Molecular dynamics simulation of pressure-driven water flow in silicon-carbide nanotubes

Many properties of silicon carbide (SiC) nanotubes, such as their high mechanical strength and resistance to corrosive environments, are superior to those of their carboneous counterparts, namely, carbon nanotubes (CNTs) and, therefore, SiC nanotubes can be a viable alternative to CNTs in a variety of applications. We employ molecular dynamics simulations to examine flow of water in SiC nanotubes and to study the differences and similarities with the same phenomenon in the CNTs. The simulations indicate that SiC nanotubes always provide larger flow enhancements than those reported for the CNTs. Moreover, a given flow enhancement in SiC nanotubes requires an applied pressure gradient that is at least an order of magnitude smaller than the corresponding value in a CNT of the same size.     

Investigation of entrance and exit effects on liquid transport through a cylindrical nanopore

The entrance and exit effects on liquid transport through a nano-sized cylindrical pore under different solid wall-liquid interactions were studied by comparing molecular dynamics (MD) results of a finite length nanopore in a membrane with those of an infinite length one. The liquid transport through a finite length nanopore in a membrane was carried out by using a pressure-driven non-equilibrium molecular dynamics (NEMD) method proposed by Huang et al. [C. Huang, K. Nandakumar, P. Choi and L. W. Kostiuk, J. Chem. Phys., 2006, 124, 234701]. The fluid motion through an infinite length nanopore, which had the same cross-stream dimension as the finite length channel in the membrane, but with periodic boundary conditions in the stream-wise direction, was carried out by using the external-field driven NEMD approach [J. Koplik, J. R. Bavanar and J. F. Willemsen, Phys. Rev. Lett., 1988, 60, 1282]. The NEMD results show that the pressure and density distributions averaged over the channel in the radial direction in both finite and infinite length channels are similar, but the radial distributions of the stream-wise velocity were significantly different when the solid wall was repulsive. The entrance and exit effects lead to a decrease in flow rate at about 39% for the repulsive wall and 6% for the neutral-like wall.     

Molecular dynamics study of ionic liquid confined in silicon nanopore

Russian Journal of Physical Chemistry A - Molecular dynamics simulations was carried to investigate the structure and dynamics of [BMIM][PF6] ionic liquid (IL) confined inside a slit-like silicon...     

Molecular dynamics simulation of liquid water between two walls

A molecular dynamics simulation, lasting ≈25 ps, has been performed with 150 ST2 water molecules between two quasi-hard repulsive walls, at a temperature of 302 K. A number of static and dynamic properties have been computed as a function of the distance from the walls, showing that water near the walls is in general more “ordered” than in the bulk, and that this bulk water behaves like ordinarv liquid ST2 water.     

液态水的分子动力学模拟

用分子动力学(MD)模拟方法在150~376K的温度范围内对液态水的微正则系统进行了研究。考察了液态水的结构及其性质。模拟采用了由从头算得出的柔性水-水相互作用势MCYL。对时间和空间的平均得出了液态中水分子几何构型及温度改变所引起的液态水结构变化。对径向分布函数gOH, gOO, gHH及配位数的分析表明, 在所考察的温度范围内, 每个水分子与相邻分子形成的氢键数为2~3, 水分子在参与的2个氢键中同时作为授受体。结合对振动谱的研究表明在低温时液态水形成的网络结构可能随温度的升高而形成小的簇结构。     

Molecular dynamics simulation of liquid trimethylphosphine

Structural and dynamical properties of liquid trimethylphosphine (TMP), (CH(3))(3)P, as a function of temperature is investigated by molecular dynamics (MD) simulations. The force field used in the MD simulations, which has been proposed from molecular mechanics and quantum chemistry calculations, is able to reproduce the experimental density of liquid TMP at room temperature. Equilibrium structure is investigated by the usual radial distribution function, g(r), and also in the reciprocal space by the static structure factor, S(k). On the basis of center of mass distances, liquid TMP behaves like a simple liquid of almost spherical particles, but orientational correlation due to dipole-dipole interactions is revealed at short-range distances. Single particle and collective dynamics are investigated by several time correlation functions. At high temperatures, diffusion and reorientation occur at the same time range as relaxation of the liquid structure. Decoupling of these dynamic properties starts below ca. 220 K, when rattling dynamics of a given TMP molecules due to the cage effect of neighbouring molecules becomes important.     

