Boundary conditions for molecular dynamics simulations of water transport through nanotubes

Docherty, Stephanie and Nicholls, William D. and Borg, Matthew K. and Lockerby, Duncan A. and Reese, Jason M. (2014) Boundary conditions for molecular dynamics simulations of water transport through nanotubes. Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science, 228 (1). pp. 186-195. ISSN 0954-4062 (https://doi.org/10.1177/0954406213481760)

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Abstract

This article compares both new and commonly used boundary conditions for generating pressure-driven water flows through carbon nanotubes in molecular dynamics simulations. Three systems are considered: (1) a finite carbon nanotube membrane with streamwise periodicity and 'gravity'-type Gaussian forcing, (2) a non-periodic finite carbon nanotube membrane with reservoir pressure control, and (3) an infinite carbon nanotube with periodicity and 'gravity'-type uniform forcing. Comparison between these focuses on the flow behaviour, in particular the mass flow rate and pressure gradient along the carbon nanotube, as well as the radial distribution of water density inside the carbon nanotube. Similar flow behaviour is observed in both membrane systems, with the level of user input required for such simulations found to be largely dependent on the state controllers selected for use in the reservoirs. While System 1 is simple to implement in common molecular dynamics codes, System 2 is more complicated, and the selection of control parameters is less straightforward. A large pressure difference is required between the water reservoirs in these systems to compensate for large pressure losses sustained at the entrance and exit of the nanotube. Despite a simple set-up and a dramatic increase in computational efficiency, the infinite length carbon nanotube in System 3 does not account for these significant inlet and outlet effects, meaning that a much smaller pressure gradient is required to achieve a specified mass flow rate. The infinite tube set-up also restricts natural flow development along the carbon nanotube due to the explicit control of the fluid. Observation of radial density profiles suggests that this results in over-constraint of the water molecules in the tube.

ORCID iDs

Docherty, Stephanie, Nicholls, William D., Borg, Matthew K., Lockerby, Duncan A. and Reese, Jason M. ORCID logoORCID: https://orcid.org/0000-0001-5188-1627;
CORE (COnnecting REpositories)