Brownian dynamics models of the chromatin fiber

In an early attempt to model the dynamics of the chromatin fiber, Ehrlich and Langowski [96] assumed a chain geometry similar to the one used later by Katritch et al. [89] nucleosomes were approximated as spherical beads and the linker DNA as a segmented flexible polymer with Debye-Huckel electrostatics. The interaction between nucleosomes was a steep repulsive Lennard-Jones type potential attractive interactions were not included. 

The missing internucleosome attraction, however, led to problems when longer nucleosome chains were simulated. Starting from an extended zig-zag conformation, folding of a 25-nucleosome chain occurred within 200 ps and the diameter of the resulting fiber-like structure was 45 nm in approximate agreement with values measured for chicken erythrocyte chromatin. On the other hand, the structure 

A more detailed view of the dynamies of a ehromatin chain was achieved in a recent Brownian dynamics simulation by Beard and Schlick [65]. Like in previous work, the DNA is treated as a segmented elastic chain however, the nueleosomes are modeled as flat cylinders with the DNA attached to the cylinder surface at the positions known from the crystallographic structure of the nucleosome. Moreover, the electrostatic interactions are treated in a very detailed manner the charge distribution on the nucleosome core particle is obtained from a solution to the non-linear Poisson-Boltzmann equation in the surrounding solvent, and the total electrostatic energy is computed through the Debye-Hiickel approximation over all charges on the nucleosome and the linker DNA. 

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