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

Table 1 Simulation

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	194^a	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%

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