Related papers: Magnetic Polymer Models for Epigenomic Organisatio…
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription,…
Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the…
We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways…
Motivated by the problem of domain formation in chromosomes, we studied a co--polymer model where only a subset of the monomers feel attractive interactions. These monomers are displaced randomly from a regularly-spaced pattern, thus…
Chromosomal crossovers play a crucial role in meiotic cell division, as they ensure proper chromosome segregation and increase genetic variability. Experiments have consistently revealed two key observations across species: (i) the number…
Cellular functions crucially depend on the precise execution of complex biochemical reactions taking place on the chromatin fiber in the tightly packed environment of the cell nucleus. Despite the availability of large data sets probing…
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…
Given the wide range of length scales, the analysis of polymer systems often requires coarse-graining, for which various levels of description may be possible depending on the phenomenon under consideration. Here, we provide a super-coarse…
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
The chromosome is a key player of cell physiology, and its dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described as a Rouse…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational…
"Epigenetic Tracking" is a model of systems of biological cells, able to generate arbitrary 2 or 3-dimensional cellular shapes of any kind and complexity (in terms of number of cells, number of colours, etc.) starting from a single cell. If…
Extrachromosomal DNA (ecDNA) can drive oncogene amplification, gene expression and intratumor heterogeneity, representing a major force in cancer initiation and progression. The phenomenon becomes even more intricate as distinct types of…
Ring polymers are prevalent in natural and engineered systems, including circular bacterial DNA, crown ethers for cation chelation, and mechanical nanoswitches. The morphology and dynamics of ring polymers are governed by the chemistry and…
A large number of studies have shown the existence of metabolic covalent modifications in different molecular structures, able to store biochemical information that is not encoded by the DNA. Some of these covalent mark patterns can be…
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene regulatory elements. These elements include chromatin remodelers,…