Mixing and Demixing Arising from Compression of Two Flexible and Semi-Flexible Polymer Chains in Nanochannels

We use molecular dynamics (MD) simulation to probe the non-equilibrium physics of two nanochannel-confined polymers in a homogeneous flow field. We find that the internal organization of the two chains takes the form of interwoven folds and circular coils for semi-flexible chains. This organization can lead to mixing or demixing depending on chain stiffness and flow speed. For sufficiently stiff chains, at low and intermediate flow, the two chains adopt a folded configuration that favors mixing. At high flow, the two chains adopt a predominantly coiled configuration that favors demixing, but only when the two chains are initialized in a demixed state. For decreasing stiffness, the chains start to aggregate locally instead of mixing smoothly. In the flexible chain limit, the two chains adopt a locally demixed configuration consisting of large aggregates that undergo complex stochastic dynamics, diffusing, disintegrating and reforming. In this low stiffness/flexible regime, new aggregates nucleate only when the two chains diffuse into a particular configuration that allows the chain closest to the barrier to penetrate through the second chain. Behavior resembling the low stiffness regime simulation results have been observed in nanofluidic experiments where two differentially labelled DNA chains inside nanochannels are compressed by buffer flow against a slit barrier that blocks the DNA while permitting buffer to escape.