Arm retraction and escape transition in semi-flexible star polymer under cylindrical confinement

Abstract

We studied the structure and dynamics of star-shaped polymers by means of coarse-grained molecular dynamics simulations and analysis of structural transitions of semi-flexible macromolecules confined in nano-channels. The conformation of star arms in narrow channels is given by the channel width, arm flexibility and number of arms aligned together in the given region along the channel. We focused on the conformation transition, where all arms are initially stretched in one direction of the narrow channel and were interested in the process of how individual arms escape into a free volume region of channel. We found that the escape transition does not proceed from arm ends but progresses by extension of a loop starting from the branch point; the arms escape in individual steps and the extension of arms depends on how many arms align in parallel in the channel.

Single molecule electrophoresis of star polymers through nanopores: Simulations

“…11,12 Understanding the behavior of star polymers under confinement has been the focus of various recent studies. [13][14][15][16][17][18][19][20][21][22][23][24] This is an interesting problem because the distribution of arms of the star polymer under confinement can lead to rich dynamics, and developing such an understanding is required in devising many applications. For asymmetric star polymers, arm length has been found to have a profound effect on the transport properties of the polymer in gel electrophoresis.…”

“…15 Langevin dynamics simulations show that a four arm star polymer inside a channel with all arms on the same side of the branch point transitions to the equilibrium configuration of two arms on each side by flipping one arm at a time by forming a loop near the branch point instead of retracting the arm end. 16 In the presence of a flowing fluid, conformational dynamics of a star polymer become even more important. 17 The critical capture rate of a star polymer into a nanopore is predicted to have a strong dependence on its functionality (number of arms) for certain arm lengths.…”

Free Energy of a Folded Polymer under Cylindrical Confinement

“…19,[21][22][23][24][25][26][27][28][29][30][31][32][33] Another related process is the arm retraction and escape transition for channel-confined star polymers. 34 Theoretical analyses of unfolding or segregation dynamics obtained from simulations typically employ analytical approximations using scaling arguments for the conformational free energy and its variation with the degree of overlap along the channel. However, such approximations are known to suffer from finite-size effects for the system sizes typically employed in these simulations.…”

“…This effect is closely related to the segregation of two initially overlapping polymers confined to a narrow channel, a process that is also driven by the increase in conformational entropy as polymer overlap decreases. Such entropy-driven polymer separation is thought to be a factor in the process of chromosome segregation of replicating bacteria , and has been extensively studied using computer simulation methods. ,− Another related process is the arm retraction and escape transition for channel-confined star polymers …”

Flow-Induced Translocation of Star Polymers through a Nanopore

“…The expression for this potential is given by where k b is the force constant, and θ is the bond angle. The bond angle is defined such that cos θ = r i j ̂ · r kj ̂, where i, j, and k denote three consecutive beads along the backbone with bead j being bonded to beads i and k. The potential U b was applied to all bond angles in the system including those involving the branch point as the central bead . The value of k b was set to 0 or 20.…”