Nick Kepper (DKFZ & Universität Heidelberg): 3D modeling and computer simulations of chromatin at different scales
Tuesday, 28.05.2013 16:15 im Raum Seminarraum 222, Institut für Angewandte Physik, Corrensstraße 2
The DNA in human cell nuclei has a diameter of ~2 nm and a length of ~2 m. In the first compaction step, DNA forms together with proteins the nucleosome, which then forms the chromatin. The spatial organization of chromatin is a central factor for controlling the DNA access of protein factors involved in transcription, DNA replication and repair. In diploid human cell nuclei DNA / chromatin is divided into 46 chromosomes. Here, three spatial models will be used to answer questions at different scales of DNA / chromatin organization. With all atom molecular dynamic simulations the interactions between DNA and proteins in the nucleosome were analyzed. Based on nucleosomes and connecting linker DNA, a coarse grain model was developed, combined with a Metropolis Monte Carlos algorithm. This model was used to analyze descriptions of more active euchromatin and more condensed heterochromatin and interpret force extension experiments. A more coarse grain model using Brownian Dynamics simulation technique was used to simulate dynamics in the cell nucleus and simulate the compaction of genes in the context of chromosome territories.