Investigation of DNA denaturation from generalized Morse potential

radouane el kinani

Abstract


In this paper, we present a non-linear model for DNA denaturation. We assume that the double-strands DNA interact via a realistic generalized Morse potential that reproduces well the features of the real interaction, as well as the used DNA model and that of Peyrard and Bishop. Using the Transfer Matrix Method, based on the resolution of a Schrödinger equation, we first determine exactly their solution, which are found to be bound states. Second, from an exact expression of the ground state, we compute the denaturation temperature and the free energy density, in terms of the potential parameters. Then, we calculate the contact probability, which is the probability to find the double-strands at a (finite) distance apart. The main conclusion is that, the present analytical study reveals that the generalized Morse potential is a good candidate for the study of DNA denaturation.


Keywords


DNA, INTERACTIONS, GENERALIZED MORSE POTENTIAL, DENATURATION TRANSITION, FREE ENERGY.

Full Text:

PDF

References


D.Poland, H.A.Scheraga, Theory of helix-coil transitions in biopolymers, Academic Press, New York (1970)

R.M.Wartell, A.S.Benight,Thermal denaturation of DNA molecules: a comparison of theory with experiment, Physics Reports, vol.126, p 67 (1985)

M.Peyrard, Nonlinear dynamics and statistical physics of DNA, Nonlinearity, vol.17, p R1 (2004)

O.Gotoh, Prediction of melting profiles and local helix stability for sequenced DNA, Advances in biophysics, vol.16, p 1 (1983)

R.Thomas, Structure secondaire et denaturation des acides nucleiques, Bulletin de la Société de Chimie Biologique, vol.35, p 609 (1953)

A.Segerer, T.A.Langworthy, K.O.Stetter, Thermoplasma acidophilum and thermoplasma volcanium sp. nov. from solfatara fields, Systematic and Applied Microbiology, vol.10, p 161 (1988)

D.Poland, H.A.Scheraga, Occurrence of a phase transition in nucleic acid models, The Journal of Chemical Physics, vol.45, p 1464 (1966)

T.Dauxois, M.Peyrard, A.R.Bishop, Thermodynamics of a nonlinear model for DNA denaturation, Physica D: Nonlinear Phenomena, vol.66, p 35 (1993)

J.A.McCammon, S.C.Harvey, Dynamics of proteins and nucleic acids, Cambridge University Press (1988)

J.Sheng, Z.Ying, Z.Xiang-Lin, S.Liang-Tian, Identity for the exponential-type molecule potentials and the supersymmetry shape invariance, Communications in Theoretical Physics, vol.36, p 641 (2001)

M.Peyrard, A.R.Bishop, Statistical mechanics of a nonlinear model for DNA denaturation, Physical Review Letters, vol. 62, p 2755 (1989)

D.J.Sears, R.A.M.Ferrell, Statistical mechanics of one-dimensional Ginzburg-Landau fields, Physical Review B, vol.6, p 3409 (1972)

J.A.Krumhansl, J.R.Schrieffer, Dynamics and statistical mechanics of a one-dimensional model Hamiltonian for structural phase transitions, Physical Review B, vol.11, p 3535 (1975)

A.R.Bishop, J.A.Krumhansl, S.E.Trullinger, Solitons in condensed matter: a paradigm, Physica D: Nonlinear Phenomena, vol.1, p 1 (1980)


Refbacks

  • There are currently no refbacks.


Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.