation of melting at the uranium γ phase by quantum and classical molecular dynamics methods

Melting at the high-temperature uranium γ phase at pressures up to 0.8 TPa and temperatures up to 2 × 104 K is studied using quantum and classical molecular dynamics methods. The position of the equilibrium melting curve is estimated based on quantum calculations according to the Lindemann criterion. An interatomic-interaction potential is developed for classical molecular dynamics simulation of the properties of uranium in the γ phase and liquid state. The melting curve is calculated using the modified Z method. The curve is in agreement with the known experimental data at pressures below 0.1 TPa and the found estimate. The calculated melting curve is also compared with the Simon–Glatzel equation theoretical model.

Gas Solubility and Rheological Behavior of Natural Deep Eutectic Solvents (NADES) via Combined Experimental and Molecular Simulation Techniques

AbstractA potential of natural deep eutectic solvent (NADES) produced with the mixture of choline chloride with lactic acid, malic acid, citric acid and fructose is studied in this work. Experimental techniques are used to collect thermophysical property data including water content, thermal strength, density and gas solubility of CO2 and N2 data at pressures up to 50 bars. Detailed rheological measurements and various models have been studied to describe the dynamic flow behavior. Moreover, a density functional theory (DFT) and classical molecular dynamics (MD) methods have been used for investigating the physicochemical properties, structuring, dynamics and interfacial behavior of the studied NADES from the nanoscopic point of view to infer its viability for extensive usage. The rheological experimental results show usual shear‐thinning effect in which the η is decreasing with shear rate at all temperatures. A trend of studied NADES viscosity profiles were found as very similar to that of common ionic liquids that were previously, where the viscosities of all studied NADES decreased with increasing temperature. DFT simulations yielded with an accurate quantification of short‐range interaction but liquid state is also characterized by middle and long‐range interaction together with volumetric effects. Molecular orientations were quantified by radial distribution functions and the developed interactions are topologically characterized.

A molecular dynamics study of nuclear quantum effect on diffusivity of hydrogen molecule.

In this paper, the nuclear quantum effect of the hydrogen molecule on its diffusivity was analyzed using the molecular dynamics (MD) method. The centroid MD (CMD) method was applied to reproduce the time evolution of the molecules. The diffusion coefficient of hydrogen was calculated using the Green-Kubo method over a wide temperature region, and the temperature dependence of the quantum effect of the hydrogen molecule on its diffusivity was addressed. The calculated results were compared with classical MD results based on the principle of corresponding state (PCS). It was confirmed that the difference in the diffusion coefficient calculated in the CMD and classical MD methods was small, and the PCS appears to be satisfied on the temperature dependence of the diffusion coefficient, even though the quantum effect of the hydrogen molecules was taken into account. It was clarified that this result did not suggest that the quantum effect on the diffusivity of the hydrogen molecule was small but that the two changes in the intermolecular interaction of hydrogen due to the quantum effect offset each other. Moreover, it was found that this tendency was related to the temperature dependence of the ratio of the kinetic energy of the quantum fluctuational motion to the classical kinetic energy.

Delivery of Cisplatin Anti-Cancer Drug from Carbon, Boron Nitride, and Silicon Carbide Nanotubes Forced by Ag-Nanowire: A Comprehensive Molecular Dynamics Study.

In this work, liberation of cisplatin molecules from interior of a nanotube due to entrance of an Ag-nanowire inside it was simulated by classical molecular dynamics method. The aim of this simulation was investigation on the effects of diameter, chirality, and composition of the nanotube, as well as the influence of temperature on this process. For this purpose, single walled carbon, boron nitride, and silicon carbide nanotube were considered. In order for a more concise comparison of the results, a new parameter namely efficiency of drug release, was introduced. The results demonstrated that the efficiency of drug release is sensitive to its adsorption on outer surface of the nanotube. Moreover, this efficiency is also sensitive to the nanotube composition and its diameter. For the effect of nanotube composition, the results indicated that silicon carbide nanotube has the least efficiency for drug release, due to its strong drug-nanotube. Also, the most important acting forces on drug delivery are van der Waals interactions. Finally, the kinetic of drug release is fast and is not related to the structural parameters of the nanotube and temperature, significantly.

Insights into Glycol Ether-Alkanol Mixtures from a Combined Experimental and Theoretical Approach.

