Instruct: Identify the main and secondary category of Arxiv papers based on the titles and abstracts
Query: Statistical Mechanics of Nucleosomes Constrained by Higher-Order
  Chromatin Structure   Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of
nucleosomes separated by stretches of linker DNA are folded into 30-nm
chromatin fibers which in turn form higher-order structures. Each nucleosome,
the fundamental unit of chromatin, has 147 base pairs of DNA wrapped around a
histone octamer. In order to describe how chromatin fiber formation affects
nucleosome positioning and energetics, we have developed a thermodynamic model
of finite-size particles with effective nearest-neighbor interactions and
arbitrary DNA-binding energies. We show that both one- and two-body
interactions can be accurately extracted from one-particle density profiles
based on high-throughput maps of in vitro or in vivo nucleosome positions.
Although a simpler approach that neglects two-body interactions (even if they
are in fact present in the system) can be used to predict sequence determinants
of nucleosome positions, the full theory is required to disentangle one- and
two-body effects. Finally, we construct a minimal model in which nucleosomes
are positioned by steric exclusion and two-body interactions rather than
intrinsic histone-DNA sequence preferences. The model accurately reproduces
nucleosome occupancy patterns observed over transcribed regions in living
cells.

12
The categories of this paper are: nucl-th
24
The categories of this paper are: dg-ga
28
The categories of this paper are: alg-geom
22
The categories of this paper are: chao-dyn
8
The categories of this paper are: hep-ex
34
The categories of this paper are: chem-ph
4
The categories of this paper are: cond-mat
20
The categories of this paper are: acc-phys
9
The categories of this paper are: nlin
14
The categories of this paper are: math-ph
33
The categories of this paper are: plasm-ph
5
The categories of this paper are: gr-qc
37
The categories of this paper are: supr-con
3
The categories of this paper are: physics
23
The categories of this paper are: solv-int
27
The categories of this paper are: comp-gas