Related papers: Quantifying the mobility of chromatin during embry…
The contributions of active deformation dynamics in cell nuclei to the intra-nuclear positioning of hetero- and euchromatin are investigated. We analyzed the behaviors of model chains containing two types of regions, one with high and the…
Nucleosome organization in eukaryotic genomes has a deep impact on gene function. Although progress has been recently made in the identification of various concurring factors influencing nucleosome positioning, it is still unclear whether…
Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene…
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of…
It has been observed that the growth of the nucleus and the cytoplasm is coordinated during cell growth, resulting in a nearly constant nuclear-to-cell volume ratio (N/C) throughout the cell cycle. Previous studies have shown that the N/C…
Recent studies have suggested that the Nuclear Pore Complex (NPC) plays a significant role in mechanotransduction. When a force is exerted, the NPC's diameter widens, leading to an increased molecular flux into the nucleus. In this study,…
Chromatin is repeatedly deformed in vivo during transcription, nuclear remodeling, and confined migration - yet how mechanical response varies from locus to locus, and how it relates to epigenetic state, remains unclear. We develop a theory…
A biophysical issue how the nuclear size dynamically scales with the cellular size remains mysterious. We develop a theoretical framework in which the interactions between polydisperse biomolecules and the mechanical elasticity of the cell…
Nucleocytoplasmic transport is essential for cellular function, presenting a canonical example of rapid molecular sorting inside cells. It consists of a coordinated interplay between import/export of molecules in/out the cell nucleus. Here,…
The structural origin of the size of the 11 nm nucleosomal disc is addressed. On the nanometer length-scale the organization of DNA as chromatin in the chromosomes involves a coiling of DNA around the histone core of the nucleosome. We…
The three-dimensional organization of chromatin is thought to play an important role in controlling gene expression. Specificity in expression is achieved through the interaction of transcription factors and other nuclear proteins with…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
We investigated the viscoelastic response of model interphase chromosomes by tracking the three-dimensional motion of hundreds of dispersed Brownian particles of sizes ranging from the thickness of the chromatin fiber up to slightly above…
Cell migration is closely linked to cell shape, yet cell size is often assumed to remain constant. This assumption is challenged by recent experiments showing that cells undergo volume loss during spreading and swelling upon activation,…
The cell nucleus houses the chromosomes, which are linked to a soft shell of lamin filaments. Experiments indicate that correlated chromosome dynamics and nuclear shape fluctuations arise from motor activity. To identify the physical…
We use Monte Carlo simulations to study attractive and excluded volume interactions between nucleosome core particles in 30 nm-chromatin fibers. The nucleosomes are treated as disk-like objects having an excluded volume and short range…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
By means of a minimal physical model, we investigate the interplay of two phase transitions at play in chromatin organization: (1) liquid-liquid phase separation (LLPS) within the fluid solvating chromatin, resulting in the formation of…
This paper deals with the possible motion of nucleons in the nucleus, which is due to realistic inter-nucleonic forces. This approach provides new or more substantiated conclusions about the nuclear structure than those based on the…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…