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

Area of Science:

• Polymer Physics
• Biophysics
• Fluid Dynamics

Background:

• Polymer chains in shear flow typically exhibit tumbling motion.
• Semiflexible polymers shorter than their persistence length are expected to behave as rigid rods.

Purpose of the Study:

• Investigate the dynamics of double-stranded DNA (dsDNA) segments in shear flow.
• Analyze Euler buckling in dsDNA fragments under varying Weissenberg numbers (Wi).

Main Methods:

• Utilized a bead-spring Hamiltonian model for extensible dsDNA fragments.
• Analyzed Euler buckling using the oriented deterministic state (ODS).
• Performed computer simulations to observe symmetry breaking and chain deformation.

Main Results:

• Euler buckling occurs in dsDNA segments even when shorter than persistence length at higher Wi.
• Observed symmetry breaking in the ODS at a critical Weissenberg number (Wi_c).
• Simulations demonstrated a unimodal to bimodal transformation in the second Rouse mode distribution with increasing Wi.

Conclusions:

• dsDNA segments do not behave as rigid rods in shear flow at higher Wi, exhibiting Euler buckling.
• Symmetry breaking is a key characteristic of dsDNA behavior in shear flow.
• Shear flow induces significant deformation in short dsDNA chains, aligning with experimental findings.