The binary liquid mixtures of glycol ethers (glymes) + 1-alkanol were characterized from the microscopic and macroscopic viewpoints through a combined experimental and theoretical study. Structuring, dynamics, and intermolecular forces were determined using density functional theory and classical molecular dynamics methods. The macroscopic behavior was studied though the measurement of relevant physicochemical properties and Raman IR studies. The changes in intermolecular forces with mixture composition, temperature, and the effects from the types of glymes as well as 1-alkanols were considered. Hydrogen bonding in the mixed fluids, its changes upon mixing, and mixture composition showed a large effect on fluids' structure and determined most of the fluids' properties together with the presence of hydrophobic domains from long 1-alkanols.

Elucidating the Properties of Graphene-Deep Eutectic Solvents Interface.

The properties of five deep eutectic solvents prepared based on the selection of choline chloride ionic liquid as hydrogen bond acceptor, which are mixed with several hydrogen bond donors with selected molecular features, were studied theoretically at graphene interfaces via both density functional theory and classical molecular dynamics methods. Molecular structuring at the interfaces, angular orientation, densification, and dynamic properties were analyzed upon adsorption on the graphene surface and when the deep eutectic solvents were confined between two graphene sheets and analyzed in terms of the role of the type of hydrogen bond donor for each solvent. Likewise, the behavior of deep eutectic solvent nanodroplets on graphene was simulated leading to the calculation of contact angles and nanowetting with further studies considering the effect of an external electric field on nanodroplet properties.

Atomistic simulation of the segregation of alloying elements close to radiation-induced defects in irradiated Fe–Cr–Ni BCC alloys

Ferritic-martensitic steels alloyed with Cr and Ni are promising structural materials for the nuclear and thermonuclear power industry. Under the influence of neutron irradiation degradation of the plastic properties of these materials takes place as a result of the generation of extended defects such as dislocation loops, and the formation of new phases (precipitates). In this work the atomistic computer simulation of thermodynamic processes of the precipitation of alloying elements is carried out using the newest model of ternary Fe–Ni–Cr bcc (body-centered cubic) alloys and the Metropolis Monte Carlo method in combination with the method of classical Molecular Dynamics. The composition and microstructure of Cr–Ni clusters formed in defect-free alloys and alloys containing dislocation loops, depending on the temperature and concentrations of Ni and Cr, are studied. An increase in the Ni solubility limit in the presence of dislocation loops by 100–200 K, depending on the Ni concentration, is detected. The synergetic effect of Ni and Cr segregation near dislocation loops in ternary alloy is established: the presence of Ni weakens Cr segregation, whereas Cr can either attenuate or amplify Ni segregation depending on the concentration of Ni in the alloy, the temperature and the type (Burgers vector) of loop. In general, in ternary Fe–Cr–Ni alloys, the total segregation effect is less pronounced than in binary Fe–Ni and Fe–Cr alloys.

Generation of phonon density of states and thermal scattering law using ab initio molecular dynamics

The operation and safety of thermal nuclear reactors is dependent on the ability to accurately predict the thermal neutron spectrum; a distribution which is correlated to the inelastic thermal neutron scattering cross-section of the neutron moderator. The inelastic thermal neutron scattering law, S(α,β), of a moderator is a fundamental property of the material describing the permitted vibrational excitations of the atoms, i.e. phonons, and may be calculated using atomistic methods. The current state-of-the-art ab initio lattice dynamics (AILD) methods have been used to calculate phonon density of states (DOS) at 0 K for use in the generation of S(α,β) under reactor conditions. Modern computational power, however, has made accessible ab initio molecular dynamics (AIMD) methods. The AIMD technique captures temperature effects and permits the calculation of the phonon DOS from first principles. This is in contrast to AILD, where temperature effects are lacking, and classical molecular dynamics methods that use semi-empirical force fields. The aim of this work is to demonstrate the use of AIMD in the generation of the phonon DOS for beryllium as an exemplar moderating material. The phonon DOS was computed from AIMD simulations at 300 K and compared to AILD. Subsequently, S(α,β) and the inelastic scattering cross-section were generated using the NJOY package for both methods. The predicted phonon DOS and inelastic scattering cross-section for the AIMD method were found to be consistent with those predicted using AILD.