Direct numerical simulation of electrokinetic translocation of a cylindrical particle through a nanopore using a Poisson-Boltzmann approach

Nanopore-based sensing of single molecules is based on a detectable change in the ionic current arising from the electrokinetic translocation of individual nanoparticles through a nanopore. In this study, we propose a continuum-based model to investigate the dynamic electrokinetic translocation of a cylindrical nanoparticle through a nanopore and the corresponding ionic current response. It is the first time to simultaneously solve the Poisson-Boltzmann equation for the ionic concentrations and the electric field contributed by the surface charges of the nanopore and the nanoparticle, the Laplace equation for the externally applied electric field, and the modified Stokes equations for the flow field using an arbitrary Lagrangian-Eulerian method. Current blockade due to the particle translocation is predicted when the electric double layers (EDLs) of the particle and the nanopore are not overlapped, which is in qualitative agreement with existing experimental observations. Effects due to the electric field intensity imposed, the EDL thickness, the nanopore's surface charge, the particle's initial orientation and lateral offset from the nanopore's centerline on the particle translocation including both translation and rotation, and the ionic current response are comprehensively investigated. Under a relatively low electric field imposed, the particle experiences a significant rotation and a lateral movement. However, the particle is aligned with its longest axis parallel to the local electric field very quickly due to the dielectrophoretic effect when the external electric field is relatively high.     

Molecular dynamics simulation of liquid sulfur dioxide

A previously proposed model for molecular dynamics (MD) simulation of liquid sulfur dioxide, SO(2), has been reviewed. Thermodynamic, structural, and dynamical properties were calculated for a large range of thermodynamic states. Predicted (P,V,T) of simulated system agrees with an elaborated equation of state recently proposed for liquid SO(2). Calculated heat capacity, expansion coefficient, and isothermal compressibility are also in good agreement with experimental data. Calculated equilibrium structure agrees with X-ray and neutron scattering measurements on liquid SO(2). The model also predicts the same (SO(2))(2) dimer structure as previously determined by ab initio calculations. Detailed analysis of equilibrium structure of liquid SO(2) is provided, indicating that, despite the rather large dipole moment of the SO(2) molecule, the structure is mainly determined by the Lennard-Jones interactions. Both single-particle and collective dynamics are investigated. Temperature dependency of dynamical properties is given. The MD results are compared with previous findings obtained from the analysis of inelastic neutron scattering spectra of liquid SO(2), including wave-vector dependent structural relaxation, tau(k), and viscosity, eta(k).     

Molecular simulation of pressure-driven fluid flow in nanoporous membranes

An extended nonequilibrium molecular dynamics technique has been developed to investigate the transport properties of pressure-driven fluid flow in thin nanoporous membranes. Our simulation technique allows the simulation of the pressure-driven permeation of liquids through membranes while keeping a constant driving pressure using fluctuating walls. The flow of argon in the liquid state was simulated on applying an external pressure difference of 2.4x10(6) Pa through the slitlike and cylindrical pores. The volume flux and velocity distribution in the membrane pores were examined as a function of pore size, along with the interaction with the pore walls, and these were compared with values estimated using the Hagen-Poiseuille flow. The calculated velocity strongly depends on the strength of the interaction between the fluid and the atoms in the wall when the pore size is approximately<20sigma. The calculated volume flux also shows a dependence on the interaction between the fluid and the atoms in the wall. The Hagen-Poiseuille law overestimates or underestimates the flux depending on the interaction. From the analysis of calculated results, a good linear correlation between the density of the fluid in the membrane pores and the deviation of the flux estimated from the Hagen-Poiseuille flow was found. This suggests that the flux deviation in nanopore from the Hagen-Poiseuille flow can be predicted based on the fluid density in the pores.     

Molecular alignment in a liquid induced by a nonresonant laser field: Molecular dynamics simulation

We carried out molecular dynamics (MD) simulations for a dilute aqueous solution of pyrimidine in order to investigate the mechanisms of field-induced molecular alignment in a liquid phase. An anisotopically polarizable molecule can be aligned in a liquid phase by the interaction with a nonresonant intense laser field. We derived the effective forces induced by a nonresonant field on the basis of the concept of the average of the total potential over one optical cycle. The results of MD simulations show that a pyrimidine molecule is aligned in an aqueous solution by a linearly polarized field of light intensity I approximately 10(13) W/cm2 and wavelength lambda = 800 nm. The temporal behavior of field-induced alignment is adequately reproduced by the solution of the Fokker-Planck equation for a model system in which environmental fluctuations are represented by Gaussian white noise. From this analysis, we have revealed that the time required for alignment in a liquid phase is in the order of the reciprocals of rotational diffusion coefficients of a solute molecule. The degree of alignment is determined by the anisotropy of the polarizability of a molecule, light intensity, and temperature. We also discuss differences between the mechanisms of optical alignment in a gas phase and a liquid phase.     

