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

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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.

Indexes of the most distant beads in a star-shaped polymer during transition. The chain is indexed from the connecting point as I = 1 to the chain’s end with I = 100 as computed for semi-flexible molecules with b = 20, in a narrow channel with D = 10. Dashed line Process of arm retraction if it proceeded from arm end (opposite to what is observed)

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Acknowledgments

This work was supported by the Slovak Research and Development Agency (Grant No. SRDA-0451-11) and the Scientific grant agency of the Ministry of Education of the Slovak Republic (VEGA Grant Nos. 2/0093/12 and 2/0068/13).

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Correspondence to Dušan Račko.

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Račko, D., Cifra, P. Arm retraction and escape transition in semi-flexible star polymer under cylindrical confinement. J Mol Model 21, 186 (2015) doi:10.1007/s00894-015-2735-9

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Keywords

  • Semi-flexible
  • DNA
  • Molecular dynamics
  • Confined
  • Nano-channel
  • Electrophoresis