The sarcomere model in XB Modeler is composed of actin and myosin filaments. Since the geometrical structure of a sarcomere model is symmetric, XB Modeler deals with a half of it. That is referred as to the half sarcomere model.
In the half sarcomere model, the actin filament is divided into segments at regular intervals. Each segment is referred as to the T/T unit. On the myosin filament, the myosin heads with their arms are lined up in a row at regular intervals as well. The T/T unit is a complex composed of the troponin and tropomyosin molecules. In the activation of muscle, a calcium ion binds with the troponin. As a result of calcium binding to the troponin, a sequence of events is initiated which results in the conformational change of tropomyosin, removing a physical obstruction to formation of the actin-myosin cross-bridges.
XB Modeler applies your state transition models to the individual T/T units and the individual myosin heads, and simulates their transitions with the Monte Carlo method. You can refer the state of T/T unit above the myosin head in defining the transition rates of the myosin head. You can refer also the states of myosin heads below the T/T unit in defining the transition rates of the T/T unit. Furthermore, you can also refer the states of neighboring myosin heads in defining the transition rates of the myosin head. This will be useful to model cooperative interactions between myosin heads. There are also cases where the T/T units are absent on the actin filament like experiments with an optically trapped actin filament. In these cases, you only have to define the state transition model for the myosin heads.