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Helicoidal transfer matrix model for inhomogeneous DNA melting

Tom Michoel (UGent) and Yves Van de Peer (UGent)
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Abstract
An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically stressed DNA with a fixed linking number constraint. Without loss of accuracy, the continuous degrees of freedom can be discretized using a minimal number of discretization points, yielding an effective transfer matrix model of modest dimension (d=36). The resulting algorithms to compute DNA melting profiles are both simple and efficient.
Keywords
DOUBLE-STRANDED DNA, PEYRARD-BISHOP MODEL, DUPLEX DESTABILIZATION, STATISTICAL-MECHANICS, SUPERHELICAL DNA, DENATURATION, MACROMOLECULES, MOLECULES, PROFILES, PHYSICS

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Citation

Please use this url to cite or link to this publication:

MLA
Michoel, Tom, and Yves Van de Peer. “Helicoidal Transfer Matrix Model for Inhomogeneous DNA Melting.” PHYSICAL REVIEW E 73.1 (2006): n. pag. Print.
APA
Michoel, T., & Van de Peer, Y. (2006). Helicoidal transfer matrix model for inhomogeneous DNA melting. PHYSICAL REVIEW E, 73(1).
Chicago author-date
Michoel, Tom, and Yves Van de Peer. 2006. “Helicoidal Transfer Matrix Model for Inhomogeneous DNA Melting.” Physical Review E 73 (1).
Chicago author-date (all authors)
Michoel, Tom, and Yves Van de Peer. 2006. “Helicoidal Transfer Matrix Model for Inhomogeneous DNA Melting.” Physical Review E 73 (1).
Vancouver
1.
Michoel T, Van de Peer Y. Helicoidal transfer matrix model for inhomogeneous DNA melting. PHYSICAL REVIEW E. 2006;73(1).
IEEE
[1]
T. Michoel and Y. Van de Peer, “Helicoidal transfer matrix model for inhomogeneous DNA melting,” PHYSICAL REVIEW E, vol. 73, no. 1, 2006.
@article{372288,
  abstract     = {{An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of freedom is shown to predict the same DNA melting properties as traditional long-range Ising models, for free DNA molecules in solution, as well as superhelically stressed DNA with a fixed linking number constraint. Without loss of accuracy, the continuous degrees of freedom can be discretized using a minimal number of discretization points, yielding an effective transfer matrix model of modest dimension (d=36). The resulting algorithms to compute DNA melting profiles are both simple and efficient.}},
  articleno    = {{011908}},
  author       = {{Michoel, Tom and Van de Peer, Yves}},
  issn         = {{1539-3755}},
  journal      = {{PHYSICAL REVIEW E}},
  keywords     = {{DOUBLE-STRANDED DNA,PEYRARD-BISHOP MODEL,DUPLEX DESTABILIZATION,STATISTICAL-MECHANICS,SUPERHELICAL DNA,DENATURATION,MACROMOLECULES,MOLECULES,PROFILES,PHYSICS}},
  language     = {{eng}},
  number       = {{1}},
  pages        = {{11}},
  title        = {{Helicoidal transfer matrix model for inhomogeneous DNA melting}},
  url          = {{http://dx.doi.org/10.1103/PhysRevE.73.011908}},
  volume       = {{73}},
  year         = {{2006}},
}

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