Related papers: Dynamics of forced biopolymer translocation
We investigate the translocation of a stiff polymer consisting of M monomers through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind onto the polymer, and partially prevent backsliding of the polymer…
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the…
We investigate the dynamics of nanoparticles in semidilute polymer solutions when the nanoparticles are comparably sized to the polymer coils using explicit- and implicit-solvent simulation methods. The nanoparticle dynamics are…
Using results from Schramm Loewner evolution (SLE), we give the expression of the fluctuation-induced force exerted by a polymer on a small impenetrable disk, in various 2-dimensional domain geometries. We generalize to two polymers and…
Cell dynamics simulation is used to investigate the phase behavior of block copolymer/homopolymer mixture subjected to a steady shear flow. Phase transitions occur from transverse to parallel and then to perpendicular lamellar structure…
Polymer translocation in three dimensions out of planar confinements is studied in this paper. Three membranes are located at $z=-h$, $z=0$ and $z=h_1$. These membranes are impenetrable, except for the middle one at $z=0$, which has a…
Monte Carlo simulations are used to study the translocation of a polymer into and out of a ellipsoidal cavity through a narrow pore. We measure the polymer free energy F as a function of a translocation coordinate, s, defined to be the…
Shear flow is known to induce huge density fluctuations in otherwise clear and uniform polymer solutions. This effect is rooted in the elasticity of the entangled polymer network, and can span distances over a thousand chains wide. It has…
Biopolymer looping is a dynamic process that occurs ubiquitously in cells for gene regulation, protein folding, etc. In cellular environments, biopolymers are often subject to tensions which are either static, or temporally fluctuating far…
In entangled polymer systems, there are several characteristic time scales, such as the entanglement time and the disengagement time. In molecular simulations, the longest relaxation time (the disengagement time) can be determined by the…
The hydrophobic effect is the dominant force which drives a protein towards its native state, but its physics has not been thoroughly understood yet. We introduce an exactly solvable model of the solvation of non-polar molecules in water,…
The locomotion of microorganisms and spermatozoa in complex viscoelastic fluids is of critical importance in many biological processes such as fertilization, infection, and biofilm formation. Depending on their propulsion mechanisms,…
The viscoelastic effect on the hydrodynamic relaxation in semidilute polymer solutions is investigated. From the linearized two-fluid model equations, we predict that the dynamical asymmetry coupling between the velocity fluctuations and…
Microfluidic channels are integral to biomedical technology and process engineering, offering versatility in handling fluids with complex properties, often a combination of viscous and elastic attributes. Despite significant advancements in…
Hydrogels have a distinct combination of mechanical and water-transport behaviors. As hydrogels stiffen, they become less permeable. Here, we combine semi-dilute polymer theory with the Kozeny-Carman equation to develop a simple scaling law…
The conformations of semiflexible (bio)polymers are studied in flow through geometrically structured microchannels. Using mesoscale hydrodynamics simulations, we show that the polymer undergoes a rod-to-helix transition as it moves from the…
Behavior of a dilute polymer solution in a random three-dimensional flow with an average shear is studied experimentally. Polymer contribution to the shear stress is found to be more than two orders of magnitude higher than in a laminar…
Inspired by recent experiments on chromosomal dynamics, we introduce an exactly solvable model for the interaction between a flexible polymer and a set of motor-like enzymes. The enzymes can bind and unbind to specific sites of the polymer…
A theoretical model is developed for predicting dynamic polymer depletion effects under the influence of fluid flow. The results are established by combining the two-fluid model and the self-consistent field theory. We consider a uniform…
Microbial flagellates typically inhabit complex suspensions of polymeric material which can impact the swimming speed of motile microbes, filter-feeding of sessile cells, and the generation of biofilms. There is currently a need to better…