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. 2005 Mar 4;88(6):3770–3779. doi: 10.1529/biophysj.104.055269

FIGURE 1.

FIGURE 1

Representation of a three-site dsDNA and its homologous three-site filament during the simulations. Each rectangle stands for one base (or basepair) with its neighborhood. All filament sites always keep the same 1.5 size, whereas the dsDNA sites' lengths can change (variables li). Variable r indicates the relative position of the filament to the DNA. Variables ni indicate which DNA site is bound to which filament site. (A) State of the system at time-step t (no bond between the filament and the DNA). (B–D) Possible state of the system at time-step t + 1. (B) Update of the li's, example of a length exchange between sites 1 and 2. (C) Update of the li's, example of a length exchange between site 1 and the thermal bath. (D) The ni update, example of the formation of a bond between DNA site 1 and filament site 2.