Compression of a confined semiflexible polymer under direct and oscillating fields

TL;DR

This study uses computer simulations to explore how confined semiflexible polymers, like DNA, collapse into knots under direct and oscillating fields, revealing confinement and field frequency as key factors influencing polymer compaction and knot formation.

Contribution

It demonstrates that external fields can induce polymer collapse and knotting in confined environments, highlighting the roles of confinement strength, field oscillation, and bending rigidity.

Findings

Stronger confinement enhances polymer compaction under direct fields.

Oscillating fields at optimal frequencies induce collapse even in moderate confinement.

Bending rigidity significantly influences folding and knotting behavior.

Abstract

The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long biopolymers tend to collapse under an external field, contrary to the previously reported stretching. These long folded structures have a tendency to form knots that has profound implications in gene regulation and various other biological functions. These knots have been mechanically induced via optical tweezers, nanochannel confinement, etc., until recently, where uniform field driven compression lead to self entanglement of DNA. In this work, we capture the compression of a confined semiflexible polymer under direct and oscillating fields, using a coarse-grained computer simulation model in the presence of long-range hydrodynamics. Within this framework, we show that subjected to direct field, chains in stronger confinements exhibit substantial compaction, contrary to the one in moderate confinements or bulk, where such compaction is absent. Interestingly, an alternating field within an optimum frequency can effectuate this compression even in moderate or no confinement. Additionally, we show that the bending rigidity has a profound influence on the chains folding favourability under direct and alternating fields. This field induced collapse is a quintessential hydrodynamic phenomenon, resulting in intertwined knotted structures, even for shorter chains, unlike DNA knotting experiments, where it happens exclusively for longer chains.