Biophysical Society Thematic Meeting | Hamburg 2022

Biophysics at the Dawn of Exascale Computers

Poster Abstracts

60-POS Board 60 ENABLING COMPUTER SIMULATIONS OF CHROMATIN AT PHYSIOLOGICAL DENSITY WITH A RESOLUTION OF INDIVIDUAL NUCLEOSOMES Tilo Zülske 1 ; Gero Wedemann 1 ; 1 University of Applied Sciences, ETI/IACS, Stralsund, Germany In chromatin DNA is wrapped around histone proteins forming nucleosomes. The nucleosome chain folds into higher order structures as topological domains, chromosomes and the whole nucleus. Despite experimental advancements in electron microscopy, single molecule techniques and mapping of nucleosomes and their modifications, many fundamental features of chromatin remain undiscovered. Due to the poor experimental accessibility of chromatin, computer simulations are valuable tools for research. Computer simulation models of chromatin are usually coarse-grained models describing the main characteristics of the chromatin-fiber. During the last decade simulation approaches mainly focus on small chains, with less than 1000 nucleosomes, because of the high computing resources and time they consume. With the advent of new high-performance computers this barrier can be overcome, and larger systems can be researched. That way the in vivo density situation in the nucleus can be represented better than before. But that is only half the truth: For better computing performance the software needs to be improved e.g., applying technique like parallelization. The application of a technique lies in the responsibility of the developers and can be a complex process. Therefore, we analysed our simulation software with different profiling tools in order to identify the computing bottlenecks. In addition, we enhanced our parallelization strategy and proved the suitability of the used data structures for better computing resource allocation. Finally, we developed a novel Monte Carlo step that enables sampling in high density regimes. We could significantly increase the computing performance of our software. On the supercomputer system HLRN, now we can simulate chains with up to 6000 nucleosomes mimicking conditions of physiological nucleosome concentrations as the interphase nucleus.

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