Related papers: Fluidification of Entangled Polymers by Loop Extru…
In cell extrusion, a cell embedded in an epithelial monolayer loses its apical or basal surface and is subsequently squeezed out of the monolayer by neighboring cells. Cell extrusions occur during apoptosis, epithelial-mesenchymal…
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…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
We investigated the elongational flows of the weakly entangled linear polymer melt using a coarse-grained molecular dynamics simulation. We extended the uniform extensional flow (UEF) method developed by Nicholson and Rutledge (D. A.…
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…
We report measurements of turbulent drag reduction of two different polyelectrolyte solutions: DNA and hydrolyzed Polyacrylamide. Changing the salt concentration in the solutions allows us to change the flexibility of the polymer chains.…
Cell layers eliminate unwanted cells through the extrusion process, which underlines healthy versus flawed tissue behaviors. Although several biochemical pathways have been identified, the underlying mechanical basis including the forces…
Polymer fibers consist of macromolecules oriented along the fiber axis. Better alignment of chains leads to an increased strength of the fiber. It is believed that the key factor preventing formation of a perfectly oriented fiber is…
We use nonequilibrium molecular dynamics simulations to verify recent tube-model predictions that associative polymer networks exhibit broad stretch fluctuations during elongational flow. Simulations further show that these fluctuating…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
Entangled ring polymers, along with blends of ring and linear polymers, continue to be a topic of great interest and debate due to the conflicting experimental results in the literature as well as the difficulty of producing entangled…
Loop formation in long molecules occurs many places in nature, from solutions of carbon nanotubes to polymers inside a cell. In this article, we review theoretical studies of the static and dynamic properties of polymer loops. For example,…
The tube model is a central concept in polymer physics, and allows to reduce the complex many-filament problem of an entangled polymer solution to a single filament description. We investigate the probability distribution function of…
Structural Maintenance Complexes (SMC) are energy consuming motors that are important in folding the genome by loop extrusion (LE) in all stages of the cell cycle. Single molecule magnetic tweezer pulling experiments have revealed that…
This study focuses on comparing the individual polymer chain dynamics in an entangled polymeric liquid under different shear and extension rates. Polymer chains under various shear rates and extension rates were simulated using a…
The deformations of flagella are important in the motility of single- and multi-flagellated bacteria. Existing numerical methods have treated flagella as extensible filaments with a large extensional modulus, resulting in a stiff numerical…
Complex flow fields govern the deformation of polymers in various manufacturing processes. However, high flow rates may trigger reaction events (i.e., bond breaking or undesirable reaction of mechanophores) in raw polymeric materials,…
The dynamics of elastocapillary thinning in high molecular weight polymer solutions are re-examined using high-speed digital video microscopy. At long times, the evolution of the viscoelastic thread deviates from self-similar exponential…
Large-scale cellular transformations are triggered by subtle physical and structural changes in individual biomacromolecular and membrane components. A prototypical example of such an event is the orchestrated fusion of membranes within an…
We briefly review the recent advances in the rheology of entangled polymers and identify emerging research trends and outstanding challenges, especially with respect to branched polymers. Emphasis is placed on the role of well-characterized…