Molecular dynamics modelling of sodium and calcium metaphosphate glasses for biomaterial applications

Many phosphate-based glasses (PBGs) for biomaterial applications have been developed from the Na2O-CaO-P2O5 system. The common base compositions for PBGs are (55-x)Na2O-xCaO-45P2O5 and 20Na2O.30CaO.50P2O5, where the later corresponds to a metaphosphate, and there is a wealth of experimental data for 50Na2O.50P2O5, 50CaO.50P2O5 and 20Na2O.30CaO.50P2O5 metaphosphate glasses. A classical molecular dynamics (MD) method has been used to model Na2O-CaO-P2O5 glass structures, and the results have been closely compared with experimental data for the same glasses. The MD models show the phosphate network to be dominated by Q2 units, as expected, and to have short range order parameters that are in good agreement with neutron and X-ray di?raction results. Typical coordination numbers of Na and Ca are 5 and 6, respectively. The modifer cation distributions have been examined in detail through the correlation functions TMM(r), with M=Na and/or Ca. The TMM(r) functions show the expected dependence of peak position on modifer cation size, and peak height on modifer cation concentration. The numbers of M-M nearest neighbours are in agreement with a statistical model, in which modifer cations are bonded to nonbridging oxygens, Onb, and M(Onb)N polyhedra are predominantly connected to each other by corner-sharing.

Effect of sharp maximum in ion diffusivity for liquid xenon

Ion diffusion in a liquid usually could be treated as a movement of an ion cluster in a viscous media. For small ions this leads to a special feature: diffusion coefficient is either independent of the ion size or increases with it. We find a different behavior for small ions in liquid xenon. Calculation of the dependence of an ion diffusion coefficient in liquid xenon on the ion size is carried out. Classical molecular dynamics method is applied. Calculated dependence of the ion diffusion coefficient on its radius has sharp maximums at the ion radiuses 1.75 and 2 Å. Every maximum is placed between two regions with different stable ion cluster configurations. This leads to the instability of these configurations in a small region between them. Consequently ion with radius near 1.75 or 2 Å could jump from one configuration to another. This increases the speed of the diffusion. A simple qualitative model for this effect is suggested. The decomposition of the ion movement into continuous and jump diffusion shows that continuous part of the diffusion is the same as for the ion cluster in the stable region.

Structure of liquid chlorobenzene in the temperature range 293-363 K

The classical molecular dynamics method is used to simulate the structure of liquid chlorobenzene in the temperature range 293-363 K. Theradial angular distribution functions for the distances between the benzene molecular planes and the angle between them; the radial distribution functions for the distances between chlorine atoms; self-diffusion coefficients, local dipole moments, and permittivities are calculated. In the entire temperature range molecules are joined into agglomerates due to contacts between chlorine atoms (halogen aggregation) and to the specific interactions of benzene rings, which causes mainly parallel and perpendicular orientations of the rings in the first coordination sphere. The molecules in the agglomerates are mostly organized in the 1D motif: chains of chlorine atoms and stacks of benzene rings. With increasing temperature, the agglomerate structure is reorganized, with the most visible changes occurring in temperature ranges 293-298 K, 313-323 K, and 343-353 K.

Mechanical properties of graphene grain boundary and hexagonal boron nitride lateral heterostructure with controlled domain size

In this paper, the mechanical properties of in-plane heterostructure with alternating stripes of graphene grain boundary (GB) and hexagonal boron nitride (h-BN) are investigated using classical Molecular Dynamics method. The graphene GB contains an array of pentagon-heptagon (5–7) defects, and has good interfacial continuity with the lateral BN domain. By studying the dynamic failure process of heterostructure with varying hybridization intervals and GB tilt angles, two different local failure types are noticed. Coupled effects of h-BN hybridization and GB tilt angle on the tensile strength of heterostructure are revealed. For heterostructure with graphene GBs of evenly spaced 5–7 defects, the tensile strength is insensitive to the h-BN hybridization and increases anomalously with the defect density. For heterostructure with graphene GB of unevenly spaced 5–7 defects, lateral h-BN hybridization enhanced the tensile strength of the heterostructure. Such strength enhancement effect is contributed to the bond length mismatch between graphene and h-BN, and deteriorates with the increase of hybridization interval. Our results give helpful insight into the strength characteristics of hybrid two-dimensional nanomaterials based electronic and optical devices.

