Figure 6

Conformational dynamics and chemical kinetics. Calculation of the MFPT from the node 2^′ through 2^′′ to ∗ on the network shown in Figure 5c can be performed using Eqs. 20 and 21as follows. First, it is sufficient to modify the initial network (a) by replacing the directed link from the node 2^′′ to the node ∗ with the link redirecteded to the node 2^′′. Then, we calculate in a such prepared network (b) the MFPT from the node 2^′ to the node 2^′′ using Monte Carlo or Hill’s method and simultaneously the steady-state occupation probability $p_{2^{\mathrm{\prime \prime }}}^{\text{st}}$ of node 2^′′, which we next multiply by the transition probability $v_{+2^{\mathrm{\prime \prime }}}$ to ∗. The inverse of this product plus the MFPT between nodes 2^′ and 2^′′, sum up to the total MFPT obtained for the original network (a).