Classical Molecular Dynamics Method Research Articles

Atomistic tribological investigation of ultrathin layer of carbon disulfide between diamond surfaces

Using the method of classical molecular dynamics the tribological properties are studied of one molecular layer of liquid carbon disulfide, pressed by two atomically smooth diamond surfaces. We treat the models of elastic spheres for carbon disulfide molecules and absolutely rigid diamond plates. The found time series of atomic level friction force at the contact is heterogeneous. An increase of the external normal pressure leads to the transition of the film to a solidlike state. This is manifested in a decrease of the diffusion constant, in the behavior of velocity autocorrelation function of liquid molecules and average friction force.

Solvation of Ethanol, Phenol, and o-Methoxyphenol in Dilute Aqueous Solutions under Normal and Supercritical Conditions

The structure of 2 wt % aqueous solutions of ethanol, phenol, and o-methoxyphenol (guaiacol) was modeled in NVT ensemble using the classical molecular dynamics method at densities of 0.997 and 0.133 g/cm3 corresponding to the normal (298 K, 0.1 MPa) and supercritical (673 K, 23.0 MPa) conditions. The self-diffusion coefficients were calculated for individual components in solutions; the radial distribution functions were calculated for the oxygen atoms of water molecules, oxygen atoms of hydroxyl groups, and centers of mass in phenol molecules. The possibility of clusterization of solute molecules was analyzed. The data obtained suggest heterogeneity of solutions, in which clusters of different compositions and structures can exist. Clusterization of up to seven ethanol and phenol molecules can occur under normal conditions, and dimerization was detected under SC conditions. The structural features of solutions under normal and SC conditions were compared. The difference in the formation of hydration shells of ethanol and phenols molecules was demonstrated. Stable shells of water molecules form around ethanol molecules under normal conditions. For phenols, the solvation shells are unstable, with a pronounced tendency toward clusterization of organic molecules.

Parameterization and validation of a new force field for Pt(II) complexes of 2‐(4′‐amino‐2′‐hydroxyphenyl)benzothiazole

AbstractUnderstanding the ways of interaction of a drug with a biological target is crucial in the pharmacology field. One methodology that allows the simulation of new drugs under in vitro conditions is the classical molecular dynamics (MD) method. However, MD simulations in systems containing metallodrugs are challenging due to the lack of specific parameters found in the literature. In this work, we propose and model a new possible anticancer platinum(II) complex: cis‐dichloro(2‐aminomethylpyridine)platinum(II) bonded to 2‐(4′‐amino‐2′‐hydroxyphenyl)benzothiazole (AHBT). The developed model consists of a new set of AMBER force field parameters based on density functional theory (DFT) calculations. The extensive validation of the parameter set shows that it adequately describes the structural properties of the complex. Overall, we expect this work to contribute significantly to future MD simulations of Pt(II) complexes in biological targets that are still not well explored, mainly due to the few parameters found in the literature.

Coupling Molecular Dynamics and Direct Simulation Monte Carlo using a general and high-performance code coupling library

A domain-decomposed method to simultaneously couple the classical Molecular Dynamics (MD) and Direct Simulation Monte Carlo (DSMC) methods is proposed. This approach utilises the MPI-based general coupling library, the Multiscale Universal Interface. The method provides a direct coupling strategy and utilises two OpenFOAM based solvers, mdFoam+ and dsmcFoam+, enabling scenarios where both solvers assume one discrete particle is equal to one molecule or atom. The ultimate goal of this work is to enable complex multi-scale simulations involving micro, meso and macroscopic elements, as found with problems like evaporation.Results are presented to show the fundamental capabilities of the method in terms of mass and kinetic energy conservation between simulation regions handled by the different solvers. We demonstrate the capability of the method by deploying onto a large supercomputing resource, with attention paid to the scalability for a canonical NVT ensemble (a constant number of atoms N, constant volume V and constant temperature T) of Argon atoms. The results show that the method performs as expected in terms of mass conservation and the solution is also shown to scale reasonably on a supercomputing resource, within the known performance limits of the coupled codes. The wider future of this work is also considered, with focus placed on the next steps to expand the capabilities of the methodology to allow for indirect coupling (where the coarse-graining capability of the DSMC method is used), as well as how this will then fit into a larger coupled framework to allow a complete micro-meso-macro approach to be tackled.

