Figure 3:

Distributions of transition-path transit times, p(t_AB), for the models of Ubiquitin folding shown in Figure 2. (a) The distributions calculated via kinetic Monte Carlo simulations of the 1-d native contacts landscape model, the topological configuration model, and the quasi-one-dimensional minimum free-energy path through the topological configuration network. To compare the shapes of the distributions, all transit times are scaled according to the mean transit time, ⟨t_AB⟩, for each model. Also shown are the ten transit times observed in all-atom MD simulations. (b) The same three distributions were fit to the theoretical distribution for a harmonic barrier, $P_{\text{AB}}^{\text{harm}}$, in order to estimate the decay constant, 𝜔^-1 of the exponential tail. The transit-time distribution calculated from the empirical 1-d landscape agrees well with the theoretical distribution using the empirical barrier height, 5.37kT, while the distribution calculated from the topological configuration model can only be fit by $P_{\text{AB}}^{\text{harm}}$ if we set the shape parameter ΔF^† equal to a much lower barrier height of 0.43kT.