Fig. 3: Validation of vesicle mobility, and mobility of molecules on vesicle surface.

a Vesicle diffusive steps experienced by a vesicle diffusing at 0.06 μm²s⁻¹ for two different choices of Δt of 0.1 ms (blue) and 1 ms (orange). b Vesicle diffusion in a cytosolic volume with varying fractions of the volume occupied. Free diffusion (yellow line) is compared to expected \({6Dt}\) solution, and increasing cytosolic occupancy of 20%, 40% and 60% show increasingly reduced mobility, as expected. c The apparent diffusion coefficient of vesicles vs time in the STEPS implementation of the MFT model of Rotham et al.⁸ showing reduced apparent diffusion rate with time due to steric interactions with mitochondria and other vesicles, agreeing with the results from that study. d Validation of active transport, with vesicles maintaining the correct speeds upon interactions with paths at 0.5 μm s⁻¹ (orange) and 0.3 μm s⁻¹ (blue). e The STEPS implementation (blue) of surface species angular displacement by the Ghosh algorithm⁵² (orange) for an example diffusion step of 2 ms for a surface species with diffusion rate on the vesicle surface of 1 μm²s⁻¹. f Mean and standard deviation of spherical surface diffusion over a range of diffusion timesteps (n = 100,000 independent simulations). The Ghosh algorithm (orange) is compared to a surface diffusion model on a spherical mesh surface in STEPS (blue).