Parameters describing the H bond in DNA

DNA-RNA transcription as an impact of viscosity

The impact of viscosity on DNA dynamics is studied both analytically and numerically. It is assumed that the viscosity exists at the segments where DNA molecule is surrounded by RNA polymerase. We demonstrate that the frictional forces destroy the modulation of the incoming solitonic wave. We show that viscosity, crucial for demodulation, is essential for DNA-RNA transcription.

Localization and delocalization of energy in a Peyrard-Bishop chain

This paper studies energy localization conditions in lattices of the type proposed by Peyrard and Bishop. Homogeneous and inhomogeneous lattices are analyzed and the role of interfaces in the latter is emphasized. Simulations allowed us to identify critical energy values for the existence of localization. After a certain energy value, it is possible to observe the loss of energy localization along the chain.

A model coupling vibrational and rotational motion for the DNA molecule

We investigate a mechanical model for the DNA molecule using an extension of the Peyrard and Bishop model. In the present model, there are two chains of oscillators linked by a Morse potential, which represent the hydrogen bonds. The rotational and vibrational motions of each base pair are considered and the coupling for these motions are introduced by a nonlinear combination of them in the Morse potential. In this context, thermodynamics and structural properties are discussed.

Energy localization in the Peyrard-Bishop DNA model

We study energy localization on the oscillator chain proposed by Peyrard and Bishop to model DNA. We search numerically for conditions with initial energy in a small subgroup of consecutive oscillators of a finite chain and such that the oscillation amplitude is small outside this subgroup on a long time scale. We use a localization criterion based on the information entropy and verify numerically that such localized excitations exist when the nonlinear dynamics of the subgroup oscillates with a frequency inside the reactive band of the linear chain. We predict a mimium value for the Morse parameter (micro>2.25) (the only parameter of our normalized model), in agreement with the numerical calculations (an estimate for the biological value is micro=6.3 ). For supercritical masses, we use canonical perturbation theory to expand the frequencies of the subgroup and we calculate an energy threshold in agreement with the numerical calculations.

Statistical Model to DNA Melting

We explore a DNA statistical model to obtain information about the behavior of the thermodynamics quantities. Special attention is given to the thermal denaturation of this macromolecule.