Bending and kinking in helical polymers

Abstract

Molecular dynamics simulations provide a powerful tool to understand the mechanics of helical polymers. We report on all-atom simulation of strong bending and buckling of a-helix (AH) filaments by compression loading. We find that the filament buckling proceeds by an abrupt transition from the extended to folded states involving the dramatic drop in the helix span. At the buckling threshold the uniform filament curvature is broken and a sharp kink arises in the AH contour. At high loads the doubly kinked filaments may appear. The bending reversibility up to the point of the kink emergence is confirmed. Simulations identify significant limitations of the popular worm-like chain model in representing the strongly curved filaments. The critical curvatures at the emergence of the doubly kinked structures in helical minicircles of AH and dsDNA are calculated. It is argued that an inclination for helix kinking, and the associated dual filament stiffness, represents a unique attribute of the compression mechanics in helical polymers.

Unfolding Kinetics of a Wormlike Chain under Elongational Flow

“…Another issue is that buckling may be sensitive to the non-uniformity of the elastic properties of the real chain or fiber. Molecular dynamics simulations performed recently on helical polymer chains indicate that the wormlike chain model may have limitations [ 13 ]. An investigation of this issue for chains or fibers buckled under elongational flow is warranted, even though they are less heterogeneous than the polymers considered by Palenc̆ár and Bleha [ 13 ].…”