Dynamics of a double-stranded DNA segment in a shear flow

TL;DR

This paper investigates how double-stranded DNA behaves in shear flow, revealing that shear can cause buckling and deformation even in segments shorter than their persistence length, through modeling and simulations.

Contribution

It introduces a bead-spring model to analyze Euler buckling in dsDNA under shear flow and demonstrates symmetry breaking phenomena through simulations.

Findings

Buckling occurs at a critical Weissenberg number Wi_c.

Shear induces strong deformation in short DNA segments.

Symmetry breaking is observed as a transition from unimodal to bimodal distribution.

Abstract

We study the dynamics of a double-stranded DNA (dsDNA) segment, as a semiflexible polymer, in a shear flow, the strength of which is customarily expressed in terms of the dimensionless Weissenberg number Wi. Polymer chains in shear flows are well-known to undergo tumbling motion. When the chain lengths are much smaller than the persistence length, one expects a (semiflexible) chain to tumble as a rigid rod. At low Wi, a polymer segment shorter than the persistence length does indeed tumble as a rigid rod. However, for higher Wi the chain does not tumble as a rigid rod, even if the polymer segment is shorter than the persistence length. In particular, from time to time the polymer segment may assume a buckled form, a phenomenon commonly known as Euler buckling. Using a bead-spring Hamiltonian model for extensible dsDNA fragments, we first analyze Euler buckling in terms of the oriented deterministic state (ODS), which is obtained as the steady-state solution of the dynamical equations by turning off the stochastic (thermal) forces at a fixed orientation of the chain. The ODS exhibits symmetry breaking at a critical Weissenberg number Wi$_{\text c}$, analogous to a pitchfork bifurcation in dynamical systems. We then follow up the analysis with simulations and demonstrate symmetry breaking in computer experiments, characterized by a unimodal to bimodal transformation of the probability distribution of the second Rouse mode with increasing Wi. Our simulations reveal that shear can cause strong deformation for a chain that is shorter than its persistence length, similar to recent experimental observations.