Main loop flow diagram.

Blue box represents the start of the program. Red box represent the diffusion processes. Green box and orange box describe the cell mechanics and cycling processes respectively. Finally, yellow boxes represent the data saving process. After initializing the microenvironment, the cells, and the current simulation time t = 0, our model tracks (internally) t_mech (the next time at which cell mechanics methods are run), t_cycle (the next time at which cell processes are run), and t_save (the simulation data output time), with output frequency Δt_save. % represents the modulo operation.