Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore.

  title={Topological jamming of spontaneously knotted polyelectrolyte chains driven through a nanopore.},
  author={Angelo Rosa and Massimiliano Di Ventra and Cristian Micheletti},
  journal={Physical review letters},
  volume={109 11},
The advent of solid state nanodevices allows for interrogating the physicochemical properties of a polyelectrolyte chain by electrophoretically driving it through a nanopore. Salient dynamical aspects of the translocation process have been recently characterized by theoretical and computational studies of model polymer chains free from self-entanglement. However, sufficiently long equilibrated chains are necessarily knotted. The impact of such topological "defects" on the translocation process… 

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  • Mod. Phys. 80, 141
  • 2008
  • Rev. Lett. 91, 265506
  • 2003
  • Natl. Acad. Sci. USA 90, 5307
  • 1993
J Chem Phys 132
  • 195101
  • 2010
Soft Matter 6
  • 243
  • 2010
  • 92, 5057
  • 1990
Macromolecules 39
  • 2621
  • 2006
  • Rev. E 76, 021803
  • 2007
  • Rev. Biophys. 39, 349
  • 2010
  • 117, 119
  • 1995