Simulations of two-dimensional unbiased polymer translocationusing the bond fluctuation model

摘要

We use the bond fluctuation model (BFM) to study the pore-blockade times of a translocatingpolymer of length N in two dimensions, in the absence of external forces on the polymer (i.e., unbiased translocation) and hydrodynamic interactions (i.e., the polymer is a Rouse polymer),through a narrow pore. Earlier studies using the BFM concluded that the pore-blockade time scales with polymer length as τ_d~N~β,with β=1+ 2v,whereas some recent studies using different polymermodels produce results consistent with β=2+ v, originally predicted by us. Here v is the Flory exponent of the polymer; v=0.75 in 2D. In this paper we show that for the BFM if the simulationsare extended to longer polymers, the purported scaling τ_d~N~(1+2v)ceases to hold. We characterize the finite-size effects, and study the mobility of individual monomers in the BFM. In particular, we findthat in the BFM, in the vicinity of the pore the individual monomeric mobilities are heavily suppressed in the direction perpendicular to the membrane. After a modification of the BFM whichcounters this suppression (but possibly introduces other artifacts in the dynamics), the apparentexponent β increases significantly. Our conclusion is that BFM simulations do not rule out ourtheoretical prediction for unbiased translocation, namely, β= 2 + v.