Genomes have complex three-dimensional architectures. The recent convergence of
genetic, biochemical, biophysical, and cell biological methods has uncovered several …

Recent progress in whole-genome mapping and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …

Loop-extrusion and phase-separation have been proposed as mechanisms that shape
chromosome spatial organization. It is unclear, however, how they perform relative to each …

A multitude of sequencing-based and microscopy technologies provide the means to
unravel the relationship between the three-dimensional organization of genomes and key …

Abstract SARS-CoV-2 can re-structure chromatin organization and alter the epigenomic
landscape of the host genome, but the mechanisms that produce such changes remain …

Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to
investigate slow biological processes that involve multiple proteins, nucleic acids, and their …

The genome is the most functional part of a cell, and genomic contents are organized in a
compact three-dimensional (3D) structure. The genome contains millions of nucleotide …

Mammalian chromosomes are organized into megabase-sized compartments that are
further subdivided into topologically associating domains (TADs). While the formation of …

Simulating chromatin is crucial for predicting genome organization and dynamics. Although
coarse-grained bead-spring polymer models are commonly used to describe chromatin, the …

The interior of the eukaryotic cell nucleus has a crowded and heterogeneous environment
packed with chromatin polymers, regulatory proteins, and RNA molecules. Chromatin …