Comparative study of the crowding-induced collapse effect in hard-sphere, flexible polymer and rod-like polymer...

A systematic Langevin simulation is performed to study the crowding-induced collapse effect on a probed chain in three typical systems: hard sphere (HS), flexible polymer and rod-like polymer. Dependence of probed chain compaction on both crowder size and concentration is investigated explicitly. Particular attention is paid to examining the significant discrepancy in collapse effect associated with the crowder structure. First, we find an opposite compaction behavior in the HS and flexible polymer systems, in consistence with previous simulation and experimental observations. Compaction decreases with HS size while it increases with flexible polymer chain length. The underlying mechanism for such a contradiction is unraveled in terms of a depletion effect. For the HS system, as the crowder size increases, the ability of accommodating the probed chain enhances with a negligible depletion effect and thus results in a reduced compaction, while a polymer crowder system introduces a local depletion effect, responsible for an intensified compaction effect with increasing polymer length. Secondly, we reveal that the anisotropic feature of the rod-like polymer is a crucial factor in compaction. A novel non-monotonous behavior against the polymer length is observed under rod-like polymer crowding, which can be ascribed to the competition between anisotropy-induced stretching and crowding-induced compaction. Lastly, we present a quantitative evaluation of the crowding-induced potential, which provides a scenario for understanding compaction from a microscopic viewpoint. The potential profiles with respect to crowder size demonstrate a consistent tendency with the corresponding collapse behavior. The study in the present work provides a deeper insight into the modeling structure and dynamics of macromolecules in crowded media.