Some aspects of a two-pore translocation problem

We report Brownian dynamics (BD) simulation results for a coarse-grained (CG) model semi-flexible polymer threading through two nanopores. Particularly we study a “tug-of-war” situation where equal and opposite forces are applied on each pore to avoid folds for the polymer segment in between the pores. We calculate mean first passage times (MFPT) through the left and the right pores and show how the MFPT decays as a function of the off-set voltage between the pores. We present results for several bias voltages and chain stiffness. Our BD simulation results validate recent experimental results and offer avenues to further explore various aspects of multi-pore translocation problem using BD simulation strategies which we believe will provide insights to design new experiments.

Crowding-Activity Coupling Effect on Conformational Change of a Semi-Flexible Polymer

The behavior of a polymer in a passive crowded medium or in a very dilute active bath has been well studied, while a polymer immersed in an environment featured by both crowding and activity remains an open problem. In this paper, a systematic Langevin simulation is performed to investigate the conformational change of a semi-flexible chain in a concentrated solution packed with spherical active crowders. A very novel shrinkage-to-swelling transition is observed for a polymer with small rigidity. The underlying phase diagram is constructed in the parameter space of active force and crowder size. Moreover, the variation of the polymer gyration radius demonstrates a non-monotonic dependence on the dynamical persistence length of the active particle. Lastly, the activity-crowding coupling effect in different crowder size baths is clarified. In the case of small crowders, activity strengthens the crowding-induced shrinkage to the chain. As crowder size increases, activity turns out to be a contrasting factor to crowding, resulting in a competitive shrinkage and swelling. In the large size situation, the swelling effect arising from activity eventually becomes dominant. The present study provides a deeper understanding of the unusual behavior of a semi-flexible polymer in an active and crowded medium, associated with the nontrivial activity-crowding coupling and the cooperative crowder size effect.