Decoherence-corrected Ehrenfest molecular dynamics on many electronic states.

Decoherence corrections increase the accuracy of mixed quantum-classical nonadiabatic molecular dynamics methods, but they typically require explicit knowledge of the potential energy surfaces of all occupied electronic states. This requirement renders them impractical for applications in which large numbers of electronic states are occupied. The authors recently introduced the collapse to a block (TAB) decoherence correction [M. P. Esch and B. G. Levine, J. Chem. Phys. 152, 234105 (2020)], which incorporates a state-pairwise definition of decoherence time to accurately describe dynamics on more than two electronic states. In this work, TAB is extended by introduction of a scheme for efficiently computing a small number of approximate eigenstates of the electronic Hamiltonian, eliminating the need for explicit knowledge of a large number of potential energy surfaces. This adaptation of TAB for dense manifolds of states (TAB-DMS) is systematically improvable by increasing the number of computed approximate eigenstates. Application to a series of one-dimensional model problems demonstrates that TAB-DMS can be accurate when even a very modest number of approximate eigenstates are computed (four in all models tested here). Comparison of TAB simulations to exact quantum dynamical simulations indicates that TAB is quite accurate so long as the decoherence correction is carefully parameterized.

Effect of Kerogen Maturity, Water Content for Carbon Dioxide, Methane, and Their Mixture Adsorption and Diffusion in Kerogen: A Computational Investigation.

The adsorption behavior of CO2, CH4, and CO2/CH4 mixtures in four different mature kerogens in the absence/presence of water was studied using grand canonical Monte Carlo and classical molecular dynamics methods. The results exhibit that the adsorption isotherms of single-component CO2 or CH4 in kerogen present similar trends and show type I Langmuir adsorption behavior according to the IUPAC classification; the total adsorbed amount of both gases follows the order of type II-A < type II-B < type II-C < type II-D kerogen under the same conditions. The changing behavior of isosteric heat decreases first and then increases, which can explain the heterogeneous characteristic of the kerogen pore surface. The Coulombic and van der Waals interactions between CO2 and kerogens play an important role on adsorption, while for CH4 adsorption, the electrostatic effect is very small, even negligible. The N-, S-, and O-containing groups in kerogen have more remarkable influence on adsorption of CO2 than CH4 because of their strong adsorption energy, therefore notably improving the selectivity of CO2 over CH4 and following the order of type II-A > type II-B > type II-C > type II-D, which is beneficial to carbon capture and storage. Both pressure and temperature have an obvious impact on gas molecule diffusion, and low pressure and high temperature correspond to a large diffusion coefficient. In addition, preabsorbed water has a negative effect on the adsorption of CO2/CH4, and for the same amount of water molecules, the effect follows the order of type II-A > type II-B > type II-C > type II-D kerogens. The binding energy of water-kerogen is stronger than that of pure CH4 or CO2-kerogen. The selectivity of CO2 over CH4 on kerogen increases with an increasing water content.

Thermodynamics and the structure of clusters in the dense Au vapor from molecular dynamics simulation.

Clusters of atoms in dense gold vapor are studied via atomistic simulation with the classical molecular dynamics method. For this purpose, we develop a new embedded atom model potential applicable to the lightest gold clusters and to the bulk gold. Simulation provides the equilibrium vapor phases at several subcritical temperatures, in which the clusters comprising up to 26 atoms are detected and analyzed. The cluster size distributions are found to match both the two-parameter model and the classical nucleation theory with the Tolman correction. For the gold liquid-vapor interface, the ratio of the Tolman length to the radius of a molecular cell in the liquid amounts to ∼0.16, almost exactly the value at which both models are identical. It is demonstrated that the lightest clusters have the chain-like structure, which is close to the freely jointed chain. Thus, the smallest clusters can be treated as the quasi-fractals with the fractal dimensionality close to two. Our analysis indicates that the cluster structural transition from the solid-like to chain-like geometry occurs in a wide temperature range around 2500 K.

