Related papers: DNA electrophoresis studied with the cage model
A theory of condensation and resolubilization of a dilute DNA solution with growing concentration of multivalent cations, N is suggested. It is based on a new theory of screening of a macroion by multivalent cations, which shows that due to…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
In this paper we consider a system of two coupled nonlinear diffusion--reaction partial differential equations (PDEs) which model the growth of biofilm and consumption of the nutrient. At the scale of interest the biofilm density is subject…
We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which…
We demonstrate a variant of the Bond Fluctuation lattice Monte Carlo model in which moves through cis conformations are forbidden. Ring polymers in this model have a conserved quantity that amounts to a topological linking number. Increased…
We measured electron paramagnetic resonance (EPR) spectra of 14N- and 15N-labeled perdeuterated TEMPONE radicals in normal and supercooled water at various radical concentrations. By fitting the EPR spectra to spectral shape functions based…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
We investigate the universality of entanglement kinetics in polymer melts. We compare predictions of a recently developed constitutive equation for disentanglement to molecular dynamics simulations of both united-atom polyethylene and…
Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time…
We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But,…
The conformational behavior of a giant DNA mediated by condensing agents in the bulk solution has been investigated through experimental and theoretical approaches. Experimentally, a pronounced conformational hysteresis is observed for…
Condensation of hundreds of mega-base-pair-long human chromosomes in a small nuclear volume is a spectacular phenomenon. This process is driven by the formation of chromosome loops. ATP consuming motor, condensin, interacts with chromatin…
Single-molecule force-extension experiments have allowed quantitative measurements of the mechanical responses of biomolecules to applied forces explaining their roles in key biological functions. Electrophoretic stretching of charged…
We develop an analytical theory that accounts for the image and surface charge interactions between a charged dielectric membrane and a DNA molecule translocating through the membrane. Translocation events through neutral carbon-based…
The transition from globular to elongated states of biopolymers in shear flow occurs at a distinct critical shear rate, $\dot{\gamma }^{*}$. The magnitude of $\dot{\gamma }^{*}$ depends on the internal potential and the polymer length. For…
We present dynamic light scattering (DLS) measurements of soft polymethyl-methacrylate (PMMA) and polyacrylamide(PA) polymer gels prepared with trapped bodies (latex spheres or maghemite nanoparticles). We show that the anomalous…
We discuss the exact solution for the properties of the recently introduced ``necklace'' model for reptation. The solution gives the drift velocity, diffusion constant and renewal time for asymptotically long chains. Its properties are also…
Herein an alternative model to reptation to describe concentrated polymer dynamics is developed. The model assumes that the chains act as blobs that are able to diffuse past each other in a compressed state. Allowing that the local…