The thermal denaturation of Peyrard-Bishop model with an external potential

نویسندگان

  • A. Sulaiman
  • F. P. Zen
  • H. Alatas
  • L. T. Handoko
چکیده

The impact of various types of external potentials to the Peyrard-Bishop DNA denaturation is investigated through statistical mechanics approach. The partition function is obtained using transfer integral method, and further the stretching of hydrogen bond is calculated using time independent perturbation method. It is shown that all types of external potentials accelerate the denaturation processes at lower temperature. In particular, it is argued that the Gaussian potential with infinitesimal width reproduces a constant force at one end of DNA sequence as already done in some previous works.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Topological origin of the phase transition in a model of DNA denaturation.

The hypothesis that phase transitions originate from some topological change of the critical level hypersurface of the potential energy receives direct evident support by our study of the Bishop-Peyrard model of DNA thermal denaturation.

متن کامل

Statistical mechanics of a nonlinear model for DNA denaturation.

In a letter [1] Peyrard and Bishop investigated the statistical mechanics of a simple lattice model for the denaturation of the DNA double helix. The model consists of two degrees of freedom u n and v n corresponding to the transverse displacements of the bases, i.e., displacements along the direction of the hydrogen bonds, which connect the two bases in a pair. The Hamiltonian for the model is...

متن کامل

Critical dynamics of DNA denaturation

We present detailed molecular dynamics results for the displacement autocor-relation spectra of the Peyrard-Bishop model of thermal DNA denaturation. As the phase transition is approached, the spectra depend on whether the wavelength is smaller than, or exceeds the correlation length. In the first case, the spectra are dominated by a single peak, whose frequency approaches the bare acoustic fre...

متن کامل

Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrizat...

متن کامل

Thermodynamics of local DNA openings.

A mechanism connecting the local untwisting and opening of DNA double helix is proposed. The presented thermodynamical approach is based on two models: the Peyrard-Bishop model that describes the denaturation of DNA due to thermal fluctuations and the model developed by the author describing solitary torsional waves, which propagate along the DNA molecule forced by advancing RNA polymerase. The...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2011