Fig. 5: A coarse-grained model for understanding motor mechanism.
From: Simulating a chemically fueled molecular motor with nonequilibrium molecular dynamics
Motor dynamics can be coarse grained onto an eight-state kinetic model based on the position of the shuttling ring relative to the two binding sites and the presence or absence of at least one C particle blocking group at each catalytic site. Due to symmetries there are seven macroscopic rates in the system, labeled as transitions between certain states. The kinetic model decomposes into four fundamental cycles, shown in purple, with mean steady-state currents oriented in the same direction as the cycle affinities.
