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

Abstract

We use Brownian dynamics (BD) simulations to probe the physics of nonequilibrium polymer compression in extreme nanoconfinement. In our system, modeled 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.

Piston Compression of Semiflexible Ring Polymers in Channels

“…The strong compression forces at tight confinement can induce multiple folding of linear chains into nested hairpins. [ 30 ] Overall, the piston compression behavior of linear semiflexible polymers shown in Figure 2 concurs with the results reported for DNA‐like polymers of N = 1000. [ 21 ]…”

“…The recent simulation of confined linear polymers suggests that compression proceeds by folding the chains into the nested S‐shaped hairpins that ultimately give rise to an organized compressed state. [ 30 ]…”

“…[ 29 ] The study of nonequilibrium piston compression of a strongly confined semiflexible chain in square channels showed the series of chain backfolding into hairpins and the emergence of the organized compressed state. [ 30 ] Simulations of the compression/relaxation cycles in the piston setup in a cylindrical channel allow to characterize the self‐entanglements arising in linear semiflexible polymers. [ 31 ] Furthermore, the piston compression was found to induce a strong tendency for a helical organization in semiflexible polymers confined in a cylinder.…”

Knot formation of dsDNA pushed inside a nanochannel

“…Previously, we have studied compression of semi-flexible polymers in nanochannels using a Langevin dynamics (LD) scheme [44,45]. These LD simulation studies and another recent study [46] have provided substantial insights about many details at smaller length scales unattainable experimentally, but are essential for microscopic understanding and interpretation of nanochannel experiments using fundamental laws of physics.…”

“…One of the advantages of these simulation studies is that, unlike an actual experiment, one can vary confining dimensions and chain stiffness easily and is thus capable of extending the simulation studies for a broader parameter space which is often quite expensive to design experimentally. In our recent LD simulation study [45] we mimicked a recent experiment in silico where dsDNA -modeled as a semi-flexible polymer -was pushed inside a rectangular open-ended nanochannel much longer than required to attain a steady state. By varying the bending rigidity of the chain we showed how the structure evolves from a disordered state to a highly organized spooled state.…”