Nick Kepper (DKFZ & Universität Heidelberg): 3D modeling and computer simulations of chromatin at different scales

Dienstag, 28.05.2013 16:15 im Raum Seminarraum 222, Institut für Angewandte Physik, Corrensstraße 2
Mathematik und Informatik

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.

Angelegt am Donnerstag, 16.05.2013 23:25 von cengw_01
Geändert am Donnerstag, 16.05.2013 23:25 von cengw_01
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