Related papers: A Random Loop Model for Long Polymers
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…
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…
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…
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…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
In entangled polymer systems, there are several characteristic time scales, such as the entanglement time and the disengagement time. In molecular simulations, the longest relaxation time (the disengagement time) can be determined by the…
A polymer folding model on the square lattice is constructed with attractive contact interactions of strength 1/c^2, 0<c<1. The corresponding model on a dynamical random lattice, with freely fluctuating co-ordination number at each vertex,…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
The statistical mechanics of polymer loops entangled in the two-dimensional array of randomly distributed obstacles of infinite length is discussed. The area of the loop projected to the plane perpendicular to the obstacles is used as a…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
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…
The statistics of randomly branching double-folded ring polymers are relevant to the secondary structure of RNA, the large-scale branching of plectonemic DNA (and thus bacterial chromosomes), the conformations of single-ring polymers…
Mesoscale behavior of polymers is frequently described by universal laws. This physical property motivates us to propose a new modeling concept, grouping polymers into classes with a common long-wavelength representation. In the same class…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
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…
The fundamental understanding of loop formation of long polymer chains in solution has been an important thread of research for several theoretical and experimental studies. Loop formations are important phenomenological parameters in many…
The rapid collapse of a polymer, due to external forces or changes in solvent, yields a long-lived `crumpled globule.' The conjectured fractal structure shaped by hierarchical collapse dynamics has proved difficult to establish, even with…
Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop…
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…