Dynamic Simulation of active/inactive Chromatin Domains

In this thesis a new model is presented, which describes the formation of higher order chromatin structures with the help of polymer physics for the first time. It is a block-copolymer model for the compactification of the 30nm Chromatin fiber into higher order structures. The idea is that basically every condensing agent (HMG/SAR, HP1, cohesin, condensin, DNA-DNA interaction...) can be modelled as an effective attractive potential of specific chain segments. This way the formation of individual 1Mbp sized rosettes from a linear chain could be observed. Furthermore several Mbp of fiber were simulated, up to an entire chromosome and finally the entire nucleus of Drosophila Melanogaster. The simulation results were compared to experimental data and good agreement was found. The results have been published in the journals Eur. Biophys. J., Int. J. Mod. Phys. C, Int. J. Biol. Phys. and Biophys. Rev. Lett. A detailed list can be found in the appendix. Part of the computation was done on the IBM Blue Gene/L supercomputer at the Forschungszentrum Jülich.

Level thesis:degree_level

thesis.doctoral

Grantor dc:publisher

Universität Heidelberg

Year

2006

Author dc:creator

• Odenheimer, Jens

Contributors dc:contributor

• Heermann, Dieter W.

Repository record source_url

http://www.ub.uni-heidelberg.de/archiv/6555

OAI identifier oai:identifier

oai:archiv.ub.uni-heidelberg.de:6555