Figure 4.

Variation of r, k₃, ξ, and β⁺ = β⁻ = β for a single protein. The red curve corresponds to the boundary conditions β₀ = 0, r₀ = 0.05 nm, and the green curve to r₀ = 0, β₀ = 0.05. Even if r₀ = 0, i.e., the protein does not change the radius of the molecule at the binding site, a change in the phase angle β₀ ≠ 0 can cause the radius to change at locations away from the binding site. Similar coupling exists among other strain parameters. The magnitudes r₀ and β₀ chosen here ensure that the change in the groove width, a parameter whose magnitude is known,¹² is in the correct range (3 Å). The decay length is l_d = ζ⁻¹ ≈ 10 bp, which is close to the one documented in literature.^7,23