Fig. 6: Organized cytoplasm optimizes short-range diffusion by reorganizing obstacle densities.

a Schematic of the model: molecular and organelle reorganization optimizes molecular diffusion by creating longer mean free paths for diffusing molecules. The green object represents a protein of interest diffusing in the cytoplasm; the blue objects represent obstacles in the cytoplasm, such as organelles, cytoskeleton elements, and macromolecular complexes. In this model, proteins in organized cytoplasm remain free to diffuse in all directions. b Diffusion effects of molecular reorganization illustrated with mean squared displacement, MSD (t) = Γt^α. The parameters {Γ, α} estimated for disorganized cytoplasm, organized cytoplasm and the cytosol are {8, 0.75}, {8.25, 0.70}, and {30, 0.85}, respectively. Note that based on the tradeoff between diffusion times and subdiffusivity in the organizing cytoplasm (Fig. 3a), we have assumed that the acceleration of protein movements over these distance scales comes at a cost of slower dynamics over longer distance scales. We also limit the comparison around the length scale of FCS measurements (~0.1–0.5 µm) since protein dynamics may show distinct characteristics at shorter and longer distance scales. Source data are provided as a Source Data file.