Molecular dynamics simulation of phase separating binary liquids in cylindrical Couette flow

We use molecular dynamics simulations to study phase separation of a 50:50 (by volume) fluid mixture in a confined and curved (Taylor-Couette) geometry, consisting of two concentric cylinders. The inner cylinder may be rotated to achieve a shear flow. In nonsheared systems we observe that, for all cases under consideration, the final equilibrium state has a stacked structure. Depending on the lowest free energy in the geometry the stack may be either flat, with its normal in the z direction, or curved, with its normal in the r or theta direction. In sheared systems we make several observations. First, when starting from a prearranged stacked structure, we find that sheared gradient and vorticity stacks retain their character for the durations of the simulation, even when another configuration is preferred (as found when starting from a randomly mixed configuration). This slow transition to another configuration is attributed to a large free energy barrier between the two states. In case of stacks with a normal in the gradient direction, we find interesting interfacial waves moving with a prescribed angular velocity in the flow direction. Because such a wave is not observed in simulations with a flat geometry at similar shear rates, the curvature of the wall is an essential ingredient of this phenomenon. Second, when starting from a randomly mixed configuration, stacks are also observed, with an orientation that depends on the applied shear rate. Such transitions to other orientations are similar to observations in microphase separated diblock copolymer melts. At higher shear rates complex patterns emerge, accompanied by deviations from a homogeneous flow profile. The transition from steady stacks to complex patterns takes place around a shear rate 1/tau(dv), where tau(dv) is the crossover time from diffusive to viscous dominated growth of phase-separated domains, as measured in equilibrium simulations.     

Molecular dynamics simulation of liquid mixtures of benzene with chlorobenzene

A molecular dynamics method is used to simulate liquid mixtures of benzene and chlorobenzene at different concentrations. Radial angular distribution functions (RADFs) for distances between the benzene ring planes and the angle between them were calculated to analyze the structure of pure components and mixtures. In chlorobenzene, the highest RADF maximum at a distance between the mass centers of the benzene rings of about 4 Å corresponds to the stacked configurations of molecules, and at 5–7 Å the number of stacked contacts are much less than that at 4 Å and is comparable with the orthogonal ones. In liquid benzene, the number of stacked and orthogonal configurations is approximately equal in a range from 4 Å to 7 Å. RADF for benzene reveals extended regions of correlation, which gives evidence of the occurrence of agglomerates bound by specific interactions between the benzene rings. These agglomerates are not characteristic of chlorobenzene, but the presence of maxima on the radial distribution function for the distances between chlorine atoms indicates chlorine aggregation. The effect of halogen aggregation on the structure of benzene-chlorobenzene mixtures is considered. The obtained results are compared with the data on molecular light scattering.     

Molecular dynamics simulation of the free surface of liquid formamide

Molecular dynamics simulations of liquid formamide (HCONH₂) were carried out using the GROMOS software. The formamide molecule is represented by all of its atoms with all internal degrees of freedom. In contrast to other simulations dealing with bulk properties, this study focuses on the interface liquid–vacuum for the first time. We show that the molecular plane is tilted out of the surface, exposing the HCO group to the vacuum. © 1997 John Wiley & Sons, Inc. Int J Quant Chem 63 : 1123–1131, 1997     

Molecular dynamics simulation of the homogeneous crystallization of liquid rubidium

The homogeneous crystallization of liquid rubidium models containing 500, 998, and 1968 particles in the basic cube was studied by the molecular dynamics method. The liquid crystallized over the temperature range 70–182.5 K predominantly with the formation of a body centered cubic (BCC) structure. The mechanism of crystallization was different from that accepted in classic nucleation theory. Crystallization developed as an increase in the number of atoms with Voronoi polyhedra of the 0-6-0-8 and 0-4-4-6 types, the formation of bound groups (clusters) from these atoms, and growth of these groups as in the coagulation of an impurity from a supersaturated solution. At the initial stage, bound groups had a very loose structure and included a fairly large number of atoms with polyhedra of other types. The linear dimension of the largest group rapidly approached the basic cube size. The atoms with the 0-6-0-8 and 0-4-4-6 Voronoi polyhedra played a leading role in crystallization and activated the transition of bound group atoms with other coordination types into a BCC coordination. The probability of formation of a bound group of a given size was found to be independent of the volume of the liquid model. Cluster size fluctuations especially strong over the temperature range 180–185 K played an important role in the formation of 0608 clusters of a threshold (“critical”) size.     

