相关论文: Locality of contacts determines the subdiffusion e…
Many researchers have been encouraged to describe the dynamics of chromosomal loci in chromatin using the classical Rouse model of polymer dynamics by the agreement between the measured mean square displacement (MSD) versus time of…
Active loop extrusion - the process of formation of dynamically growing chromatin loops due to the motor activity of DNA-binding protein complexes - is firmly established mechanism responsible for chromatin spatial organization at different…
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…
The classic model of eukaryotic gene expression requires direct spatial contact between a distal enhancer and a proximal promoter. Recent Chromosome Conformation Capture (3C) studies show that enhancers and promoters are embedded in a…
We investigate the conformational and dynamical properties of a partially active Rouse chain, where activity is localized within a specific segment, positioned at various locations along the chain and spanning any given length. Through…
We use Brownian dynamics simulations to study the formation of chromatin loops through diffusive sliding of slip-link-like proteins, mimicking the behaviour of cohesin molecules. We recently proposed that diffusive sliding is sufficient to…
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…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
Chromatin loop extrusion is a popular model for the formation of CTCF loops and topological domains. Recent HiC data have revealed a strong bias in favour of a particular arrangement of the CTCF binding motifs that stabilize loops, and…
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
The Rouse model can be regarded as the standard model to describe the dynamics of a short polymer chain under melt conditions. In this contribution, we explicitly check one of the fundamental assumptions of this model, namely that of a…
Chromatin and associated proteins constitute the highly folded structure of chromosomes. We consider a self-avoiding polymer model of the chromatin, segments of which may get cross-linked via protein binders that repel each other. The…
A living cell is an active environment where the organization and dynamics of chromatin are affected by different forms of activity. Optical experiments report that loci show subdiffusive dynamics and the chromatin fiber is seen to be…
An active loop-extrusion mechanism is regarded as the main out--of--equilibrium mechanism responsible for the structuring of megabase-sized domains in chromosomes. We developed a model to study the dynamics of the chromosome fibre by…
Motivated by the recent experimental observations of the DNA loop extrusion by protein motors, in this paper we investigate the statistical properties of the growing polymer loops within the ideal chain model. The loop conformation is…
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…
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…
The formation of interface from an initial sharp interface in polydisperse A/B blends is studied using the external potential dynamic method. The present model is a nonlocal coupling model as we take into account the correlation between…
Chromatin looping is a major epigenetic regulatory mechanism in higher eukaryotes. Besides its role in transcriptional regulation, chromatin loops have been proposed to play a pivotal role in the segregation of entire chromosomes. The…