Partially active polymer barrier crossing retains kink mechanism similar to a long passive polymer

Abstract

Using Brownian dynamics simulations (BD), we study two-dimensional (2D) barrier crossing of a long passive self-avoiding polymer that becomes active upon reaching the trans side, mimicking biomolecular translocation into nonthermally active regions across membrane pores. We find an analytical time-dependent kink solution or soliton-like solution for a passive Rouse polymer with N monomers crossing a one-dimensional asymmetric barrier, where the average translocation time, ⟨tc⟩ ∼ N. This manifests a kink, a polymer conformation stretched over the barrier that moves along the chain backbone at constant speed, opposite to the translocation direction. The analytical result agrees with our simulation results for passive phantom and self-avoiding polymers crossing a 2D barrier within the l ≪ Rg ≪ L limit, where Rg is the radius of gyration in its free state, l is its Kuhn length, and L is the barrier width. Within the same limit, the partially active self-avoiding polymer with varying self-propulsion forces follows a similar time-dependent kink mechanism at higher trans side monomer activities, which facilitate translocation by pulling the cis side chain segments. Interestingly, for all geometrical limits, the kink mechanism is retained by the partially active polymer at high self-propulsion forces when unbiased. In contrast, the passive self-avoiding polymer translocation deviates from the kink motion as ⟨tc⟩ ∼ Nα, α ∼ 2–2.5, irrespective of the limit of L when unbiased and l ≈ L ≤ Rg in driven translocations. The mechanism provides insights into translocations relevant to living matter and nanotechnology.