dorsal/arxiv
View SchemaTheoretical investigation of finite size effects at DNA melting
| Authors | Sahin Buyukdagli, Marc Joyeux |
|---|---|
| Categories | |
| ArXiv ID | physics/0703082 |
| URL | https://arxiv.org/abs/physics/0703082 |
| DOI | 10.1103/PhysRevE.76.021917 |
| Journal | Physical Review E 76 (2007) 021917 |
Abstract
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both extensive (partition function, entropy, specific heat, etc) and non-extensive (order parameter and correlation length) thermodynamic quantities of finite sequences with open boundary conditions, and applied the modified procedure to two different dynamical models. We showed that rounding of the transition clearly takes place when the length of the sequence is decreased. We also performed a finite-size scaling analysis of the two models and showed that the singular part of the free energy can indeed be expressed in terms of an homogeneous function. However, both the correlation length and the average separation between paired bases diverge at the melting transition, so that it is no longer clear to which of these two quantities the length of the system should be compared. Moreover, Josephson's identity is satisfied for none of the investigated models, so that the derivation of the characteristic exponents which appear, for example, in the expression of the specific heat, requires some care.
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"abstract": "We investigated how the finiteness of the length of the sequence affects the\nphase transition that takes place at DNA melting temperature. For this purpose,\nwe modified the Transfer Integral method to adapt it to the calculation of both\nextensive (partition function, entropy, specific heat, etc) and non-extensive\n(order parameter and correlation length) thermodynamic quantities of finite\nsequences with open boundary conditions, and applied the modified procedure to\ntwo different dynamical models. We showed that rounding of the transition\nclearly takes place when the length of the sequence is decreased. We also\nperformed a finite-size scaling analysis of the two models and showed that the\nsingular part of the free energy can indeed be expressed in terms of an\nhomogeneous function. However, both the correlation length and the average\nseparation between paired bases diverge at the melting transition, so that it\nis no longer clear to which of these two quantities the length of the system\nshould be compared. Moreover, Josephson\u0027s identity is satisfied for none of the\ninvestigated models, so that the derivation of the characteristic exponents\nwhich appear, for example, in the expression of the specific heat, requires\nsome care.",
"arxiv_id": "physics/0703082",
"authors": [
"Sahin Buyukdagli",
"Marc Joyeux"
],
"categories": [
"physics.bio-ph"
],
"doi": "10.1103/PhysRevE.76.021917",
"journal_ref": "Physical Review E 76 (2007) 021917",
"title": "Theoretical investigation of finite size effects at DNA melting",
"url": "https://arxiv.org/abs/physics/0703082"
},
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