Regensburg 2022 – scientific programme

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BP: Fachverband Biologische Physik

BP 7: Poster 1

BP 7.20: Poster

Monday, September 5, 2022, 18:00–20:00, P1

Enabling computer simulations of chromatin at physiological density with a resolution of individual nucleosomes — •Tilo Zülske, Aymen Attou, and Gero Wedemann — University of Applied Sciences Stralsund, System Engineering and Information Management, 18435 Stralsund, Germany

The spatial structure of chromatin in the nucleus is important for processes such as the regulation of transcription by facilitating contacts over long distances or by hindering spatial accessibility. Despite extensive research, the spatial structure of chromatin remains enigmatic. Coarse-grained computer simulation models of chromatin help to understand the existing variation of experimental data. Nucleosomes were modelled as spherocylinders connected by elastic segments describing linker DNA. Interactions include stretching, bending, torsion, electrostatic and internucleosomal interactions. Nucleosomes were spaced equidistantly and randomly. Configurations were sampled utilizing Metropolis Monte Carlo and replica exchange algorithms. We studied synthetic fibers of 1.1 Mbp utilizing with periodic boundary conditions that mimic density behavior at different concentrations. The systems comprised 6000 nucleosomes which was more than an order of magnitude larger than the systems computed by us so far. Comparison with experimental results deliver crucial insights how nucleosome positions and density affect the spatial structure and contacts.