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. 2018 May 29;14(5):e1006159. doi: 10.1371/journal.pcbi.1006159

Table 1. Simulation parameters at different coarse-grainings for a semi-flexible, self-avoiding polymer with L/Le = 70 and ρ = 0.009 bp/nm3 (drosophila case).

Lattice volumic fraction Φ, Kuhn size Nkνlk/b (in kbp), bond length of the polymer b (in nm) and Kuhn length lk (in nm) at different coarse-grainings (CG) of ν = 0.2, 2, 5, and 10 kbp. Each fifth subcolumn represents the time in msec equivalent to one Monte-Carlo steps (MCS). Similar tables for the yeast and mammalian cases are given in the supplementary text.

200 bp 2 kbp 5 kbp 10 kbp
Φ0 Nk0 b0 lk0 MCS Φ Nk b lk MCS Φ Nk b lk MCS Φ Nk b lk MCS
0.043 1.0 10.6 55.4 0.015 0.027 29 20.5 305 0.002 0.09 44 41.9 374 0.4 0.37 44 83.8 372 8.71
0.039 23 23.1 273 0.010 0.17 29 51.3 304 1.2 0.68 29 102.5 304 17.3
0.049 20 24.9 252 0.040 0.24 23 57.6 271 1.7 0.97 23 115.3 274 22.1
0.076 15 28.8 218 0.083 0.29 20 61.5 252 2.5
0.113 11 32.9 190 0.181 0.45 15 70.9 220 5.4