相关论文: The repton model of gel electrophoresis

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…

Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…

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…

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…

A model for the motion of ring-shaped DNA in a gel is introduced and studied by numerical simulations and a mean-field approximation. The ring motion is mediated by finger-shaped loops (hernias) that move in an amoeba-like fashion around…

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…

The process of diagnosing a disease from the 2D gel electrophoresis image is a challenging problem. This is due to technical difficulties of generating reproducible images with a normalized form and the effect of negative stain. In this…

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…

Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when…

Two-dimensional electrophoresis of proteins has preceded, and accompanied, the birth of proteomics. Although it is no longer the only experimental scheme used in modern proteomics, it still has distinct features and advantages. The purpose…

We study a model for the gel degradation by an enzyme, where the gel is schematized as a cubic lattice, and the enzyme as a random walker, that cuts the bonds over which it passes. The model undergoes a (reverse) percolation transition,…

We introduce a microscopically realistic model of a physical gel and use computer simulations to study its static and dynamic properties at thermal equilibrium. The phase diagram comprises a sol phase, a coexistence region ending at a…

A simple growth model for DNA evolution is introduced which is analytically solvable and reproduces the observed statistical behavior of real sequences.

We study a microscopically realistic model of a physical gel and use computer simulations to investigate its static and dynamic properties at thermal equilibrium. The phase diagram comprises a sol phase, a coexistence region ending at a…

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…

DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…

The Rubinstein-Duke or repton model is one of the simplest lattice model of reptation for the diffusion of a polymer in a gel or a melt. Recently, a slightly modified model with hardcore interactions between the reptons has been introduced.…

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…

In this manuscript we present an in vitro model based on agarose gel that can be used to simulate a dirty, oily, bloody, and morphologically complex surface of, for example, an open wound. We show this models effectiveness in simulating…

For economic nonlinear model predictive control and dynamic real-time optimization fast and accurate models are necessary. Consequently, the use of dynamic surrogate models to mimic complex rigorous models is increasingly coming into focus.…