Scaling properties of gel electrophoresis of DNA

Barkema, G. T.; Caron, Cathy; Marko, John F.

doi:10.1002/(sici)1097-0282(199605)38:5<665::aid-bip10>3.0.co;2-7

Cited by 30 publications

(23 citation statements)

References 24 publications

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“…A few years later, simulation results [11] became available that clearly supported this field-dependent scaling of the drift velocity in the region of plateau mobility, and later this was also verified in experiment [12]. Actually, this scaling was already clearly evident in earlier experimental results (but not noticed), for instance in those obtained by Hervet and Bean [13], Fig.…”

Section: General Featuressupporting

confidence: 66%

Lattice models of DNA electrophoresis

Heukelum

Barkema

2002

Electrophoresis

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This article presents an overview of lattice polymer models used to study DNA electrophoresis. Three commonly used models--the bond fluctuation model, the cage model, and the repton model--are discussed, as well their extension to include electric fields, and simulation results obtained. Physical properties that are shared amongst these models are identified, and differences between the models are discussed.

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Section: General Featuressupporting

confidence: 66%

Lattice models of DNA electrophoresis

Heukelum

Barkema

2002

Electrophoresis

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“…This gives rise to simple expressions of the boundary rates in terms of the reservoir densities. Using the boundary conditions ρ 0 = ρ L and ρ N +1 = ρ N +2 = ρ R extends the validity of the recursion (20) to the range 0 ≤ i ≤ N . In this way ρ N can be expressed as a function of ρ R and j and this was the reason of choosing the direction of the recursion from the right to the left.…”

Section: A Mean Fieldmentioning

confidence: 89%

“…For general boundary densities we did not find a solution of the recursion (20) in closed form, but it is easily solved numerically on a computer. It is sufficient to choose a density ρ R and a current j and apply the recursion relation for drawing the density profile.…”

Section: A Mean Fieldmentioning

confidence: 99%

Asymmetric exclusion process with next-nearest-neighbor interaction: Some comments on traffic flow and a nonequilibrium reentrance transition

2000

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We study the steady-state behavior of a driven non-equilibrium lattice gas of hard-core particles with next-nearest-neighbor interaction. We calculate the exact stationary distribution of the periodic system and for a particular line in the phase diagram of the system with open boundaries where particles can enter and leave the system. For repulsive interactions the dynamics can be interpreted as a two-speed model for traffic flow. The exact stationary distribution of the periodic continuous-time system turns out to coincide with that of the asymmetric exclusion process (ASEP) with discrete-time parallel update. However, unlike in the (single-speed) ASEP, the exact flow diagram for the two-speed model resembles in some important features the flow diagram of real traffic. The stationary phase diagram of the open system obtained from Monte Carlo simulations can be understood in terms of a shock moving through the system and an overfeeding effect at the boundaries, thus confirming theoretical predictions of a recently developed general theory of boundary-induced phase transitions. In the case of attractive interaction we observe an unexpected reentrance transition due to boundary effects.

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“…In the framework of the repton model introduced by Rubinstein 8 and Duke 10,11 (further on to be called RD model), which incorporates CLF, it is possible to calculate viscosity, diffusion coefficient and other quantities of interest. Good agreement both with theoretical and experimental results is found 6,7,14,15 . Using the RD model with periodic boundary conditions Kooiman and van Leeuwen 12 analytically calculated the proportionality constant c for the diffusion constant in the limit for infinite chain length: lim L→∞ DL 2 = c.…”

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confidence: 87%

Diffusion in a generalized Rubinstein-Duke model of electrophoresis with kinematic disorder

2003

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Using a generalized Rubinstein-Duke model we prove rigorously that kinematic disorder leaves the prediction of standard reptation theory for the scaling of the diffusion constant in the limit for long polymer chains D ∝ L −2 unaffected. Based on an analytical calculation as well as Monte Carlo simulations we predict kinematic disorder to affect the center of mass diffusion constant of an entangled polymer in the limit for long chains by the same factor as single particle diffusion in a random barrier model.

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Scaling properties of gel electrophoresis of DNA

Cited by 30 publications

References 24 publications

Lattice models of DNA electrophoresis

Lattice models of DNA electrophoresis

Asymmetric exclusion process with next-nearest-neighbor interaction: Some comments on traffic flow and a nonequilibrium reentrance transition

Diffusion in a generalized Rubinstein-Duke model of electrophoresis with kinematic disorder

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