Table 1.

Parameter values used to simulate the restrained bead-chain polymer model of chromatin and to provide a physically realistic approximation of the mechanical properties of chromatin, as currently known from experiments

Parameter	Symbol	Reduced units	SI units
Thermal energya		1.0
Bead massb	m	1.0
Lennard–Jones size parameter		1.0	30 nm
Lennard–Jones energy parameter
Bead separation			30 nm
Contact distancec			45 nm
Bond spring constantd
Persistence lengthe			120 nm
Bending energy constant
Time step/damping constantf

^aEnergy per bead per degree of freedom at T = 300 K.

^bRepresentative value based on the experimental measurement of 23.3 MDa for a 15.5-kb fragment of 30-nm chromatin upstream of the chicken -globin locus (42).

^cFollowing Rosa et al. (35), equivalent to assuming that contacts between chromatin fibers are mediated by proteins of 15-nm diameter.

^dFrom experiments, the stretching modulus is 5–150 pN (43), hence ranges from to .

^eFrom experiments, 30 – 200 nm (43).

^fTo maximize conformation sampling efficiency, we used the largest value of found to maintain stability of the BD simulations. A lower bound for can be estimated by considering a chromatin sphere of radius r = 15 nm and using with the viscosity of water = 890 µPa s at 25°C and 1 bar (44). Then, 18 ns.