Fig. 5: Simulations for the transition between O → B transition.
From: Theory and simulations of condensin mediated loop extrusion in DNA
a Left panel: Representative pictures from the simulation. Red, blue, light blue, orange, and green spheres are the heads, hinge, CC, elbows, and DNA, respectively. Right panel: The trajectory for the change in head-hinge distance (R). ΔtL is the time step of simulation (SI Sec. I). b Predicted distributions, P(R)s, of the head-hinge distance during one catalytic cycle of the motor. The peak positions for open state and closed state (R1 = 38 nm and R2 = 16 nm, respectively). The large width and the overlap between the two distributions implies a great deal of conformational heterogeneity that contributes also to broad step size distribution. c The distribution for R taken (digitized) from Ryu et al.19. The agreement between the simulations and experiments is remarkable, especially considering that the model has no fitting parameters. d Histograms in orange are the distribution of L in the open shape, and the blue histograms are the distribution in the closed shape. The inset shows the distributions for L > 90 nm. We performed 50 simulations from which 100,000 sample points were used to create the histograms. Data plotted in a–d are provided as a Source Data file.
