Figure 6.

Dependence of geometry on free lipid (D₀) and apparent diffusion constant (D), encounter frequency, and ${\text{G}}^{\ast }$ production rate. (A) In the free-diffusion case (free), R (purple), ${\text{R}}^{\ast }$ (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, ${\text{R}}^{\ast }$ can be part of the mobile fraction (racks$R^{\ast }$free) or be part of an immobile rack (racks$R^{\ast }$in rack). (B and C) Dependency of D₀ (first row), D (second row), ${\text{R}}^{\ast }$-G encounter rate (third row), and ${\text{G}}^{\ast }$ 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 ${\text{G}}^{\ast }$-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 ${\text{R}}^{\ast }$ in rack case). As a consequence, apparent diffusion, encounter frequency, and ${\text{G}}^{\ast }$ 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 ${\text{G}}^{\ast }$ catalysis. To see this figure in color, go online.