Organized states arising from compression of single semiflexible polymer chains in nanochannels

We use molecular dynamics simulation to probe the nonequilibrium physics of single nanochannel-confined semiflexible 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. 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 folds and circular coils. For stiff chains at low flow, we find that the organization is dominated by repeated hairpin folds. For stiff chains 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. Chain organization is retained even when the chain persistence length is on order of the channel width. We show that the global polymer organization, consisting of a number of defined folds and coiled loops, arises from the minimization of the total chain free energy.

Automated summary

In this study, molecular dynamics simulation was used to investigate the nonequilibrium physics of single nanochannel-confined semiflexible polymers in a homogeneous flow field. The results showed that the flow-based compression of the polymer against the end of the nanochannel led to a distinct organization of folds and circular coils. The organization varied with the stiffness of the chains and the flow speed, but was ultimately determined by the minimization of the total chain free energy.