J. M. D. MacElroy

Nonequilibrium molecular dynamics simulation of diffusion and flow in thin microporous membranes

A new nonequilibrium molecular dynamics method for simulating flow and diffusion within membranes is presented. The method involves two fixed volumes, separated by the permeable medium, which are maintained at fixed, though different, chemical potential. By monitoring the flow and diffusion of the fluid particles through the nonequilibrium interstitial region one can simulate mass transfer processes in a manner which parallels real laboratory experiments. The method is applied to a simple microporous membrane system and it is shown that slip flow, rather than viscous shear, is the predominant mechanism governing the permeation of moderately dense hard‐sphere fluids in very fine pores.

Molecular dynamics simulations of microwave heating of water

Nonequilibrium molecular dynamics simulations of water in an intense external microwave field have been performed using a rigid/polarizable and a flexible/nonpolarizable potential model, from ambient conditions to supercriticality. The heating profiles were compared to that predicted from a macroscopic energy balance, and the polarizable model was found to be superior in this regard.

Adsorption and diffusion of a Lennard-Jones vapor in microporous silica

The properties of a dilute Lennard‐Jones vapor in contact with an adsorbing microporous medium are investigated using grand canonical ensemble Monte Carlo and molecular dynamics techniques. The bulk structure of the microporous system is modeled as an assembly of randomly distributed interconnected solid spheres, and vapor/surface interactions are treated in two ways: (i) using a smooth continuous interaction potential and (ii) using a molecular model for the surface structure of the solid. The microporous solid representation employed in these simulations is chosen to conform in realistic manner with the bulk and surface properties of silica gel. The results obtained from the simulations include equilibrium partition coefficients, diffusivities, and related microscopic properties. By comparing these results with available experimental data it is shown that the properties of simple nonpolar gases in microporous silica may be predicted with reasonable accuracy. This is particularly true when the molecular ...

Hydrogen bonding and molecular mobility in liquid water in external electromagnetic fields

Nonequilibrium molecular dynamics simulations of water have been performed in the isothermal–isobaric ensemble in the presence of external electromagnetic fields of varying intensity in the microwave to far-infrared frequency range, using a rigid/polarizable and a flexible/nonpolarizable potential model, from 260 to 400 K. Significant alterations in molecular mobility and hydrogen bonding patterns were found vis-a-vis zero-field conditions. In addition, the influence of the isothermal–isobaric ensemble on these observations was gauged by means of comparison with pure Newtonian simulation findings in the presence of external fields, and the former results were in reasonable accord with the latter.

Structural and dynamical properties of methane clathrate hydrates

Equilibrium molecular dynamics (MD) simulations have been performed in both the NVT and NPT ensembles to study the structural and dynamical properties of fully occupied methane clathrate hydrates at 50, 125, and 200 K. Five atomistic potential models were used for water, ranging from fully flexible to rigid polarizable and nonpolarizable. A flexible and a rigid model were utilized for methane. The phonon densities of states were evaluated and the localized rattling modes for the methane molecules were found to couple to the acoustic phonons of the host lattice. The calculated methane density of states was found to be in reasonable agreement with available experimental data.

Computer simulation of moderately dense hard-sphere fluids and mixtures in microcapillaries

Grand canonical ensemble Monte Carlo and molecular dynamics simulations of partitioning and diffusion of rigid sphere fluids and mixtures in cylindrical pores have been carried out for a wide range of pore sizes. The formal linear diffusion theory employed in an earlier paper is extended to binary mixtures and is used to analyse the simulation data. The results obtained show that continuum-mechanical theory may be used to quantitatively predict the diffusion fluxes of small, nonadsorbing solutes as well as macromolecular solutes in micropores as long as the sum of the solute and solvent particle sizes is less than the size of the pore. In addition, the existence of viscous slip for dense fluids observed earlier is confirmed, and it is shown that selective partitioning of solutes in simple fluid mixtures can lead to solvent diffusion barriers in very small pores.

