A molecular dynamics study of the electrophoresis of bottle‐brush polyelectrolytes (BPEs) through nanochannels is reported. The BPE molecules consist of a neutral backbone with charged side chains. For strong attractive interactions between the BPE and the wall, the BPE is being trapped on the channel surface. A stretching–shrinking migration of the BPE in a channel of radius 6σ is observed at relatively strong electric fields. The stretching–shrinking transition is periodic for intermediate electric fields but not for stronger electric fields. The BPE also shows a transverse migration toward the wall at weak electric fields, while toward the center with further enhancing the electric field. For a channel with larger radius 12σ, the BPE does not migrate in the stretching–shrinking manner.