Molecular dynamics studies on spark plasma sintering of Ge–Si based thermoelectric material

The development of new fabrication technologies for Ge–Si thermoelectric materials requires a corresponding theoretical description of physical processes lying behind the synthesis. In the present paper, we investigated the interdiffusion of Si and Ge atoms at the Ge/Si interface, which takes place during spark plasma sintering of Ge and Si powders for fabrication of thermoelectric bulk. The calculation was performed using numerical simulation based on the classical molecular dynamics method. The diffusion coefficients of Si in Ge and vice versa were found at sintering temperatures of 900 K–1300 K and an external pressure of 7 MPa. The calculation results were used to analyze the experimental data derived from the measurements of Ge and Si profiles at the interface of thin Ge/Si plates subjected to spark plasma sintering at the temperature of 1160 K (887 °C). The comparison of measured and calculated diffusion profiles has shown good agreement with one another.

Evolution of the Ni-Al Janus-like clusters under the impacts of low-energy Ar and Ar13 projectiles

The evolution of free 390-atom Janus-like Ni-Al clusters along 100 and 500 ps under impacts of up to 1.0 keV Ar and Ar13 projectiles is simulated by the classical molecular dynamics method. The initial metastable Janus-like clusters have two mono-component parts, equal in number of atoms, with a small spatial overlap. After an impact of the projectiles and rapid expansions accompanied by sputtering at a high-temperature spike for less than 0.5 ps, where critically different kinetics are found in the cases of Ar1 and Ar13 projectiles, the resulting Ni-Al clusters gradually evolve due to exothermic mixing of the components and the tendency of surface segregation of Al atoms. The surface enrichment by Al atoms after 500 ps is clearly seen in the case of Ar1 impacts whereas at Ar13 impacts with the energies above 100 eV this tendency is masked by intense sputtering, which includes both collisional and long-term thermal contributions, with a large preferential yield of Al atoms.

Linking tracks in mica crystals with phase transitions in a bistable lattice

Since the middle of the last century, scientific research has been conducted to explain the nature of the tracks visible to the naked eye in mica muscovite crystals. In the present work, an attempt to link the appearance of tracks with a phase transition in a bistable medium is made using classical molecular dynamics method. For this purpose, a two-dimensional triangular lattice simulating one row of potassium atoms in mica is considered. Interactions between atoms are described via pairwise Morse potential and a local potential, whose minima create a hexagonal lattice. In order to create a bistability in the system, a mismatch between the equilibrium distance of the triangular lattice and the period of the local potential is artificially introduced. The phase transitions arising from a monotonic increase or decrease of the depth of the local potential are described. It is revealed that at lower temperatures the domains of different phases can coexist, but at higher temperatures the domain with lower potential energy grows with heat release by reducing the high energy domain. It is speculated that the considered model, which provides the possibility of coexistence of two different phases, can be used to explain at qualitative level the nature of dark tracks visible with the naked eye in transparent crystals of mica muscovite.

A map between excitation magnitude and critical stable temperature for screwing oscillators built on double-walled nanotubes

Abstract The influence of excitation amplitude and temperature on oscillation behavior of a novel oscillator is investigated via the classic molecular dynamics (MD) method. The oscillator is built on carbon@MoS2 heterogeneous nanotubes (CNT@MST) and has dual-signal screwing output. A map between the excitation magnitude and the critical stable temperature is generated to show the maximum service temperature at which the inner tube can perform a stable screwing oscillation under different pull-rotation excitations. The results indicate that, under the same pull-rotation excitation, the CNT@MST screwing oscillators exhibit lower energy dissipation, higher axial oscillation frequency and higher stable temperature than those from the traditional CNT@CNT screwing oscillators with the same inner tube.

Thermal Conductivity of Alkali Metal Chlorides: Calculation with Molecular Dynamics Method

The classical molecular dynamics method was used to calculate the thermal conductivity of molten salts MCl (M = Li, Na, K, Rb, Cs) in the temperature range of two hundred degrees above the melting temperatures. The simulated system had 4000 nonequivalent ions (2000 metal and chlorine ions each) with periodic boundary conditions. The Born–Mayer potential with the Coulomb term was used in the simulation. It is shown that the thermal conductivity of alkali metal chlorides decreases with an increase in the cation number in line Li+ → Na+ → K+ → Rb+ → Cs+. Moreover, the thermal conductivity for all melts weakly depends on temperature.

