Related papers: Quantifying the mobility of chromatin during embry…
Kinetics of the first order phase transition has been investigated. The case when the droplets sizes have a limit value is considered. An analytical theory for such process has been constructed and all main characteristics of the process…
Quantum Chromodynamics, the microscopic theory of strong interactions, has not yet been applied to the calculation of nuclear wave functions. However, it certainly provokes a number of specific questions and suggests the existence of novel…
Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in…
The classical nucleation theory finds the rate of nucleation proportional to the monomer concentration raised to the power, which is the `critical nucleaus size', ${n_c}$. The implicit assumption, that amyloids nucleate in the same way, has…
The nucleus of eukaryotic cells typically makes up around 30% of the cell volume and has significantly different mechanics, which can make it effectively up to ten times stiffer than the surrounding cytoplasm. Therefore it is an important…
Nuclear modifications of the nucleon's structure function $F_2^N$ have been investigated mainly since the discovery of the EMC nuclear effect in 1983, and there were many experimental measurements from the deuteron to a heavy nucleus. Now,…
Polymer translocation in crowded environments is a ubiquitous phenomenon in biological systems. We studied polymer translocation through a pore in free, one-sided (asymmetric), and two-sided (symmetric) crowded environments. Extensive…
Gastrulation, namely cell internalization, is a significant milestone during the development of metazoans from worm to human, which generates multiple embryonic layers with distinct cell fates and spatial organizations. Although many…
The chromosome is a key player of cell physiology, and its dynamics provides valuable information about its physical organization. In both prokaryotes and eukaryotes, the short-time motion of chromosomal loci has been described as a Rouse…
We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium…
Numerical results on the translocation of long biopolymers through mid-sized and wide pores are presented. The simulations are based on a novel methodology which couples molecular motion to a mesoscopic fluid solvent. Thousands of events of…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene…
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which…
Cells in an epithelial monolayer coordinate motion with their neighbors giving rise to collectively moving packs of sizes spanning multiple cell diameters. The physical mechanism controlling the pack size, however, remains unclear. A…
We discover a surprising relation between the collective motion of nucleons within atomic nuclei, traditionally understood to be driven by long-range correlations, and short-range nucleon-nucleon interactions. Specifically, we find that…
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 volume occupied by unconstrained bacterial DNA in physiological solutions exceeds 1000 times the volume of the cell. Still, it is confined to a well defined region of the cell called the nucleoid, which occupies only a fraction of the…
This paper focuses on mechanical aspects of chromatin biological functioning. Within a basic geometric modeling of the chromatin assembly, we give for the first time the complete set of elastic constants (twist and bend persistence lengths,…
Many diatoms follow a size diminuation - size restoration cycle in their vegetative phase, leading to daughter cells that differ in size. For the diatom Seminavis robusta, we investigated by cell tracking over several generations whether…