Coarse grained modeling of ion transport through a hydrophobic nanopore*

Transport phenomena at the nanoscale are dramatically influenced by confinement effects and the presence of interfaces. Reversible formation of vapor bubbles may occur inside hydrophobic nanopores as a consequence of water confinement [1]. In electrolyte solutions, this is accompanied by a drop in the channel conductance, resulting in a hydrophobic gate for ionic current which is relevant in several biological channels [2].
We studied hydrophobic gating in a model nanopore system with a NaCl solution via Restrained Molecular Dynamics (RMD) simulations [3]. We computed the free energy map and the diffusion coefficients as a function of the number of water molecules inside the nanopore and the axial coordinate of both ions.
Based on the data from RMD simulations, we developed a coarse grained model for the dynamics of the water inside the pore and computed the conductivity of both ions as a function of the number of water molecules inside the pore. The model can be used to simulate the combined effect of multiple channels on timescales not easily accessible for molecular dynamics simulations.

[1] A.Tinti et al., PNAS (2017)
[2] P. Aryal et al., J. Mol. Bio. (2015)
[3] L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. (2006)