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. 2014 Aug 14;42(16):10425–10432. doi: 10.1093/nar/gku759

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© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 6. — Supercoiling decreases the average duration of the off state (<t_off>) without significantly changing the average duration of the on state (<t_on>). Shown profiles of the evolution of <t_on> and <t_off> correspond to the data presented in Figure 1 where 3000 bp plasmids having two sites with the mutual affinity set to ε = 10 k_BT were supercoiled to different extents. The inset schematically shows the telegraphic profile registering durations of individual on and off states during Brownian dynamics simulations. The on state is characterized by the distance between centres of the beads representing enhancer and promoters being smaller than 6 nm (bead diameter corresponds to 3 nm). If the distance is larger it is classified as the off state. The time is measured in reduced Lennard-Jones units used within HooMD simulation program.