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- W4296179789 abstract "The relationship between chromatin architecture and function defines a central problem in biology and medicine. Many computational chromatin models with atomic, coarse-grained, mesoscale, and polymer resolution have been used to shed light onto the mechanisms that dictate genome folding and regulation of gene expression. The associated simulation techniques range from Monte Carlo to molecular, Brownian, and Langevin dynamics. Here, we present an efficient Compute Unified Device Architecture (CUDA) implementation of Brownian dynamics (BD) to simulate chromatin fibers at the nucleosome resolution with our chromatin mesoscale model. With the CUDA implementation for computer architectures with graphic processing units (GPUs), we significantly accelerate compute-intensive hydrodynamic tensor calculations in the BD simulations by massive parallelization, boosting the performance a hundred-fold compared with central processing unit calculations. We validate our BD simulation approach by reproducing experimental trends on fiber diffusion and structure as a function of salt, linker histone binding, and histone-tail composition, as well as Monte Carlo equilibrium sampling results. Our approach proves to be physically accurate with performance that makes feasible the study of chromatin fibers in the range of kb or hundreds of nucleosomes (small gene). Such simulations are essential to advance the study of biological processes such as gene regulation and aberrant genome-structure related diseases." @default.
- W4296179789 created "2022-09-18" @default.
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- W4296179789 date "2023-07-01" @default.
- W4296179789 modified "2023-09-30" @default.
- W4296179789 title "Brownian dynamics simulations of mesoscale chromatin fibers" @default.
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- W4296179789 doi "https://doi.org/10.1016/j.bpj.2022.09.013" @default.
- W4296179789 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36116007" @default.
- W4296179789 hasPublicationYear "2023" @default.
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