Related papers: Chromosome Compaction and Chromatin Stiffness Enha…
Twisted coronal loops should be ubiquitous in the solar corona. Twisted magnetic fields contain excess magnetic energy, which can be released during magnetic reconnection, causing solar flares. The aim of this work is to investigate…
By means of a minimal physical model, we investigate the interplay of two phase transitions at play in chromatin organization: (1) liquid-liquid phase separation (LLPS) within the fluid solvating chromatin, resulting in the formation of…
Understanding how stick-slip dynamics manifests in diverse physical conditions is a crucial topic in tribology. Although it has been extensively studied in simple frictional configurations, the characterization of stick-slip behavior in…
Eukaryotic DNA is packaged into chromatin: one-dimensional arrays of nucleosomes separated by stretches of linker DNA are folded into 30-nm chromatin fibers which in turn form higher-order structures. Each nucleosome, the fundamental unit…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
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…
We discuss the stick-slip motion of an elastic block sliding along a rigid substrate. We argue that for a given external shear stress this system shows a discontinuous nonequilibrium transition from a uniform stick state to uniform sliding…
Long-distance regulatory interactions between enhancers and their target genes are commonplace in higher eukaryotes. Interposed boundaries or insulators are able to block these long distance regulatory interactions. The mechanistic basis…
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…
The rotor-router walk model is proposed to describe the sub-diffusive behavior of double-strand breaks in chromatin caused by external factors such as heavy ions, $\gamma$-irradiation, etc. The mechanism of the double-strand breaks…
Active and diffusive motion in Brownian particles are regularly observed in fluidic environments, albeit at different time scales. Here, we experimentally study the dynamics of highly asymmetric microclusters trapped in air employing…
We propose that the degree of sweeling of the 30nm chromatin fiber (a "measure" of its transcriptional activity) is mainly determined by the short-ranged electrostatical interaction between different sections of the "folded" DNA chain.…
Large deformations of soft materials are customarily associated with strong constitutive and geometrical nonlinearities that originate new modes of fracture. Some isotropic materials can develop strong fracture anisotropy, which manifests…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
Trypsin and chymotrypsin are both serine proteases with high sequence and structural similarities, but with different substrate specificity. Previous experiments have demonstrated the critical role of the two loops outside the binding…
The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…
Current biophysical models for transcriptionally active chromatin view this as a polymer with sticky sites, mimicking transcription units such as promoters and enhancers which interact via the binding of multivalent complexes of…
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…
The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…