Polymer segregation in cylindrical confinement revisited: A three-dimensional free energy landscape

We study the dynamic separation process of two identical polymers confined in a cylinder, allowing both ends of the polymer chains to be free, based on a three dimensional (3D) free energy landscape combined with direct molecular dynamics (MD) simulations. The landscape suggests that the probability distribution curves of induction time (segregation time) reduced by corresponding average values would collapse into a single one under the so-called blob constraint, i.e., κ ≡ ND ^-1/ is a constant, where N is the number of monomers in a chain, D is the channel diameter, and ν ≃ 3/5. Such a collapse behavior is well demonstrated by direct MD simulations and further by Brownian dynamics simulations of an effective particle on the 3D landscape. Interestingly, Brownian dynamics shows that the average induction time $$ or segregation time $$ decreases monotonically with κ in a power-law dependence if the diffusion coefficient $$ is fixed, suggesting a distinct mechanism of the induction process which is neither diffusion nor barrier-crossing, in accordance with trajectory analysis by using MD simulations. In addition, we find that both $$ and $$ show good power-law dependencies on the polymer length N under the blob constraint.