Acid activation mechanism of the influenza A M2 proton channel

The homotetrameric influenza A M2 channel (AM2) is an acid-activated proton channel responsible for the acidification of the influenza virus interior, an important step in the viral lifecycle. Four histidine residues (His37) in the center of the channel act as a pH sensor and proton selectivity filter. Despite intense study, the pH-dependent activation mechanism of the AM2 channel has to date not been completely understood at a molecular level. Herein we have used multiscale computer simulations to characterize (with explicit proton transport free energy profiles and their associated calculated conductances) the activation mechanism of AM2. All proton transfer steps involved in proton diffusion through the channel, including the protonation/deprotonation of His37, are explicitly considered using classical, quantum, and reactive molecular dynamics methods. The asymmetry of the proton transport free energy profile under high-pH conditions qualitatively explains the rectification behavior of AM2 (i.e., why the inward proton flux is allowed when the pH is low in viral exterior and high in viral interior, but outward proton flux is prohibited when the pH gradient is reversed). Also, in agreement with electrophysiological results, our simulations indicate that the C-terminal amphipathic helix does not significantly change the proton conduction mechanism in the AM2 transmembrane domain; the four transmembrane helices flanking the channel lumen alone seem to determine the proton conduction mechanism.

Molecular Dynamics Study on Proton Transport in Supported Nafion Ionomer Thin Films on Lennard-Jones Walls

The catalyst layer, one of the components of membrane electrode assembly in polymer electrolyte fuel cells, was modeled by molecular dynamics methods, and proton transport in ionomer thin films was simulated to elucidate the effect of surface wetting interaction on the ionomer thin film morphology and proton transport property. Ionomer thin film properties are considered to be affected by the surface property of supported carbon due to their nano-scale thickness (4-10 nm thick). One of the surface properties is surface wetting interaction basically attributed to the physical or chemical property of surfaces.In this study, modeled Nafion thin films with 4 nm and 10 nm thick were generated on the two ideal LJ smooth surfaces which have different strength of interactions to focus on the effect of the surface wetting interaction on the ionomer thin film morphology and proton transport. Protons exist as hydronium ions in ionomer thin films for chemical stability and are transported by the two transport mechanisms which are the vehicle mechanism (just move as hydronium ions) and the Grotthuss mechanism called proton hopping. It is common that proton transport model is restricted to only the vehicle mechanism when using classical molecular dynamics method, however, our proton transport model includes the Grotthuss mechanism by using aTS-EVB method (anharmonic two-state empirical valence bond method) in order to make proton transport model more reproducible.From the analysis in the ionomer thin films with 4 nm thick, surface wetting interaction was found to affect the orientation of sulfonic group near the surface. The orientation is well-ordered on the higher hydrophobic surface, and the sulfonic groups point to the gas phase direction, while it is randomly distributed on the lower hydrophobic surface, which make differences in the water cluster connectivity and size in ionomer thin films between the two surfaces. Proton transport property was evaluated by the self-diffusion coefficient. The proton self-diffusion coefficient in ionomer thin films was indicated to be improved on higher hydrophobic surface probably because higher hydrophobic surface makes ideal water cluster structures for proton transport in ionomer thin films.As compared to the ionomers with the different film thickness, the proton self-diffusion coefficient in ionomer thin films on higher hydrophobic surface was indicated to decrease in the increase of the film thickness, while that on lower hydrophobic surface was indicated to increase slightly. This result is expected to come from the confinement and interface effects which can be remarkable when the thickness decrease. The ionomer morphology on higher hydrophobic surface has advantages for proton transport probably thanks to the effects as observed in the ionomer with 4 nm thick, while that on lower hydrophobic surfaces has disadvantage. Since the effects can be weaker with the increase in the film thickness, the proton self-diffusion coefficient in ionomer thin films on higher hydrophobic surface was found to decrease with the increase in the film thickness, while that on lower hydrophobic surface was found to increase slightly.

Mechanism of 1,12-Dicarba-closo-dodecaborane Mobility on Gold Substrate as a Nanocar Wheel

We studied the mobility of p-carborane on a gold surface by analyzing the potential energy surfaces (PES) and simulating the motion of p-carborane using the classical molecular dynamics (MD) method. In the first section, we calculated the PES of p-carborane molecules on a gold surface during pure translation (sliding) and pure rotation independently and then employed this PES to predict the probable motion of p-carborane. These calculations were performed in several major orientations during sliding as well as different fixed positions during rotational movements to enable us to find the p-carborane motion threshold on a gold surface. In the second section, we use classical MD in isothermal conditions to specify the regime of motion of p-carborane at different temperatures. We found that by raising the temperature, three different regimes of motion may be observed: jumps to adjacent cells, long jumps, and continuous motion. To better understand the change of motion regime of p-carborane on the gold surfac...

