Dependence of geometry on free lipid (D0) and apparent diffusion constant (D), encounter frequency, and production rate. (A) In the free-diffusion case (free), R (purple), (yellow), and G (blue) are all mobile. In the rack geometry, 80% of R is set as immobile in racks of dimers, whereas the other molecules diffuse freely. Here, can be part of the mobile fraction (racksfree) or be part of an immobile rack (racksin rack). (B and C) Dependency of D0 (first row), D (second row), -G encounter rate (third row), and production, given the geometries in A. Note the smaller scale of the y axis between the plots of free lipid and apparent diffusion constant. In B, the D0 of the free-diffusion case is imposed for all geometries. Consequently, the crowding effects of the geometry can be seen in the apparent diffusion constant and the resulting encounter and -production rates. In C, the crowding effects of the geometry are compensated by imposing higher free-lipid-diffusion constants on the particles (note that the diffusion of G is set to compensate the loss of diffusion contribution from the immobilized R in the in rack case). As a consequence, apparent diffusion, encounter frequency, and production are similar in all geometries. All data shown are averages and standard errors of six simulations per scenario. Simulation timescales are 100 μs for diffusion analysis, 1 ms for encounter analysis, and 10 ms for catalysis. To see this figure in color, go online.