Related papers: Nucleosome positioning and energetics: Recent adva…
The insertion of HIV and other DNA elements within genomes underpins both genetic diversity and disease when unregulated. Most of these insertions are not random and occupy specific positions within the genome but the physical mechanisms…
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…
In this work we examine how volume exclusion caused by regions of high chromatin density might influence the time required for proteins to find specific DNA binding sites. The spatial variation of chromatin density within mouse olfactory…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient…
We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as…
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…
Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from…
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…
In this study, structural stability, electronic, optical and vibrational properties of DNA nucleobase adsorbed Graphene Quantum Dot (GQD) has been investigated using density functional theory. Based on state-of-art electronic structure…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture…
In a certain way, this paper presents the continuation of the previous one which discussed the harmonic structure of the genetic code (Rakocevic, 2004). Several new harmonic structures presented in this paper, through specific unity and…
This article presents a physical biology approach to understanding organization and segregation of bacterial chromosomes. The author uses a "piston" analogy for bacterial chromosomes in a cell, which leads to a phase diagram for the…
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…
We solve a hydrodynamic model of active chromatin dynamics, within a confined geometry simulating the cell nucleus. Using both analytical and numerical methods, we describe the behavior of the chromatin polymer driven by the activity of…
We investigated the effect of torsional rigidity of a semiflexible chain on the wrapping transition around a spherical core, as a model of nucleosome, the fundamental unit of chromatin. Through molecular dynamics simulation, we show that…
Motivated by recent experiments probing shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such…
While the main features of atomic nuclei are well described by nuclear mean-field models, there is a large and growing body of evidence which indicates an important additional role played by spatially-correlated nucleon-nucleon structures.…
Prokaryotes do not make use of a nucleus membrane to segregate their genetic material from the cytoplasm, so that their nucleoid is potentially free to explore the whole volume of the cell. Nonetheless, high resolution images of bacteria…
How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes…
Nucleic acids and proteins are not only biologically important polymers: They have recently been recognized as novel functional materials surpassing in many aspects the conventional ones. Although Herculean efforts have been undertaken to…