arXiv subjects

Sahin Buyukdagli

Publications and source records attributed to Sahin Buyukdagli.

58 records · Page 4Linked to original sources

arXiv2007

Theoretical investigation of finite size effects at DNA melting

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.

physics.bio-ph↗

arXiv2006

On scaling laws at the phase transition of systems with divergent order parameter and/or internal length : the example of DNA denaturation

We used the Transfer-Integral method to compute, with an uncertainty smaller than 5%, the six fundamental characteristic exponents of two dynamical models for DNA thermal denaturation and investigate the validity of the scaling laws. Doubts concerning this point arise because the investigated systems (i) have a divergent internal length, (ii) are described by a divergent order parameter, (iii) are of dimension 1. We found that the assumption that the free energy can be described by a single homogeneous function is robust, despite the divergence of the order parameter, so that Rushbrooke's and Widom's identities are valid relations. Josephson's identity is instead not satisfied. This is probably due to the divergence of the internal length, which invalidates the assumption that the correlation length is solely responsible for singular contributions to thermodynamic quantities. Fisher's identity is even wronger. We showed that this is due to the d=1 dimensionality and obtained an alternative law, which is well satisfied at DNA thermal denaturation.

physics.bio-ph↗

arXiv2005

Towards more realistic dynamical models for DNA secondary structure

We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate perpendicular to the sequence axis. We show, through molecular dynamics simulations, that the model has the correct behaviour at the denaturation transition.

physics.bio-ph↗

arXiv2005

Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation

We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbour calculations. Within this model, the finiteness of stacking enthalpies is shown to be responsible for the sharpness of calculated melting curves. Transfer-integral and molecular dynamics calculations are performed to demonstrate that the proposed model leads to good agreement with known experimental results for both homogeneous and inhomogeneous DNA.

physics.bio-ph↗