Reverse osmotic characteristics and mechanism of hydrogenated porous graphene

Graphene-based materials have aroused great interest for their potential applications in water desalination and purification membranes attributed to their ultrathin thickness, high mechanical strength, and anti-foiling properties. Reverse osmosis (RO) technology is currently the most progressive, energy-saving and efficient separation technology by membranes, therefore the new materials with high strength, strong pollution resistance and excellent performance are urgently needed. The ability of porous graphene to serve as a kind of novel advanced RO membrane is due to two major potential strengths of this atomically thin two-dimensional material, i.e., ultrahigh permeability and super selectivity. Thus, the reverse osmotic properties of the porous graphene membranes should be further investigated theoretically. In this paper, classical molecular dynamics method is used to investigate the reverse osmosis characteristics of brine in hydrogenated porous graphene reverse osmosis membrane. The results show that the water permeation rate increases with the driving force, pore size and temperature increasing, for the pore diameter larger than the hydration radius. The ion rejection rate decreases with the driving force and temperature increasing. Interestingly, as the porous graphene moves in the tangential direction to perform a shearing process, the interception rate of the salt ions can be effectively improved and the concentration difference polarization phenomenon can be reduced with the tangential velocity increasing, although the water flux decreases slightly. The influence mechanism of each parameter on permeability and on water flux are explored by analyzing the hydrogen bond distribution, the ionic hydration in feed solution, and the energy barrier of the water molecules in penetrating process. In order to further evaluate the effects of various parameter changes on the benefits of reverse osmosis membranes, both the selectivity and permeability are calculated to evaluate the tradeoff between permeability and selectivity, indicating that the increase of the pore diameter can obtain both high permeability and selectivity under the shearing circumstance of the membrane. The research results in this paper will provide a theoretical understanding of porous graphene-based desalination membrane and also may be helpful in designing the shearing graphene-based water filtration devices.

Temperature-dependent negative Poisson’s ratio of monolayer graphene: Prediction from molecular dynamics simulations

Abstract A temperature-dependent intrinsic property of monolayer graphene, the negative Poisson’s ratio (NPR), is investigated in the present study. The classical molecular dynamics (MD) method is employed and the Erhart-Albe hybrid potential, i.e. the combination of the reactive empirical bond order (REBO) and the Tersoff potentials, is used for the graphene sheet in the numerical simulation. In the simulation process, the graphene sheet is assumed to be free standing with in-plane periodical boundary condition and under an ambient temperature up to 1000 K. Our study shows that the graphene NPR is decreased with the increase of temperature. Besides, we also perform the simulation of the graphene negative temperature expansion coefficient (NTEC) as an indirect validation of the present MD model. The characteristics of the nonlinear variations for both the NPR and the NTEC of a pristine graphene sheet are investigated. Our MD results at low temperature (0.1 K) further prove the intrinsic and anisotropic property of NPR for graphene.

Computational Study of Lithium Intercalation in Silicene Channels on a Carbon Substrate after Nuclear Transmutation Doping

Silicene is considered to be the most promising anode material for lithium-ion batteries. In this work, we show that transmutation doping makes silicene substantially more suitable for use as an anode material. Pristine and modified bilayer silicene was simulated on a graphite substrate using the classical molecular dynamics method. The parameters of Morse potentials for alloying elements were determined using quantum mechanical calculations. The main advantage of modified silicene is its low deformability during lithium intercalation and its possibility of obtaining a significantly higher battery charge capacity. Horizontal and vertical profiles of the density of lithium as well as distributions of the most significant stresses in the walls of the channels were calculated both in undoped and doped systems with different gaps in silicene channels. The energies of lithium adsorption on silicene, including phosphorus-doped silicene, were determined. High values of the self-diffusion coefficient of lithium atoms in the silicene channels were obtained, which ensured a high cycling rate. The calculations showed that such doping increased the normal stress on the walls of the channel filled with lithium to 67% but did not provoke a loss of mechanical strength. In addition, doping achieved a greater battery capacity and higher charging/discharging rates.

Theoretical Insights into CO2 Adsorption by MoS2 Nanomaterials

The properties of MoS2-based nanomaterials regarding gaseous CO2 are studied using a theoretical approach considering quantum chemistry and classical molecular dynamics methods. Geometries for one-dimensional (nanotubes) and two-dimensional (nanosheets) materials were explored, as well as cylindrical nanopores. A large trend of CO2 molecules to be adsorbed at nanomaterial interfaces was inferred as quantified by interaction energies. Adsorption layers developed are on the studied surfaces, and fast confinement in the studied cylindrical geometries was inferred. Diffusion through cylindrical pores was shown to be largely dependent on pore diameters, with small pores hindering diffusion, whereas the increase of pore sizes allows a fast diffusion through well-defined diffusion channels. The reported results provide a detailed picture of the nanoscopic mechanisms of CO2–MoS2 interactions, showing the promising properties of these nanomaterials for CO2-capturing purposes.

