Related papers: Magnetic Polymer Models for Epigenomic Organisatio…
Epigenetic inheritance during cell division is essential for preserving cell identity by stabilizing the overall chromatin organisation. Heterochromatin,the condensed and transcriptionally silent fraction of chromatin,is marked by specific…
Several orders of magnitude typically separate the contour length of eukaryotic chromosomes and the size of the nucleus where they are confined. The ensuing topological constraints can slow down the relaxation dynamics of genomic filaments…
Morphogen profiles play a vital role in biology by specifying position in embryonic development. However, the factors that influence the shape of a morphogen profile remain poorly understood. Since morphogens should provide precise…
Polymers with active segments constitute prospective future materials and are used as a model for some biological systems such as chromatin. The directions of the active forces are typically introduced with temporal or spatial correlations…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
It has been demonstrated that the observed ratio of phenotypes of marker enzymes in some sugarbeet plants produced by mitotic agamospermy can be explained by different degrees of endoreduplication of chromosomes carrying different alleles…
The fundamental processes of biological development are governed by multiple signaling molecules that create non-uniform concentration profiles known as morphogen gradients. It is widely believed that the establishment of morphogen…
Conducting Polymer Dendrites (CPD) can engrave sophisticated patterns of electrical interconnects in their morphology with low-voltage spikes and few resources: they may unlock in operando manufacturing functionalities for electronics using…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
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…
We study a continuous quasi-two-dimensional order-disorder phase transition that occurs in a simple model of a material that is inhomogeneously strained due to the presence of dislocation lines. Performing Monte Carlo simulations of…
In a uniform radio-frequency (RF) plasma between a large electrode pair, the addition of an axial magnetic field induces diverse longitudinal filaments. To reveal its pattern dynamics, we conduct two-dimensional (2D) Particle-In-Cell (PIC)…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our…
Electropolymerization is a bottom-up materials engineering process of micro and nano-scale that utilizes electrical signals to deposit conducting dendrites' morphologies by a redox reaction in the liquid phase. It resembles synaptogenesis…
Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…
Natural supports of information are given by random copolymers such as DNA or RNA where information is coded in the sequence of covalent bonds. At the molecular scale, the stochastic growth of a single copolymer with or without a template…
We study the dynamics of an ideal polymer chain in a crowded, viscoelastic medium and in the presence of active forces. The motion of the centre of mass and of individual monomers is calculated. On time scales that are comparable to the…
Magnetic particles underpin a broad range of technologies, from water purification and mineral processing to bioseparations and targeted drug delivery. The dynamics of magnetic particles in high-gradient magnetic fields-encompassing both…