Influence of Crowder Geometry and Flexibility on Polymer Translocation Dynamics

Abstract

The interplay between polymer dynamics and molecular crowding is a crucial aspect of many biological and synthetic systems. In this study, we employ coarse-grained molecular dynamics simulations to investigate the translocation of a polymer through a nanopore under varying crowding conditions. The crowders are modelled as rigid rods of different lengths, and their influence on translocation probability and time is systematically analyzed by varying the area fraction (ϕ), crowder length (L), and bending rigidity (kθ). We find that increasing ϕ leads to a significant reduction in translocation probability, with longer and more rigid crowders imposing a stronger steric hindrance, thereby amplifying the entropic barrier. Translocation time follows a non-monotonic trend, suggesting a competition between entropic compression and active pushing from the crowders. These findings highlight how crowding geometry and rigidity influence polymer transport, with implications for biological processes such as DNA translocation and applications in synthetic nanopores. However, limitations arise due to the lack of explicit hydrodynamic interactions and the idealized nature of crowder-polymer interactions.