Physics – Condensed Matter – Mesoscale and Nanoscale Physics
Scientific paper
2011-10-14
Physics
Condensed Matter
Mesoscale and Nanoscale Physics
11 pges, 14 figures
Scientific paper
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension characteristics of the polymer chain with the convexity properties of the energy vs. stretch profile of its individual monomer subunits. Namely, if the inter-atomic interaction potentials within the monomer are such that its is described by a uniformly convex (concave down) energy function, the stretching of the entire chain is single phase and uniform. However, if the monomer stretching energy as a function of extension has a non-convex (concave up) region, the stretching of the polymer chain separates into two phases: weakly and strongly stretched monomers. We use simplified planar and 3D polymer models to illustrate the basic principles of the proposed model. Specifically, we show that when the secondary structure of a polymer is mostly due to weak non-covalent interactions, the stretching is two-phase, and the force-stretching diagram has the characteristic plateau. This scenario is realized in alpha-helix, consistent with earlier observations based on all-atom molecular dynamics simulations. Using a coarse-grained model of the DNA with realistic potentials, we show explicitly that the double helix exhibits the two-phase behaviour under stretching, in agreement with single molecule experiments. The predicted end points of the force-extension plateau are in close quantitative agreemnt with experiment, while a reasonable qualitative agreement is obtained for the tension value at the plateau. Detailed analysis demonstrtates that breaking of Watson-Crick bonds is not necessary for the existence of the plateau, although some of the bonds do break as the double-helix extends.
Kikot Irina P.
Mazo Mikhail A.
Onufriev Alexey V.
Savin Alexander V.
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