Opposite translocation of long and short oligomers through a nanopore

Abstract

We consider elongated cylindrical particles, modeling, e.g., DNA fragments or nanorods, while they translocate under the action of an externally applied voltage through a solid state nanopore. Particular emphasis is put on the concomitant potential energy landscape encountered by the particle on its passage through the pore due to the complex interplay of various electrohydrodynamic effects beyond the realm of small Debye lengths. We find that the net potential energy difference across the membrane may be of opposite sign for short and long particles of equal diameters and charge densities (e.g., oligomers). Thermal noise thus leads to biased diffusion through the pore in opposite directions. By means of an additional membrane gate electrode it is even possible to control the specific particle length at which this transport inversion occurs.

Influence of concentration polarization on DNA translocation through a nanopore

“…Indeed, a similar continuum model has suggested that nanopores can be used to sort DNA fragments based on their size by controlling a gate membrane electrode. 45 …”

Reluctance of a neutral nanoparticle to enter a charged pore

“…Introducing (37) into (41,42) it follows that both p 1 (r) and ρ 1 (r) are independent of c 0 . The free energy per unit length g 1 thus follows with (32,37) as g 1 = −sign(σ)πU 0 ln(c 0 ) Qσ − Q 0 dr rρ(r) + .…”

“…through the pore center), Figs. 3 (c) and (d) provide a more detailed picture of the numerically obtained fields for c 0 = 1 mM together with the analytical approximations (37) and (42) for low concentrations.…”

“…The units in (d) are now 10 6 Pa. (e) and (f): Same, but for c0 = 100 mM. In addition, the analytical approximations (37) and (42) for high concentrations are shown as blue (lower) lines. (g) and (h): Same, but for c0 = 1000 mM.…”

“…It, however, turns out that the numerical treatment of the fully three-dimensional problem is still very demanding, even on modern computers, if a satisfactory numerical accuracy is required. Consequently, similar previous studies are restricted to onedimensional [35], two-dimensional [25], or axisymmetric problems [24,[39][40][41][42] problems. In the latter case, which is also at the focus of our present work, an effectively two-dimensional problem is readily recovered when going over to cylindrical coordinates (see e.g.…”