Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers
(Panel A) Scheme of a polymer (red), partially covered by ligands (green), under a tension F. (Panel B) Zoom of a ligand bound to a polymer. Each ligand covers m monomers, and the end-to-end distance of the DNA segment covered by one ligand is given by the parameter a. (Panel C) Effective mechanical decomposition of the partially covered polymer in two chains: one chain corresponds to the naked region and the other chain corresponds to the covered region. Note that distribution of ligands along the polymer is important for thermodynamic properties, this effective mechanical decomposition was done to effectively compute the extension. An extensible worm-like chain (XWLC) model is considered for the naked region, while a freely-jointed chain (FJC) model is assumed for the covered region.