Highlights•Standard force fields prescribe overly attractive DNA-DNA and DNA-protein
interactions.•Recently improved force fields enable simulations that reproduce and predict …

Gene regulation in eukaryotes requires the controlled access of sequence-specific
transcription factors (TFs) to their sites in a chromatin landscape dominated by …

Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly
wrap∼ 147 DNA base pairs around an octamer of histone proteins. How nucleosome …

ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …

The very chemical structure of DNA that enables biological heredity and evolution has non‐
trivial implications for the self‐organization of DNA molecules into larger assemblies and …

DNA dynamics can only be understood by taking into account its complex mechanical
behavior at different length scales. At the micrometer level, the mechanical properties of …

The intricacies of the 3D hierarchical organization of the genome have been approached by
many creative modeling studies. The specific model/simulation technique combination …

Chromatin organization plays a critical role in cellular function by regulating access to
genetic information. However, understanding chromatin folding is challenging due to its …

Eukaryotic cells must fit meters of DNA into micron-sized cell nuclei and, at the same time,
control and modulate the access to the genetic material. The necessary amount of DNA …

Nucleosomes containing the histone variant H2A. Z are important for gene transcription
initiation and termination, chromosome segregation and DNA double-strand break repair …