Quasi-equilibrium translocation of short polymers through thin nanopores: Implications from forward flux sampling simulations

Abstract

We present a comprehensive computational study of unbiased translocation of uncharged, coarse-grained polymers of short and intermediate length through thin nanopores. Simulations combine Langevin dynamics with forward flux sampling to monitor translocation without external bias. The results demonstrate quasi-equilibrium behavior such that the process is well described by projection onto a single, physically meaningful reaction coordinate. Essential dynamics analysis reveals a simple internal motion closely similar to dilute bulk conformational dynamics, where fluctuations along the end-to-end vector dominate the collective motion. These findings validate single-coordinate free energy descriptions for the parameter regime studied and indicate that hysteresis and hidden multidimensional complexities are negligible when an appropriate coordinate is chosen. Our results suggest that, in agreement with previous assumptions for thin pores and short to intermediate polymers, reduced descriptions capture the essential thermodynamic and dynamical features of translocation and can guide both theoretical and experimental studies.