Properties of solvate shells and the mobility of ions, according to molecular dynamics data

The solvate shells of an ion, its velocity autocorrelation function, and diffusion coefficient D are found, and the interrelations between them are analyzed. A single ion in the system of atoms of a liquid is considered a model system. The interaction between the ion and atoms of the liquid is described by polarization potential U(r); the interaction between atoms of the liquid alone is described by the Lennard–Jones potential. A classical molecular dynamics method is used. Five solvate shells around the ion are found, and the lifetimes of atoms on each shell are calculated. It is found that the velocity autocorrelation function is of a vibrating nature. The spectrum of the autocorrelator and the frequency of cluster vibrations in a linear approximation are compared. Dependences D on parameters of potential U(r) are found. No dependence D on the ion mass is found; this is explained by solvation. The Einstein–Stokes formula and the HSK approximation are used in discussing the results. It is shown that at small radii of the ion, dependence D on parameters U(r) is described by such a model. When the ion radius is increased, the deviation from this dependence and an increase in D are observed. The results are compared to experimental mobilities of O 2 - and Ar 2 + ions in liquid argon.

Structural Evolutions of ZnS Nanoparticles in Hydrated and Bare States

Suitable optoelectronic properties and the nontoxic nature of ZnS quantum dots capacitate exciting applications for these nanomaterials especially in the field of biomedical imaging. However, the structural stability of ZnS nanoparticles has been shown to be challenging since they potentially are prone to autonomous structural evolutions in ambient conditions. Thus, it is essential to build an understanding about the structural evolution of ZnS nanoparticles, especially in aqueous environment, before implementing them for in vivo applications. In this study we compared the structure of ZnS nanoparticles relaxed in a vacuum and in water using a classical molecular dynamics method. Structural analyses showed that the previously observed three-phase structure of bare nanoparticles is not formed in the hydrated state. The bulk of hydrated nanoparticles has more crystalline structure; however, the dynamic heterogeneity in their surface relaxation makes them more polar compared to bare nanoparticles. This heter...

Structural analysis and atomic simulation of Ag/BN nanoparticle hybrids obtained by Ag ion implantation

The present paper describes fabrication of Ag/BN nanoparticle hybrids by means of Ag ion implantation into the hollow BN nanoparticles (BNNPs) with a petal-like surface. The structural transformations occurring during Ag ion implantation into BNNPs are studied by low- and high-resolution transmission electron microscopy (TEM), high angle annular dark field scanning TEM (HAADF-STEM) paired with energy-dispersive X-ray (EDX) spectroscopy mapping. The experimental results are theoretically verified in the framework of the classical molecular dynamics (MD) method. Our results have demonstrated that by changing Ag ion energy in the range of 2–20kV it is possible to selectively fabricate Ag/BNNP nanohybrids with crystalline or amorphous BNNP structures and various Ag NPs distributions over the BNNP thicknesses.

Molecular dynamics simulation of bipartite bimetallic clusters under low-energy argon ion bombardment

The evolution of bipartite bimetallic atomic clusters within 5 ps under bombardment with monoenergetic argon ions at the initial energy ranging from 1 eV to 1.4 keV has been simulated by the classical molecular dynamics method with a target obtained from Ni‒Al and Cu‒Au clusters consisting of 78 and 390 atoms, equally divided between the corresponding monometallic parts, the simulated pairs of which have different heats of intermixing. The changes in the potential energy and temperature, the sputtering yields, and the intensity of the ion-stimulated movement of atoms at the interface of the monometallic parts of clusters of both sizes have been determined as functions of the energy of the bombardment.

Strain energy analysis of screw dislocations in 4H-SiC by molecular dynamics

We simulated screw dislocations with the Burgers vector parallel to the [0001] direction in 4H-SiC by a classical molecular dynamics method. A stable structure of an extended dislocation generated by the dissociation of a screw dislocation was identified by calculating the strain energy caused by dislocation cores and stacking faults. As a result, we conclude that the most expected structure of the extended dislocation is made of partial dislocations with the Burgers vector b = 1/2c + 1/2c (c is equal to the thickness of one period in the c-axis direction of 4H-SiC) and the stacking fault that is parallel to the a-plane, and that the distance between the dislocation cores is less than about 44 Å.