Fig. 1

Molecular random walks with surface dependent diffusion. a) Geometry of the testing environment. The plane the molecules are diffusing on is separated into two parts. A molecules diffusion coefficient can be set depending on the surface it is diffusing on. b Example of a single molecule random walk crossing from a fast diffusion environment to a slow diffusion environment. The blue line indicates the path of the molecule, the grey line indicates the separation between the fast and the slow diffusing environment. c The mean square displacement (MSD) of 20 particles diffusing in different diffusion environments shows anomalous diffusion. d Simulations of a simple reaction system using the geometry depicted in a). Purple Simulations performed using Smoldyn and SmoldynM produce identical results when the simulation setup is identical (same random number seed and therefore seperate simulations for the “fast” (dark purple) and “slow” (light purple) triangular surface. Blue: It is possible to run simulations with SmoldynM where molecules cross over from one triangle to the other and back adopting a new diffusion constant in the process. The development of PIP3 is shown in dark blue for the “fast” and light blue for the “slow” triangle surface