Thermodynamics and kinetics analysis of simulated passive diffusion. (A) Coarse-grained model of the passive diffusion through the NPC, with the NPC modeled as a cylindrical scaffold, with flexible FG repeats anchored to its walls. (B) Simulated and experimental exponential time constants of transport ± 95% confidence intervals, plotted as a function of molecular mass, with solid lines showing fits to power functions. The absolute values of the simulated time constants are scaled by a single constant value, to allow direct comparison with the experimental data, but without affecting the slope or the relative magnitude of the data points in any way. (C) As in B for simulated NPCs depleted in FG chains from 100% (top) to 50% (bottom). (D, top) As in B and C for FG domains with increasing cohesiveness. The legend indicates the interaction force k between pairs of FG motifs in units of kT/Å over a range of 6 Å. Results did not change significantly for k values in the range 0.0–1.7 kT/Å. (bottom) Energy for the same molecules and cohesiveness level as in the top panel; see also F. (E) The free energy barrier for diffusing macromolecules of different molecular masses in units of kT (color bar), along a cross section of the NPC going parallel to the NE through the NPC central axis (x axis) and from the nucleus to the cytoplasm (Z axis). (F) The free energy barrier projected along the z axis, by integrating over a tube of radius 12 nm about the NPC central axis. The top panel shows the free energy barrier as a function of Z for each substrate; the bottom panel shows the magnitude of the barrier as a function of molecular mass ± 95% confidence intervals.