Molecular dynamics simulation of liquid water: hybrid density functionals

The structure, dynamical, and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first-principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta-functional, four gradient-corrected functionals, and the local density and Hartree-Fock approximations. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self-diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and understructured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller average numbers of hydrogen bonds than pure density functionals but similar hydrogen bond populations. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than those of the corresponding pure density functionals.     

Molecular dynamics simulation of liquid water and ice nanoclusters using a new effective HFD‐like model

We have determined a new two‐body interaction potential of water by the inversion of viscosity collision integrals of water vapor and fitted to achieve the Hartree–fock dispersion‐like (HFD‐like) potential function. The calculated two‐body potential generates the thermal conductivity, viscosity, and self‐diffusion coefficient of water vapor in an excellent accordance with experimental data at wide temperature ranges. We have also used a new many‐body potential as a function of temperature and density with the HFD‐like pair‐potential of water to improve the two‐body properties better than the SPC, SPC/E, TIP3P, and TIP4P models. We have also used the new corrected potential to simulate the configurational energy and the melting temperatures of the (H₂O)₅₀₀, (H₂O)₈₆₄, (H₂O)₂₀₄₈, and (H₂O)₆₉₁₂ ice nanoclusters in good agreement with the previous simulation data using the TIP4P model. The extrapolated melting point at the bulk limit is also in better agreement with the experimental bulk data. The self‐diffusion coefficients for the ice nanoclusters also simulated at different temperatures. © 2017 Wiley Periodicals, Inc.     

Kinetic theory of gas separation in a nanopore and comparison to molecular dynamics simulation

Kinetic mesoscopic theory derived from an atomistic model is applied to study permeation and separation of gases in a single rectangular pore. The goal is to judge the analytical method against the results of molecular dynamics simulation and to demonstrate the ease and relevance of analytical theories to calculate density profiles, flux, permeance, and separation factors. The permeance is linked to the amount of gas adsorbed in the pore and the effect of the effective gas-wall interaction on adsorption is explored. The effects of pore size, temperature, and the parameters of the pore wall interaction are investigated and reproduce the trends found in the numerical simulation of permeation of a mixture of methane and carbon dioxide in a carbon nanopore.     

Molecular dynamics study of atomic transport properties in rapidly cooling liquid copper

Based on Mei's embedded atom model molecular dynamics simulations have been performed to investigate the rapidly cooling processes of Cu. The atomic transport property, namely the self-diffusion coefficient, is computed in the liquid state, and the results near the melting point of Cu are in good agreement with experimental data and other computational values. The atom diffusion movements during the long period of relaxation have been also studied around the solidification temperature Tc. To describe the complex microstructural evolutions during the rapidly cooling processes and the long relaxation processes, the pair correlation function and the pair analysis technique are used. It is demonstrated that the crystallization of amorphous Cu is caused by the atomic diffusion.     

Molecular dynamics simulation of nanostructural organization in ionic liquid/water mixtures

Molecular dynamics simulations have been carried out to investigate nanostructural organization in mixtures of 1-octyl-3-methylimidazolium nitrate ionic liquid and water at multiple water concentrations. Evolution of the polar network, water network, and micelle structures is visualized and analyzed via partial radial distribution functions. The calculated static partial structure factors show that within the range of water contents examined, polar networks, water networks, and micelles possess an approximately invariant characteristic length at around 20 A. Furthermore, the above calculations point out that, as the amount of water increases, the polar network is continuously broken up (screened) by the intruding water, while the structural organization of the water network and the micelle exhibits a turnover. At the turnover point, the most ordered micelle (cation-cation) structure and water (water-anion-water) network are formed. Thereafter, the structural organization abates drastically, and only loose micelle structure exists due to the dominant water-water interactions. The simulated turnover of structural organization agrees with the sharpest peak in the experimentally obtained structure factor in aqueous solutions of similar ionic liquids; the simulated water structure reveals that water can form liquidlike associated aggregates due to the planar symmetry and strong basicity of NO(3)-, in agreement with experiment. The turnover of structural organization of micelles results from the persistent competition between the hydrophobic interactions of the nonpolar groups and the breakup of the charged polar network with increasing water content, whereas the turnover of the water network results from the competition between the water-water and water-anion interactions.