Ricerc@Sapienza

The experimental and computational study of solid state nanopores as synthetic counterpart of biological ion channels has been a major research topic in nanofluidics and biotechnology in the last decade. Ideally, such biomimetic devices should be designed to have the desired properties in terms of selectivity and gating. Selectivity refers to the difference in terms of flux of different ionic species under the same chemical potential difference, while gating refers to the mechanism of transition between open (conductive) and closed (nonconductive) configurations. Hydrophobic gating has recently emerged as a gating mechanism found in several biological channels. The mechanism of hydrophobic gating is related to the reversible formation of a vapour bubble inside hydrophobic nanopores due to the extreme water confinement, resulting in stochastic transitions between a dry and a wet state. Since ions can only go through the pore in the wet state, controlling the wet and dry transitions with voltage or hydrostatic pressure tunes the channel conductance. There is considerable interest in understanding hydrophobic gating in biology and in the design of synthetic gated channels. However, a clear understanding of the dynamics of the hydrophobic gate in response to external stimuli and the dependence of such dynamics on the microscopic features of the pore is still to be achieved. Here, a coarse graining approach is proposed to extract the long time behaviour of the pore from an atomistic model of hydrophobic nanopore. Restrained molecular dynamics simulations will be used to extract the free energy and diffusivity as a function of two coarse grained variables: the pore filling and the axial position of a tagged ion. The outcome of these simulations will be used to perform Langevin simulations to extract the rates of ion crossing and of pore wetting and drying, which are out of the range of Molecular Dynamics simulations due to their computational cost.