Microwave heating and non-thermal effects of sodium chloride aqueous solution

ABSTRACTThe dielectric thermal and non-thermal properties of sodium chloride aqueous solution under the microwave region have been estimated. The dielectric properties, hydrogen bonding, transport properties, energy distribution and local structure have been evaluated by classical molecular dynamics method. In the process of microwave energy distribution, the direct coupling of rotational motion, vibration and redirection is revealed. Microwave energy is converted into kinetic energy and interaction energy between two molecules. A mechanism for exploring the effects of microwaves on the non-thermal effects of brine systems over a longer simulation time and a wider microwave range is proposed. The increase in field intensity is usually accompanied by local damage to the water structure near the hydrated ions. More specifically, above the field threshold, the residence time of water molecules near the ions significantly decreases.HighlightsMicrowave energy is transferred to the kinetic energy and the energy between the molecules.The increase in field intensity is usually accompanied by local damage to the water structure near the hydrated ions.The larger electric field strength amplifies the effect of frequency.The residence time of water molecules near the ions significantly decreases.

Electrolyte in heterogeneous water-glucose mixtures: A view from experiment and molecular modeling

The mobilities and activities of ions in NaCl-glucose-water mixtures are probed by means of conductometry and potentiometry. A positive deviation of the limiting conductance from the Stokes-Einstein (SE) relation is observed. This striking effect is discussed in terms of ‘excluded volume’ concept for strongly heterogeneous liquids. A drastic difference between sodium cations and chloride anions is argued resting on measurements with ion selective electrodes. The microscopic structure of water-glucose solutions is thoroughly addressed by classical molecular dynamics (MD) method. The MD simulations reproduce qualitatively the main experimental findings; trends in the behavior of the Na+ and Cl− ions are attributed to a noticeable difference in the structure and dynamics of their solvation shells.

Water Effects on Molecular Adsorption of Poly(N-vinyl-2-pyrrolidone) on Cellulose Nanocrystals Surfaces: Molecular Dynamics Simulations.

Models of interaction between a poly(N-vinyl-2-pyrrolidone) macromolecule and a fragment of Iβ-cellulose were built in a vacuum and water environment. The models were made to interpret the mechanism of interaction of the polymer and cellulose nanocrystals by the classical molecular dynamics method. The structural behavior of a poly(N-vinyl-2-pyrrolidone) macromolecule in water has been studied in terms of the radius of gyration, atom–atom radial distribution functions and number of hydrogen bonds. It was found that the polymer has a high affinity with the solvent and each monomer unit has on average 0.5 hydrogen bonds. The structural and energy characteristics of the polymer adsorption were investigated at different initial positions of the poly(N-vinyl-2-pyrrolidone) macromolecule relative to the cellulose fragment. It was observed that the polymer macromolecule was mainly adsorbed on the cellulose fragment in the globular form. Moreover, in the solvent the interaction of poly(N-vinyl-2-pyrrolidone) with the cellulose hydrophobic surface was stronger than that with the hydrophilic one. This study will show that the presence of water makes the interaction between the polymer and cellulose weaker than in a vacuum, and the polymer and cellulose mainly interact through their solvation shells.

Dynamical behavior and high-pressure study of C20@Tube peapod structure

The classical molecular dynamics (MD) method and density functional theory are utilized to study the dynamics and high-pressure behaviors of C20@Tube peapod structure. Results show that the critical and most suitable diameters of the tube for filling the C20 molecule are 9.5 and 10.86 Å, respectively. The mean free path and frequency of collision between the host and guest molecules are analyzed. Competition between the tube’s confinement effect and the temperature on the molecular motion is studied. Two superhard carbon phases with a large bulk modulus are obtained under high pressure. The encapsulated C20 molecule induces a decrease in the band gap under ambient conditions and a lower pressure of closure of band gap. In addition, the application of pressure leads to a redistribution of electric charge between the host and guest molecule. The encapsulation induces a red shift of the vibrational optic modes for both the tube and the C20 molecule.