Molecular dynamics simulation of hindered diffusion in microcapillaries

A general model for diffusion in membranes is employed to illustrate that the individual contributions of diffusion relative to the membrane and self-diffusion in the pore fluid are simply related to the autocorrelation function for the instantaneous centre of mass velocity of the pore fluid and the usual autocorrelation function for the particle velocities. These results are used to analyse molecular dynamics simulation data for hindered diffusion of rigid sphere fluids in cylindrical pores over a wide range of pore fluid densities and pore sizes. Two reflection conditions, specular and diffuse scattering from the pore wall, are also investigated. The results obtained for diffuse scattering are in qualitative agreement with experimental data reported in the literature. These results also suggest that dense fluids and liquids may undergo a small, nonzero degree of slip during flow past a rigid boundary.

Simulation Studies of a Lennard-Jones Liquid in Micropores

Abstract In this paper grand canonical ensemble Monte Carlo and molecular dynamics simulation techniques are used to establish the degree to which the equilibrium and transport properties of fluids in micropores are influenced both by confinement in the narrow pore space and by the lattice structure of the pore wall. Partition coefficients, solvation forces, and diffusion coefficients for a Lennard-Jones liquid confined within two model cylindrical pores are determined over a range of effective micropore sizes. In one model the cylindrical pore wall is described by a structureless, continuum interaction potential similar to that which is frequently employed in theoretical studies of adsorption. In the second model a single embedded layer of lattice atoms is placed at the solid/fluid interface. The results obtained are compared with the prediction of a bulk fluid approximation and the Fischer-Methfessel approximation to the Yvon-Born-Green equation and the recently developed kinetic theory of Davis for mic...

Carbon nanotube assisted water self-diffusion across lipid membranes in the absence and presence of electric fields

Water self-diffusion has been investigated by molecular dynamics (MD) simulation through armchair single-walled carbon nanotubes (SWCNTs) implanted in 1-palmytoil-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) membrane patches. Four systems were investigated, each containing one of (5,5), (6,6), (8,8) and (11,11) CNTs with diameters of 6.89, 8.20, 11.04 and 15.02 Å respectively and a length of 36.9 Å, oriented normal to the membrane. The CHARMM27 potential was used, in conjunction with TIP3P water, with particle-mesh Ewald electrostatics. Equilibrium and non-equilibrium MD simulations were performed in the respective absence and presence of a static electric field with an intensity of 0.0065 V/Å, applied along the axis normal to the membrane, i.e. approximately along the axis of the CNTs. It was found that the permeation rate of tracer water molecules was enhanced from 1.13 to 2.6 particles per nanosecond in the presence of the field in the case of (5,5) CNT, whilst the permeation rate per unit area declined in the larger nanotubes vis-à-vis equilibrium zero-field conditions. Single-file diffusion was observed in the (5,5) and (6,6) cases, compared with classical diffusion in the larger pores. From an analysis of the molecular dipole moment distributions, the number of water molecules present in the CNTs and the hydrogen-bonding characteristics of water inside the CNTs and at their mouth, these trends have been rationalised. A significant decrease in the fluctuations in the number of water molecules in the (5,5) CNT due to an enhanced dipole alignment in the electric field resulted in an increased rate of incorporation of the water molecules into this CNT, whereas a sharper alignment of the water dipoles with the field coupled with the greater rotational freedom of the water molecules in the (6,6) nanotube tended to reduced water self-diffusion.

Atomistic simulations of liquid water using Lekner electrostatics

Equilibrium molecular dynamics simulations have been performed for liquid water using three different potential models in the NVT and NPT ensembles. The flexible SPC model, the rigid TIP4P model and the rigid/polarizable TIP4P-FQ potential were studied. The Lekner method was used to handle long range electrostatic interactions, and an efficient trivariate cubic spline interpolation method was devised for this purpose. A partitioning of the electrostatic interactions into medium and long range parts was performed, and the concomitant use of multiple timestep techniques led to substantially enhanced computation speeds. The simulations were carried out using 256 molecules in the NVT ensemble at 25°C and 997 kg m−3 and in the NPT ensemble at 25°C and 1 bar. Various dynamic, structural, dielectric, rotational and thermodynamic properties were calculated, and it was found that the simulation methodologies performed satisfactorily vis-à-vis previous simulation results and experimental observations.