dorsal/arxiv
View SchemaA helicoidal transfer matrix model for inhomogeneous DNA melting
| Authors | Tom Michoel, Yves Van de Peer |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0507036 |
| URL | https://arxiv.org/abs/q-bio/0507036 |
| DOI | 10.1103/PhysRevE.73.011908 |
| Journal | Phys. Rev. E 73, 011908 (2006) |
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.
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"abstract": "An inhomogeneous helicoidal nearest-neighbor model with continuous degrees of\nfreedom is shown to predict the same DNA melting properties as traditional\nlong-range Ising models, for free DNA molecules in solution, as well as\nsuperhelically stressed DNA with a fixed linking number constraint. Without\nloss of accuracy, the continuous degrees of freedom can be discretized using a\nminimal number of discretization points, yielding an effective transfer matrix\nmodel of modest dimension (d=36). The resulting algorithms to compute DNA\nmelting profiles are both simple and efficient.",
"arxiv_id": "q-bio/0507036",
"authors": [
"Tom Michoel",
"Yves Van de Peer"
],
"categories": [
"q-bio.BM",
"q-bio.QM"
],
"doi": "10.1103/PhysRevE.73.011908",
"journal_ref": "Phys. Rev. E 73, 011908 (2006)",
"title": "A helicoidal transfer matrix model for inhomogeneous DNA melting",
"url": "https://arxiv.org/abs/q-bio/0507036"
},
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