FIGURE 9.

(A) A sample refolding trajectory starting from the stretched state. The hairpin was initially unfolded to a fully stretched state and f_Q was set to zero at t ≈ 20 μs. End-to-end distance monitored as a function of time shows that refolding occurs in steps. (B) The deviation of dihedral angles from their values in native state as a function of time. The large deviation of the dihedral angles in the loop region can be seen in the red strip. Note that this strip disappears around t ≈ 300 μs, which coincides with the formation of bonds shown in C. The value f_B is the fraction of bonds with pink color, indicating that the bond is fully formed.