Simple model for the DNA denaturation transition.

@article{Causo2000SimpleMF,
  title={Simple model for the DNA denaturation transition.},
  author={Maria Serena Causo and Barbara Coluzzi and Peter Grassberger},
  journal={Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics},
  year={2000},
  volume={62 3 Pt B},
  pages={
          3958-73
        }
}
  • M. S. Causo, B. Coluzzi, P. Grassberger
  • Published 13 October 1999
  • Mathematics, Physics, Biology, Medicine
  • Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
We study pairs of interacting self-avoiding walks ¿omega(1), omega(2)¿ on the 3d simple cubic lattice. They have a common origin omega(1)(0)=omega 20, and are allowed to overlap only at the same monomer position along the chain: omega(1)(i) not equal omega(2)(j) for i not equal j, while omega(1)(i)=omega(2)(i) is allowed. The latter overlaps are indeed favored by an energetic gain epsilon. This is inspired by a model introduced long ago by Poland and Sheraga [J. Chem. Phys. 45, 1464 (1966)] for… 
Three-dimensional models for homogeneous DNA near denaturation
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On the disordered SAW model for DNA denaturation
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Sufficient minimal model for DNA denaturation: Integration of harmonic scalar elasticity and bond energies.
TLDR
Free-energy profiles along the denaturation pathway allow to detect stable or meta-stable partial denaturation states, composed of bubble, as local free-energy minima separated by barriers, and elucidate the self-averaging property of the system.
Denaturation patterns in heterogeneous DNA.
  • M. Zoli
  • Physics, Medicine
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2010
TLDR
These findings establish a link between microscopic and macroscopic signatures of the transition between heterogeneous DNA sequences and show an enhanced degree of cooperativity at about the same temperatures for which the specific-heat peaks occur.
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TLDR
The results show that the entropy associated with semiflexibility of DNA sensitively affects the size distribution and lifetime of bubble, and the lifetime grows with bubble size m as m(2.7) at temperature close to T(c), which is consistent with the analysis based on a stochastic model of bubble size dynamics.
Two-dimensional wetting with binary disorder: a numerical study of the loop statistics
Abstract.We numerically study the wetting (adsorption) transition of a polymer chain on a disordered substrate in 1+1 dimension. Following the Poland-Scheraga model of DNA denaturation, we use a
Numerical study of DNA denaturation with self-avoidance: pseudo-critical temperatures and finite size behaviour
We perform an extensive numerical study of the disordered Poland-Scheraga (PS) model for DNA denaturation in which self-avoidance is completely taken into account. In complement to our previous work,
Unified description of poly- and oligonucleotide DNA melting: nearest-neighbor, Poland-Sheraga, and lattice models.
TLDR
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References

SHOWING 1-10 OF 49 REFERENCES
Statistical Mechanics of Torque Induced Denaturation of DNA
A unifying theory of the denaturation transition of DNA, driven by temperature $T$ or induced by an external mechanical torque $\ensuremath{\Gamma}$ is presented. Our model couples the hydrogen-bond
Denaturation of Heterogeneous DNA
The effect of heterogeneous sequence composition on the denaturation of double-stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the
Phase transitions and critical phenomena
  • D. Landau
  • Physics, Mathematics
    Computing in Science & Engineering
  • 1999
The examination of phase transitions and critical phenomena has dominated statistical physics for the latter half of this century--there is a great theoretical challenge in solving special
"J."
however (for it was the literal soul of the life of the Redeemer, John xv. io), is the peculiar token of fellowship with the Redeemer. That love to God (what is meant here is not God’s love to men)
J. Chem Phys
  • J. Chem Phys
  • 1966
Phys
  • 45, 1456, 1464
  • 1966
J. Chem. Phys
  • J. Chem. Phys
  • 1456
A 32
  • 2931
  • 1999
J. Phys. A
  • J. Phys. A
  • 1999
Phys
  • Rev. E 59, R16
  • 1999
...
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