Polymer segregation under confinement: Free energy calculations and segregation dynamics simulations

Abstract

Monte Carlo simulations are used to study the behavior of two polymers under confinement in a cylindrical tube. Each polymer is modeled as a chain of hard spheres. We measure the free energy of the system, F, as a function of the distance between the centers of mass of the polymers, lambda, and examine the effects on the free energy functions of varying the channel diameter D and length L, as well as the polymer length N and bending rigidity, kappa. For infinitely long cylinders, F is a maximum at lambda=0, and decreases with lambda until the polymers are no longer in contact. For flexible chains, the polymers overlap along the cylinder for low lambda, while above some critical value of lambda they are longitudinally compressed and non-overlapping while still in contact. We find that the free energy barrier height, scales as Delta F/k_BT~ND^{-1.93+/-0.01}. In addition, the overlap free energy scales as F/k_BT=Nf(lambda/N;D), where f is a function parameterized by D. For channels of finite L, the free energy barrier height increases with increasing confinement aspect ratio L/D at fixed volume fraction phi, and it decreases with increasing phi at fixed L/D. Increasing the polymer bending rigidity kappa monotonically reduces the overlap free energy. For strongly confined systems, F varies linearly with lambda with a slope that scales as F'(lambda)~-k_BT D^{-beta} P^{-alpha}, where beta approx 2 and alpha approx 0.37 for N=200 chains. These exponent values deviate slightly from those predicted using a simple model, possibly due to insufficiently satisfying the conditions defining the Odijk regime. Finally, we use Monte Carlo dynamics simulations to examine polymer segregation dynamics for fully flexible chains and observe segregation rates that decrease with decreasing entropic force magnitude. The polymers are not conformationally relaxed at later times during segregation.