[(a)–(f)] A series of snapshots showing an example of a polymer reversal event observed in simulations. Also shown in (a) is the definition of reversal reaction coordinate, equal to the difference of the positions of the first and last monomers measured along the pore axis. (g) An example of a trajectory showing several chain reversal events.
The free energy plotted as a function of the reaction coordinate for a polymer confined inside pores of different radius. is a double well symmetric with respect to . Here we show only the left side of the double well. The kink observed at small values of is due to the discrete nature of the end beads, which are in close proximity at .
(a) The reversal rate constant plotted as a function of the pore radius for a chain consisting of monomers. Comparison of transition state theory, Kramers’ theory, the forward flux sampling method and brute-force simulations. See text for the details of the calculations. (b) The reversal rate constant plotted as a function of the pore radius for a chain consisting of monomers. Comparison of transition state theory, Kramers’ theory, and the forward flux sampling.
Comparison of the actual dynamics along the reaction coordinate with those approximated by a one-dimensional Langevin equation in the potential of mean force . For one-dimensional Langevin dynamics, the effective friction coefficient was estimated from Eq. (17). The data are for and . (a) The time-dependent transmission factor defined by Eqs. (24) and (25). (b). The position autocorrelation function used to evaluate the friction coefficient according to Eq. (17).
The reversal rate constant plotted as a function of the polymer length for : Comparison of different methods.
The reversal free energy barrier plotted as a function of the chain length for different values of the pore radius. See Fig. 2 and Sec. III for the description of .
The mean radial compression force per monomer [Eq. (31)] for a ring polymer and linear polymer confined inside a pore of radius . For the linear polymer, the straight line shown is the best fit for and is described by the equation , which is consistent with the theoretical scaling law. For the ring polymer, the straight line shown fits the data for and is described by .
The TST prefactor as a function of the pore radius for different chain length. The lines are described by the formula .
The transmission factor plotted as a function of the polymer length for . The solid line is described by .
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