Concept of implementing the reaction-diffusion model of apoptosis execution. The model was implemented by assigning a spatially progressing permeabilisation of the outer mitochondrial membrane. Through membrane pores, Smac and cyt-c are released into the cytosol (red dots) where they initiate the apoptosis execution network. Cyt-c induces apoptosome formation, while Smac inhibits caspase inhibitor XIAP. As visualised here by multiple panes of the signalling map, the spatially progressing activation of the apoptosis execution network was modelled in discrete steps (n = 300) across distance (30 μm). The reaction network was calculated by partial differential equations and allowed for diffusive exchange of the reactants along spatial concentration gradients.