Related papers: Effects of Molecular Crowding on stretching of pol…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
Biomolecular condensates are essential for cellular organization and result from phase separation in systems far from thermodynamic equilibrium. Among various models, chemically active droplets play a significant role, consisting of…
We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times, but anomalous…
During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the…
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…
The structure and function of polymers in confined environments, e.g., biopolymers in the cytoplasm of a cell, are strongly affected by macromolecular crowding. To explore the influence of solvent quality on conformations of crowded…
A brief review of our recent studies aiming at a better understanding of the scaling behaviour of polymers in disordered environments is given. The main emphasis is on a simple generic model where the polymers are represented by…
We study the effect of the crowded nature of the cellular cytoplasm on the translocation of a polymer through a pore in a membrane. By systematically treating the entropic penalty due to crowding, we show that the translocation dynamics are…
We derive an analytical pair potential of mean force for Brownian molecules in the liquid-state. Our approach accounts for many-particle correlations of crowding particles of the liquid, and for diffusive transport across the spatially…
The emergence of collective motion, also known as flocking or swarming, in groups of moving individuals who orient themselves using only information from their neighbors is a very general phenomenon that is manifested at multiple spatial…
Depletion-induced interactions between colloids in colloid-polymer mixtures depend in range and strength on size, shape, and concentration of depletants. Crowding by colloids in turn affects shapes of polymer coils, such as biopolymers in…
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…
The cytoplasm of a living cell is crowded with several macromolecules of different shapes and sizes. Molecular diffusion in such a medium becomes anomalous due to the presence of macromolecules and diffusivity is expected to decrease with…
We study flexible polymer macromolecules in a crowded (porous) environment, modelling them as self-attracting self-avoiding walks (SASAW) on site-diluted percolative lattices in space dimensions d=2, 3. The influence of stretching force on…
Intrinsically disordered proteins (IDPs) abound in cellular regulation. Their interactions are often transitory and highly sensitive to salt concentration and posttranslational modifications. However, little is known about the effect of…
Macromolecular crowding can influence polymer shapes, which is important for understanding the thermodynamic stability of polymer solutions and the structure and function of biopolymers (proteins, RNA, DNA) under confinement. We explore the…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
The interaction of polymers with small-scale velocity gradients can trigger a coil-stretch transition in the polymers. We analyze this transition within a direct numerical simulation of shear turbulence with an Oldroyd-B model for the…
We study the peculiarities of stretching of globular polymer macromolecules in a disordered (crowded) environment, using the model of self-attracting self-avoiding walks on site-diluted percolative lattices in space dimensions d=3. Applying…
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…