ArticleBiophysical journal2023
Brownian dynamics simulations of mesoscale chromatin fibers.
Article in Biophysical journal, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.Nucleic acids research · 2026Article
- Multiscale chromatin modeling of chromosome X structural changes upon inactivation highlights the differential regulatory mechanism ofbioRxiv : the preprint server for biology · 2026Article
- Physical models reveal indirect reader protein interactions that facilitate epigenetic crosstalk.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.bioRxiv : the preprint server for biology · 2025Article
- Incorporating multiscale methylation effects into nucleosome-resolution chromatin models for simulating mesoscale fibers.The Journal of chemical physics · 2025Article
- Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis.The Journal of chemical physics · 2025Article
- The impact of charge regulation and ionic intranuclear environment on the nucleosome core particle.The Journal of chemical physics · 2024Article
- The Impact of Charge Regulation and Ionic Intranuclear Environment on the Nucleosome Core Particle.bioRxiv : the preprint server for biology · 2024Article
- Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis.bioRxiv : the preprint server for biology · 2024Article
- Article
- Genome structural dynamics: insights from Gaussian network analysis of Hi-C data.Briefings in functional genomics · 2024Article
- Embracing exascale computing in nucleic acid simulations.Current opinion in structural biology · 2024Review
- Article
- Regulation of chromatin architecture by protein binding: insights from molecular modeling.Biophysical reviews · 2024Review
- Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics.Nucleic acids research · 2024Article
- Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin.Research square · 2023Article
- Biophysics at the dawn of exascale computers.Biophysical journal · 2023Article
- Genome modeling: From chromatin fibers to genes.Current opinion in structural biology · 2023Review
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3 authors.
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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.
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