Related papers: Organization and Dynamics of Chromosomes
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…
One of the central problems in epigenetics is how epigenetic modification patterns and chromatin structure are regulated in the cell nucleus. The polymer Potts model, a recently studied model of chromatins, is introduced with an offset in…
We discover a new type of nonequilibrium phase transition in a model of chromatin dynamics, which accounts for the coherent motions that have been observed in experiment. The coherent motion is due to the long-range cooperation of molecular…
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a…
Inter- or intramolecular coupling processes between chromophores such as excimer formation or H- and J-aggregation are crucial to describing the photophysics of closely packed films of conjugated polymers. Such coupling is highly distance…
The spatial organization of chromatin within the nucleus plays a crucial role in gene expression and genome function. However, the quantitative relationship between this organization and nuclear biochemical processes remains under debate.…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
The ability of eukaryotic cells to squeeze through constrictions is limited by the stiffness of their large and rigid nucleus. However, migrating cells are often able to overcome this limitation and pass through constrictions much smaller…
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene…
We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active…
This study presents an enhanced method for analyzing cluster dynamics, with a particular focus on tracking clusters' continuity over time using time-series data from molecular dynamics (MD) simulation. The proposed method was applied to…
Investigating the dynamics of chromatin and the factors that are affecting it, has provided valuable insights into the organization and functionality of the genome in the cell nucleus. We control the expression of Lamin-A, an important…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
The transport of biomolecules across a cell membrane is an important phenomena that plays a pivotal role in the functioning of biological cells. In this paper, we investigate such processes by modeling the translocation of polymers through…
Topological constraints can affect both equilibrium and dynamic properties of polymer systems, and can play a role in the organization of chromosomes. Despite many theoretical studies, the effects of topological constraints on the…
Heteroclinic cycles are widely used in neuroscience in order to mathematically describe different mechanisms of functioning of the brain and nervous system. Heteroclinic cycles and interactions between them can be a source of different…
We perform large scale three-dimensional molecular dynamics simulations of unlinked and unknotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a…