Let the channel length be and assume uniform solution conductivity. Its Ohmic resistance scales as , whereas access resistance of a reservoir mouth scales as . The fraction of voltage in the entrance regions is therefore of order . Most of the potential drop lies inside the long channel; the small entrance field region is neglected in the model, not asserted identically zero.
Write for inserted contour length and choose to pull the chain inward. The charge already inside feels force , giving
Confinement removes polymer configurations. In the stiff-chain regime, the confinement deflection length obeys , hence . A free-energy cost of order per deflection gives a roughly constant resisting entropic force . The insertion barrier of a charged polymer follows from , with an entry maximum at when that point lies within the insertion interval. Its height is . The field supplies work against this confinement entropy.
Put , so . After capture, neglect the entry barrier, exterior-chain drag and thermal corrections to strong directed motion. Then
The confined-polymer entry and recoil times have different length dependence; this entry graph is linear through the origin. Charge and drag both grow with inserted length, leaving a constant velocity. The same cancellation explains length-independent mobility in an ideal free-draining electrophoresis model. It does not include a capture waiting time or claim that every free-solution chain has identical hydrodynamic drag.
A measured superlinear entry time can arise when exterior-coil drag, tension propagation, wall adsorption or nonuniform friction adds length dependence absent from this model. For example with the same drive gives for . Under the assumptions of uniform wall charge and polymer entry scaling, a homogeneous thin-double-layer electro-osmotic model adds a length-independent fluid velocity . It changes the drift coefficient, not its length exponent. This does not rule out charge heterogeneity, adsorption or near-cancellation followed by diffusion in a real channel; those are additional mechanisms.
With the field off, the confinement entropy drives outward motion. Assuming the constant force and the same local friction,
The small final end region lies outside the long-confined-segment approximation but gives only a small correction. Thus ideal insertion scales as , while recoil scales as .
TODO: user-deferred DNA-specific numerical stopping-voltage estimate and its biological parameter-based inference. No biological quantities are evaluated.
For entropic-trap length separation, a reservoir/channel array can repeat length-dependent capture, confinement and relaxation delays, turning them into different mean residence times. The uniform inside-channel drift speed derived above is itself length independent, so that drift alone cannot separate lengths. Separation must retain length dependence of the barrier or of the capture/recoil dynamics and can be tuned with a forward-biased time-dependent field. For large bulk throughput, pressure-driven advection is preferable to diffusion alone; a pressure gradient can be combined with electric capture control. In the unobstructed continuum limit . Excessive driving erases trapping differences, so throughput and resolution compete; the question supplies no geometry or adsorption law selecting a unique optimal drive.
Figure 1.
Original dimensionless insertion barriers and the distinct insertion and recoil length scalings
. Details.