Paper Citing NAMD - Abstract
Garate, J. -A.; English, N. J.; MacElroy, J. M. D.
Carbon nanotube assisted water self-diffusion across lipid membranes in the absence and presence of electric fields
MOLECULAR SIMULATION, 35:3-12, 2009
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 respectively and a length of 36.9, 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 0.0065V/, 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-a-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.
