Nanopore Measurements of Filamentous Viruses Reveal a Sub-nanometer-Scale Stagnant Fluid Layer

We report measurements and analyses of nanopore translocations by fd and M13, two related strains of filamentous virus that are identical except for their charge densities. The standard continuum theory of electrokinetics greatly overestimates the translocation speed and the conductance associated with counterions for both viruses. Furthermore, fd and M13 behave differently from one another, even translocating in opposite directions under certain conditions. This cannot be explained by Manning condensed counterions or a number of other proposed models. Instead, we argue that these anomalous findings are consequences of the breakdown of the validity of continuum hydrodynamics at the scale of a few molecular layers. Next to a polyelectrolyte, there exists an extra-viscous, sub-nanometer-thin boundary layer that has a giant influence on the transport characteristics. We show that a stagnant boundary layer captures the essential hydrodynamics and extends the validity of the electrokinetic theory beyond the continuum limit. A stagnant layer with a thickness of about half a nanometer consistently improves predictions of the ionic current change induced by virus translocations and of the translocation velocity for both fd and M13 over a wide range of nanopore dimensions and salt concentrations.