相关论文: Inhomogeneous Reptation of Polymers

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…

We present quantitative results for the drift velocity of a polymer in a gel if a force (e.g. through an electric or magnetic field) acts on a tag, attached to one of its ends. This is done by introducing a modification of the…

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,…

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.…

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…

We analyze the motion of individual beads of a polymer chain using a discrete version of De Gennes' reptation model that describes the motion of a polymer through an ordered lattice of obstacles. The motion within the tube can be evaluated…

The cage model for polymer reptation, proposed by Evans and Edwards, and its recent extension to model DNA electrophoresis, are studied by numerically exact computation of the drift velocities for polymers with a length L of up to 15…

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…

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…

Gel electrophoresis allows to separate knotted DNA (nicked circular) of equal length according to the knot type. At low electric fields, complex knots being more compact, drift faster than simpler knots. Recent experiments have shown that…

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…

The effect of sequence heterogeneity on polynucleotide translocation across a pore and on simple models of molecular motors such as helicases, DNA polymerase/exonuclease and RNA polymerase is studied in detail. Pore translocation of RNA or…

We use computer simulations to study the (driven) dynamics of a charged polymer in a disordered medium, thus mimicking the setting used in gel electrophoresis. In agreement with experiments, we find that inside the gel the mobility of the…

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…

Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule…

We study knotted polymers in equilibrium with an array of obstacles which models confinement in a gel or immersion in a melt. We find a crossover in both the geometrical and the topological behavior of the polymer. When the polymers' radius…

We study of the dynamics of ring polymers confined to diffuse in a background gel at low concentrations. We do this in order to probe the inter-play between topology and dynamics in ring polymers. We develop an algorithm that takes into…

Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in…

We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…

Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…