Molecular Dynamics Simulation of Fast Water Transport though Aquaporin-Mimic Nanpores

Abstract

The aquaporin water channel allows efficiently fast water transport while rejecting ions and protons. We perform molecular dynamics simulations with flexible hourglass-shaped pores by mimicking aquaporin water channels. The simulation model includes a uniform applied external force field to mimic osmotic gradient environment and an added harmonic constraint to achieve nanopore flexibility. We estimated the osmotic permeability from simulation and it is consistent with experimental results to confirm the validity of our model. We performed non-equilibrium molecular dynamics simulation with Nose-Hoover thermostat, the SPC/E water model, and carbon pore atoms. The occupancy (number of water molecules inside the pore) is maintained as a fixed value as long as the pore geometry is the same. The simplified model also successfully captures the important physics of real aquaporin, e.g. a single-file arrangement of water molecules, the reorientation of water dipoles. We found that the model pore has the capacity to house more water molecules. We also found that water flow is up to 5 times than predicted by continuum hydrodynamic theory. This finding suggests that deforming straight nanopores into the hourglass shape (if possible) enhances the ability of water transport in thin membranes. The future work includes the simulations with a longer hourglass-shaped nanopore (maybe up to 1 μm) and changing the chemical characteristics (e.g. surface charge, hydrophobicity) of a membrane surface.