Geometry of the multi-compartment reaction–diffusion model used to simulate myoplasmic Ca²⁺ movements. The myoplasm of a half-sarcomere of one myofibril is divided into 18 equal-volume radially symmetric compartments (six longitudinal by three radial) at a half-sarcomere length of 2 µm. Ca²⁺ release (large downward arrow) occurs into the compartment located at the periphery of the myofibril about ∼0.5 µm from the z-line, the location of the triadic junctions in mammalian fibers (Smith, 1966; Eisenberg, 1983; Brown et al., 1998; Gómez et al., 2006). Ca²⁺ pumping (small upward arrows) is restricted to the six outermost compartments at the periphery of the myofibril (the location of the SR membrane), troponin is restricted to the nine compartments located within 1 µm of the z-line (the location of the thin filaments), and free Ca²⁺ and the soluble Ca²⁺ buffers (e.g., ATP, parvalbumin, and the Ca²⁺ indicator) have access to all compartments via diffusion. The buffer concentrations and reaction rate constants vary with the fiber type and compartment location (see text and Table 2). A set of first-order differential equations is specified for each compartment to describe the Ca²⁺ concentration changes that take place in that compartment caused by release, binding, pumping, and/or diffusion across compartment boundaries. The full set of equations can be integrated simultaneously once the SR Ca²⁺ release flux is specified.