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
|
- 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
-
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%