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lammps/tools/moltemplate/examples/coarse_grained/chromosome_metaphase_Naumova2013/README_FIRST.txt
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This is an implementation of the "two-stage" model used by Maxim Imakaev
in the Naumova et Al 2013 Science paper on metaphase chromatin.
(Download the supplemental materials section and scroll down to the section:
"Two-stage process: linear compaction - axial compression")
---- SMALL MODIFICATION ----
Unlike that study, I did not use "softened" Lennard-Jones potentials
(which allow the chains to pass through each other).
--- Why use moltemplate? ---
Honestly, you don't need to use moltemplate to build this polymer.
It is almost counter-productive to use moltemplate to build this kind of
polymer because it is so simple. (The polymer has only 1 bead per atom.
It just makes it more complicated to introduce all these extra
files including monomer.lt, condensin.lt and system.lt, especially considering
that system.lt is a complex file which is generated by a separate script.)
However building the sytem using moltemplate may pay off if you
replace each point-like monomer with a multi-atom molecule later on.
(Right now, using moltemplate to build this system is sort of overkill.
I'll post an example of building more complex models of chromatin eventually.)
Anyway, the two-stage model at the end of Naumova et al Science 2013 uses the "30nm-fiber" model, whose details are (somewhat vaguely) described in the supplemental materials section.
---- 10-nm fiber model: ----
For the 10nm model,
n=128000,
L=200,
U(alpha)=5*(1 - cos(alpha))
bond_length=1.0 (=10nm)
sigma=1.0 (particle radius = 10nm)
---- 30-nm fiber model: ----
"The 30nm-like fiber was modeled by increasing the volume of each monomer and the amount of DNA represented by each monomer by a factor of 4.25, while keeping other parameters the same at the monomer level."
I interpret this to mean that, for the 30nm model,
n=128000/4.25~=30117 (however I rounded up to 32768=2^15)
L=200/4.25~=47 (however I rounded up to 51)
U(alpha)=1.17647*(1 - cos(alpha)) (5/4.25=1.17647)
To increase the volume by a factor o 4.25, I increase both the diameter of each
bead (the "sigma" parameter), and the bond-lengths connecting them from
1.0 (corresponding to 10nm) to 4.25^(1/3)~=1.6198 (corresponding to 16.198nm).
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