Organized States Arising from Compression of Single Semi-Flexible Polymer Chains in Nanochannels

We use molecular dynamics (MD) simulation to probe the non-equilibrium physics of single nanochannel-confined semi-flexible polymers in a homogeneous flow field. The flow field compresses the polymer against the end of the nanochannel, simulating an experiment of a nanochannel confined chain compressed against a slit barrier. For sufficiently stiff chains inside a cylindrical channel, we observe that the flow-based compression gives rise to a packing of the chain against the channel end that possesses a striking organization, consisting of interweaving of hairpin folds and circular coils along the channel walls. At low flow, we find that the organization is dominated by repeated folds. At higher flow, we observe that circular coils arise along with the folds, with folding and coiling domains becoming interwoven at the highest flow speeds. Notably, such chain organization starts appearing even when the chain persistence length is only on order of the channel width. We show that the global polymer organization, consisting of a number of defined folds and coils, arises from the minimization of the total chain free energy.