Mesoscopic Model and Free Energy Landscape for Protein-DNA Binding Sites: Analysis of Cyanobacterial Promoters
Figure 1
Simplified illustration of the DNA-particle interaction model.
The one-dimensional chain (solid spheres) models the DNA chain considering a single relevant degree of freedom per base pair, and two phenomenological potentials [
and
]. The brownian particle, with coordinate
(dim ellipse), diffuses along the chain interacting with open regions through the potential
.