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Table 1 Simulation

From: Inferring the physical properties of yeast chromatin through Bayesian analysis of whole nucleus simulations

Parameter Notation Unit Range Wong 2012 MAP Best model
Chromatin persistence length P nm 27–252 30 88 69
Chromatin compaction C bp/nm 25–110 83 61 50
Chromatin fiber width W nm 30–60 20 37 30
Microtubule length L nm 200–400 380 390 400
rDNA diameter W rDNA nm 194a 200 NA 194
Radius of nucleus R N nm 1000 1000 NA 1000
  1. This table lists the main parameters used in our model (first column), together with their notation (second column), and units (third column). The fourth column indicates the range over which the parameters are varied (for parameters that are not varied but held fixed in all simulations, a single value is given). The fifth column indicates values used in our previous model by Wong et al. [35]. The sixth column indicates the maximum a posteriori (MAP) estimate of each inferred parameter as obtained by our method using the whole set of experimental data. The seventh column lists the parameters of the “best model” used for Figs. 4 and 5. NA: not applicable. Additional file 2 lists all 144 models and their parameter values. More details on model parameters are provided in Additional file 1: Supplementary Methods
  2. aThis diameter corresponds to a net volume of the 150 rDNA beads that equals V = 14% of the nuclear volume, i.e. an effective volume (considering free space between rDNA beads) of ~2 V ~30% of the nucleus. For the parameter mismatch analysis, W rDNA was varied over a range of 138–251 nm, corresponding to a net volume fraction V = 5–30%, and an effective fraction of ~2 V = 10–60%