Related papers: Quantifying the mobility of chromatin during embry…
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…
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 migration of cells is relevant for processes such as morphogenesis, wound healing, and invasion of cancer cells. In order to move, single cells deform cyclically. However, it is not understood how these shape oscillations influence…
Spatial distributions are presented that quantitatively capture how polymer properties (e.g., segment alignment, density, and potential energy) vary with distance from nascent polymer crystals (nuclei) in prototypical polyethylene melts. It…
Zygotic genome activation (ZGA), the onset of transcription after initial quiescence, is a major developmental step in many species, which occurs after ten cell divisions in Zebrafish embryos. How transcription factor-chromatin interactions…
Searches for modified gravity in the large-scale structure try to detect the enhanced amplitude of density fluctuations caused by the fifth force present in many of these theories. Neutrinos, on the other hand, suppress structure growth…
It is widely discussed in the literature that the wave function of the nucleon bound in a nucleus is modified due to the interaction with the surrounding medium. We argue that the modification should strongly depend on the momentum of the…
Due to the electron correlation, a fast removal of an electron from a molecule may create a coherent superposition of cationic states and in this way initiate pure electronic dynamics in which the hole-charge left by ionization migrates…
Successful cell division requires a tight regulation of chromosome motion via the activity of molecular motors. Many of the key players at the origin of the forces generating the movement have been identified, but their spatial and temporal…
One of the biggest challenges in biology is to understand how activity at the cellular level of neurons, as a result of their mutual interactions, leads to the observed behavior of an organism responding to a variety of environmental…
We developed and applied rapid scanning laser-emission microscopy to detect abnormal changes in cell nuclei for early diagnosis of cancer and cancer precursors. Regulation of chromatins is essential for genetic development and normal cell…
Genome organization in eukaryotes during interphase stems from the delicate balance between non-random correlations present in the DNA polynucleotide linear sequence and the physico/chemical reactions which shape continuously the form and…
Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to explore the role of 3D…
Independent particle model in nuclear physics assumes that the nucleon in the nucleus moves in the average (mean field) potential generated by all other nucleons. This chapter gives a short overview of basic features of the independent…
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…
Genome sizes have evolved to vary widely, from 250 bases in viroids to 670 billion bases in amoeba. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as point mutation…
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…
We present a model improving the two-angle model for interphase chromatin (E2A model). This model takes into account the cylindrical shape of the histone octamers, the H1 histones in front of the nucleosomes and the vertical distance $d$…
The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or…
External electromagnetic fields can provoke stress, and thus modifications of the internal structure of nucleons. Working with this hypothesis, one can derive a simple description of the charge dependence of the EMC effect. This first…