Moving breathers in a bent DNA model

Abstract

We study the properties of moving breathers in a bent DNA model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bonds within each base pair. We show that the movement of a breather is hindered by the bending of the chain analogously to a particle in a potential barrier.

Breather statics and dynamics in Klein-Gordon chains with a bend

“…[15]: if K Ͻ U c , the value of K is fixed and X o is the point where the breather is reflected (turning point), then K = U͑X o ͒.…”

Bubble generation in a twisted and bent DNA-like model

“…[23,30,36]. The dimensionless stacking parameter then becomes C = 0.075, which we use throughout the paper.…”

“…Recently, both long-range dipole-dipole interaction [23,24], helicity [25,26] and curvature [27][28][29] have been included in the nonlinear transport theory, as well as combinations of these effects [30][31][32][33][34]. It has been shown that chain geometry induces effects similar to those of impurities [27][28][29]32].…”

High-order nonlinear excitations in the Joyeux-Buyukdagli model of DNA

“…This model describes, by a simplified approach, the hydrogen bond and has been applied successfully to many applications such as energy localization [15] and calculation of solitonic speed [16]. In this model, the double strand corresponds to a Klein-Gordon chain, the variable parameters are the distances between nucleotides within each base pair, and only short-range interactions are considered because of the stacking coupling [17]. It is well known that the Peyrard-Bishop (PB) model can produce solitons due to the balanced competition between dispersion and nonlinear effects [18][19][20].…”