Related papers: Chromatin Folding in Relation to Human Genome Func…
The state of chromatin in individual cells is directly related to the state of the whole organism and may be used for assessment of the state of the whole organism. Many hereditary diseases are connected with chromatin rearrangements.…
The fractal globule state is a popular model for describing chromatin packing in eukaryotic nuclei. Here we provide a scaling theory and dissipative particle dynamics (DPD) computer simulation for the thermal motion of monomers in the…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
We review the mechanism and consequences of the "bridging-induced attraction", a generic biophysical principle which underpins some existing models for chromosome organisation in 3-D. This attraction, which was revealed in polymer…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Nucleosomes organize the folding of DNA into chromatin and significantly influence transcription, replication, regulation and repair. All atom molecular dynamics simulations of a nucleosome and of its 146 basepairs of DNA free in solution…
In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles,…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
We study a simple solvable model describing the genesis of monomer sequences for hetero-polymers (such as proteins), as the result of the equilibration of a slow stochastic genetic selection process which is assumed to be driven by the…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
Using a bead-spring model of bacterial DNA polymers of {\em C. crescentus} and {\em E. coli} we show that just $33$ and $38$ effective cross-links at special positions along the chain contour of the DNA can lead to the large-scale…
We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem…
The interaction between protons and graphene is attracting a large interest due to recent experiments showing that these charged species permeate through the 2D material following a low barrier (~ 0.8 eV) activated process. A possible…
There are many experimental data indicating the correlations of the changes in high level of organization of chromatin in human cells and changes in the state of the whole organism related to disease, state of tiredness or aging. In our…
Nucleosome core particle is a dynamic structure -- DNA may transiently peel off the histone octamer surface due to thermal fluctuations or the action of chromatin remodeling enzymes. Partial DNA unwrapping enables easier access of…
The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with…
It has been shown that genome spatial structures largely affect both genome activity and DNA function. Knowing this, many researchers are currently attempting to accurately model genome structures. Despite these increased efforts there…
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…