Fig. 7: Schematic summary of kinetic processes.

Each kinetic process (columns) is schematically explained by representing entities involved in it along with their states before (first row) and after (second row) the kinetic process happens. The type of entities involved is represented by different shapes, as indicated on the bottom left part of the figure. The role that the entities play in the kinetic process is indicated by their color (see bottom right legend). Species can either have a specific 3D position (point species and link species) or be held as a count in a well-mixed container (species in tetrahedrons, triangles, vesicle lumen, and raft surface). In addition, vesicles also have a specific 3D position and rafts are centered on specific triangles. Schematics on the top row (before the kinetic process happens) indicate in red which entities can be consumed by the process, in blue which species can be a dependency for the process (the process cannot happen unless these dependencies are met) and in purple species that are an anti-dependency for the process (the process can be prevented from happening by the presence of species). When dependencies are not met, or when anti-dependencies are met, the kinetic process has rate 0 in the SSA and thus cannot happen. Different colors on rafts indicate the different roles that species on the surface can take. Schematics on the bottom row (after the kinetic process happens) indicate in green the entities that are produced or modified by the process. Exocytosis can either release the species on the surface of the vesicle in a patch triangle or as a newly created raft. Endocytosis happens on an endocytic zone which consists in a set of patch triangles (represented by the red dashed line); all the species in these triangles are moved to the surface of the newly created vesicle. A more detailed summary of the kinetic processes can be found in Supplementary Table 1.