Related papers: Topological interactions between ring polymers: Im…
Chromatin is a complex of DNA and specific proteins forming an intermediary level of organization of eukaryotic genomes, between double-stranded DNA and chromosome. Within a generic modeling of the chromatin assembly, we investigate the…
Chromatin loop extrusion by Structural Maintenance of Chromosome (SMC) complexes is thought to underlie intermediate-scale chromatin organization inside cells. Motivated by a number of experiments suggesting that nucleosomes may block loop…
Vitrimers are polymer networks that can undergo bond exchange reactions. They dynamically rearrange their structures while maintaining their overall integrity, thus resulting in unique properties such as self-healing, reprocessability,…
Some recent results on the rotational dynamics of polymers are reviewed and extended. We focus here on the relaxation of a polymer, either flexible or semiflexible, initially wrapped around a rigid rod. We also study the steady polymer…
We investigate the conformational and dynamical properties of a partially active Rouse chain, where activity is localized within a specific segment, positioned at various locations along the chain and spanning any given length. Through…
Spatiotemporal coordination of chromatin and subnuclear compartments is crucial for cells. Numerous enzymes act inside nucleus\textemdash some of those transiently link and pass two chromatin segments. Here we study how such an active…
Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically…
Monte Carlo simulations of coarse-grained polymers provide a useful tool to deepen the understanding of conformational and statistical properties of polymers both in physical as well as in biological systems. In this study we sample compact…
Understanding and controlling the rheology of polymeric complex fluids that are pushed out-of-equilibrium is a fundamental problem in both industry and biology. For example, to package, repair, and replicate DNA, cells use enzymes to…
Linear polymers are represented as chains of hopping reptons and their motion is described as a stochastic process on a lattice. This admittedly crude approximation still catches essential physics of polymer motion, i.e. the universal…
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…
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…
Transposable elements (TEs) constitute a significant portion of eukaryotic genomes, yet their role in chromatin organization remains poorly understood. This study investigates the distribution patterns of TEs around chromatin ligation…
Polymers are a primary building block in many biomaterials, often interacting with anisotropic backgrounds. While previous studies have considered polymer dynamics within nematic solvents, rarely are the the effects of anisotropic viscosity…
We perform large scale three-dimensional molecular dynamics simulations of unlinked and unknotted ring polymers diffusing through a background gel, here a three-dimensional cubic lattice. Taking advantage of this architecture, we propose a…
Flocking is a fascinating phenomenon observed across a wide range of living organisms. We investigate, based on a simple self-propelled particle model, how the emergence of ordered motion in a collectively moving group is influenced by the…
Biopolymer length regulation is a complex process that involves a large number of subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length…
The dynamics of loop formation by linear polymer chains has been a topic of several theoretical/experimental studies. Formation of loops and their opening are key processes in many important biological processes. Loop formation in flexible…
By using long-range interacting polygons, we experimentally probe the coupling between particle shape and long-range interaction. For two typical space-filling polygons, square and triangle, we find two types of coupling modes that…
Scaffold proteins organize cellular processes by bringing signaling molecules into interaction, sometimes by forming large signalosomes. Several of these scaffolds are known to polymerize. Their assemblies should therefore not be understood…