Related papers: DNA electrophoresis studied with the cage model
The cage model for polymer reptation is extended to simulate DC electrophoresis. The drift velocity v of a polymer with length L in an electric field with strength E shows three different regions: if the strength of field is small, the…
We investigate the Rubinstein-Duke model for polymer reptation by means of density-matrix renormalization group techniques both in absence and presence of a driving field. In the former case the renewal time \tau and the diffusion…
Diffusion of a polymer in a gel is studied within the framework of de Gennes' model for reptation. Our results for the scaling of the diffusion coefficient D and the longest relaxation time tau are markedly different from the most recently…
We propose a new method for electrophoretic separation of DNA in which adsorbed polymers are driven over a disordered two-dimensional substrate which contains attractive sites for the polymers. Using simulations of a model for long polymer…
Reptation governs motion of long polymers through a confining environment. Slack enters at the ends and diffuses along the polymer as stored length. The rate at which stored length diffuses limits the speed at which the chain can drift.…
We study the motion of long polymers (eg DNA) in a gel under the influence of an external force acting locally on small segments of the polymer. In particular, we examine the dependence of the drift velocity on the position where the force…
The repton model is a simple model of the "reptation" motion by which DNA diffuses through a gel during electrophoresis. In this paper we show that the model can be mapped onto a system consisting of two types of particles with hard-sphere…
Polymer dynamics at large fields in Rubinstein-Duke repton model is investigated theoretically. Simple diagrammatic approach and analogy with asymmetric simple exclusion models are used to analyze the reptation dynamics of polymers. It is…
Motivated by DNA electrophoresis near a nanopore, we consider the flow field around an "elongated jet", a long thin source which injects momentum into a liquid. This solution qualitatively describes the electro-osmotic flow around a long…
A systematic study of electron or hole transfer along DNA dimers, trimers and polymers is presented with a tight-binding approach at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters…
A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. The proposed model governs the discrete movement of the RNA polymerase along a DNA template, with no consideration given to elastic…
Theoretical results for the extension of a polymer confined to a channel are usually derived in the limit of infinite contour length. But experimental studies and simulations of DNA molecules confined to nanochannels are not necessarily in…
Based on our formulation of the DNA electrophoresis near a pore [P. Rowghanian and A. Y. Grosberg, Phys. Rev. E 87, 042723 (2013)], we address the electrophoretic DNA capture into a nanopore as a steady-state process of particle absorption…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
A hydrodynamic model for determining the electrophoretic speed of a polyelectrolyte through a nanopore is presented. It is assumed that the speed is determined by a balance of electrical and viscous forces arising from within the pore and…
We give a lower bound on the diffusion coefficient of a polymer chain in an entanglement network with kinematic disorder, which is obtained from an exact calculation in a modified Rubinstein-Duke lattice gas model with periodic boundary…
The transfer of electrons and holes along DNA dimers, trimers and polymers is described at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters between successive base-pairs. The temporal and…
We report results of extensive Dynamical Monte Carlo investigations on self-assembled Equilibrium Polymers (EP) without loops in good solvent. (This is thought to provide a good model of giant surfactant micelles.) Using a novel algorithm…
Charge inversion of a DNA double helix by an oppositely charged flexible polyelectrolyte (PE) is considered. We assume that, in the neutral state of the DNA-PE complex, each of the DNA charges is locally compensated by a PE charge. When an…
We present in this paper an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows to address theoretically the influence of complex position along DNA, as well as…