DNA electrophoresis studied with the cage model

DOI10.1006/JCPH.2002.7095zbMATH Open1001.82568arXivcond-mat/0101467OpenAlexW2071452023MaRDI QIDQ697782FDOQ697782

Authors: A. van Heukelum, G. T. Barkema, R. H. Bisseling 

Publication date: 17 September 2002

Published in: Journal of Computational Physics (Search for Journal in Brave)

Abstract: 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 monomers. The computations show the Nernst-Einstein regime (v ~ E) followed by a regime where the velocity decreases exponentially with the applied electric field strength. In agreement with de Gennes' reptation arguments, we find that asymptotically for large polymers the diffusion coefficient D decreases quadratically with polymer length; for the cage model, the proportionality coefficient is DL^2=0.175(2). Additionally we find that the leading correction term for finite polymer lengths scales as N^{-1/2}, where N=L-1 is the number of bonds.

Full work available at URL: https://arxiv.org/abs/cond-mat/0101467

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zbMATH Keywords

DNA electrophoresiscage modelpolymer reptation

Mathematics Subject Classification ID

Statistical mechanics of polymers (82D60)

Cites Work

• Free fermion approximation for the Ising model with further-neighbor interactions on a triangular lattice
• Title not available (Why is that?)

Cited In (6)

• The model of DNA chain motion in pulsed field gel electrophoresis
• Parallel multilevel algorithms for hypergraph partitioning
• Title not available (Why is that?)
• Parallel Jacobi-Davidson with block FSAI preconditioning and controlled inner iterations.
• Nonlocal pagerank
• A Truncated Taylor Series Algorithm for Computing the Action of Trigonometric and Hyperbolic Matrix Functions

Uses Software

• BSPlib

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