Dynamics of DNA breathing in the Peyrard–Bishop model with damping and external force

Abstract

The impact of damping effect and external forces to the DNA breathing is investigated within the Peyrard-Bishop model. In in the continuum limit, the dynamics of the breathing of DNA is described by the forced-damped nonlinear Schrodinger equation and studied by means of variational method. The analytical solutions are obtained for special cases. It is shown that the breather propagation is decelerated in the presence of damping factor without the external force, while the envelope velocity and the amplitude increase significantly with the presence of external force. It is particularly found that the higher harmonic terms are enhanced when the periodic force is applied. It is finally argued that the external force accelerates the DNA breathing.

Physics of base-pairing dynamics in DNA

“…These damped mechanical models lead to the same conclusions: viscous damping induces a quick stoppage of the soliton which thus travels less than 10 bp [107,125] and decreases drastically the soliton velocity [152,142], and the "bubble" lifetimes which becomes on the order of a few picoseconds only [155,156,157]. Deng [150], using a stochastic differential PBD equation, found base-pair opening times of about 10-400 ps.…”

“…Several attempts to introduce a friction force in the mechanical models have been proposed [107,141,142,148,149,150]. For instance, in the geometry of the PBD model, this friction force is written as −ζ 0 ∂y/∂t where ζ 0 6πηa ∼ 10 −11 kg/s is the friction coefficient of a base-pair.…”

Improving energy transfer in QD-DNA photonic networks

“…In contrast, the Förster-weighted spacing estimated for the four QD:(1.0×R 0 ) n assemblies is 74.2 ± 9Å or ~1.5×R 0 which is ~20% larger. We ascribe this difference to the DNA sequence that is hybridized to the 1.0×R 0 template and hypothesize that this may reflect some, incomplete hybridization or "breathing" in this end portion of the DNA 15,16 . Alternatively, there may be some interactions between the Cy3 dye label on this DNA and the PEG layer that surrounds the QD during assembly.…”

On The Features Solitary Wave Solutions for the DoubleStructures Model of DNA

“…Since the structure of DNA double helix has been discovered by Watson and Crick in 1953 [2]. Many researchers, especially ones in theoretical physics and nonlinear dynamics and also triggered the formulation of several simple models of nonlinear DNA dynamics corresponding to geometric structure, namely, the DNA double-stranded [3][4][5][6][7][8][9][10][11][12][13][14] or the double helix [15][16][17][18][19][20][21][22][23][24][25][26][27][28]. These models had been developed during the past decade to describe the nonlinear dynamics properties of open base-pairs in DNA, which commonly called denaturation bubbles [29].…”