Figure 2.

Visualization of actin density field reveals Arp2/3-driven changes to actin organization. (a) We visualize representative final snapshots from our simulations at various Arp2/3 concentrations as a density field. Cylindrical reaction volume is discretized into voxels of size (100, 100, 100) nm to define local F-actin density. The ends of cylindrical volume are shown as 50-nm-thick yellow cylinders. Please refer to the materials and methods for more information on the actin density field computation. Red squares represent the center of mass of voxels that contain actin above the threshold concentrations (listed above). (b) Plot of the number of domains identified when viewing the actin density field at various threshold concentrations from last 100 s of snapshots (sampling frequency = 5 s) of six replicates. Solid line represents mean, and shaded area represents standard deviation. The X axis is shown on a logarithmic scale, and the bulk actin concentration is shown as a dotted line. Note that the apparent fine structure of fluctuations observed in 25- and 50-nM profiles between 40- and 200-μM thresholds correspond to small (1–2 unit) fluctuations in the number of domains identified. (c) The fraction of total actin monomers included in identified domains was found by integrating over the density field and is plotted versus threshold actin concentrations. The dotted line represents bulk actin concentration (20 μM). Solid lines represent mean, and shaded area represents standard deviation. The fraction of total actin included in the domains reduces with increasing [Arp2/3]. To see this figure in color, go online.