Evolution of Nested Folding States in Compression of a Strongly Confined Semiflexible Chain

We use Brownian dynamics (BD) simulations to probe the physics of non-equilibrium polymer
compression in extreme nanoconfinement. In our system, modelled on the ‘nanodozer assay’, a gasket
translating at a fixed sliding speed impinges on a nanochannel extended chain. In square channels
with diameter much smaller than the chain persistence length, we find that chain compression
proceeds through a unique folding kinetics driven by repeated double fold nucleation events and
growth of nested folds. We show that the folding kinetics can be understood by coupling a theory
for deterministic contour spooling across the folds with a dynamically varying energy landscape for
fold nucleation. These findings are critical for understanding compression of nanochannel confined
DNA in the sub-persistence length (Odijk) regime.