Bubble generation in a twisted and bent DNA-like model

Larsen, Peter Ulrik Vingaard; Christiansen, Peter Leth; Bang, Ole; Archilla, Juan F. R.; Gaididei, Yuri

doi:10.1103/physreve.70.036609

Cited by 15 publications

(14 citation statements)

References 44 publications

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“…(We point out that for the new parameter J, a value of 0.05 has been proposed by Larsen et al (2004).) Equation (4.7) has the energy integral These results are interesting because the formation of a localized coherent structure seems to need a geometrical deformation to modify the substrate interactions.…”

Section: Breathers and Pulsesmentioning

confidence: 96%

“…By oversimplifying the mathematics, it is possible to obtain some analytical results considering a dimer. This approach has been proposed in Larsen et al (2004), where the effect of the bending (and also of the twisting) has been represented by a harmonic modification of the Morse potential. This means that we can modify equation (3.1) as…”

Section: Breathers and Pulsesmentioning

confidence: 99%

“…(We point out that for the new parameter J, a value of 0.05 has been proposed by Larsen et al (2004).) Equation (4.7) has the energy integral It is easy to check that F mod ðFÞ has a double zero in FZ0 and another simple zero F Ã s0.…”

Section: Breathers and Pulsesmentioning

confidence: 99%

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The relevance of nonlinear stacking interactions in simple models of double-stranded DNA

Saccomandi

Sgura

2006

J. R. Soc. Interface.

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Single molecule DNA experiments provide interesting data that allow a better understanding of the mechanical interactions between the strands and the nucleotides of this molecule. In some sense, these experiments complement the classical ones about DNA thermal denaturation. It is well known that the original Peyrard-Bishop (PB) model by means of a harmonic stacking potential and a nonlinear substrate potential has been able to predict the existence of a critical temperature of full denaturation of the molecule. In the present paper, driven by the findings of single molecule experiments, we substitute the original harmonic intra-strand stacking potential with a Duffing type potential. By elementary and analytical arguments, we show that with this choice it is possible to obtain a sharp transition in the classical domain wall solution of the PB model and the compactification of the classical solitary wave solutions of other models for the dynamics of DNA. We discuss why these solutions may improve our knowledge of the DNA dynamics in several directions.

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Section: Breathers and Pulsesmentioning

confidence: 96%

Section: Breathers and Pulsesmentioning

confidence: 99%

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The relevance of nonlinear stacking interactions in simple models of double-stranded DNA

Saccomandi

Sgura

2006

J. R. Soc. Interface.

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“…The dipole-dipole interactions between different base pairs should never be ignored and they may play a crucial role for the dynamical properties of DNA, for example when the geometry of the double strand of DNA is taken into account, as the distance between base pairs and, therefore, the intensity of the coupling between them, depends on the shape of the molecule [5,6,7,8,9,10,11].…”

Section: Introductionmentioning

confidence: 99%

Breather trapping and breather transmission in a DNA model with an interface

et al. 2006

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We study the dynamics of moving discrete breathers in an interfaced piecewise DNA molecule. This is a DNA chain in which all the base pairs are identical and there exists an interface such that the base pairs dipole moments at each side are oriented in opposite directions. The Hamiltonian of the Peyrard-Bishop model is augmented with a term that includes the dipole-dipole coupling between base pairs. Numerical simulations show the existence of two dynamical regimes. If the translational kinetic energy of a moving breather launched towards the interface is below a critical value, it is trapped in a region around the interface collecting vibrational energy. For an energy larger than the critical value, the breather is transmitted and continues travelling along the double strand with lower velocity. Reflection phenomena never occur.The same study has been carried out when a single dipole is oriented in opposite direction to the other ones. When moving breathers collide with the single inverted dipole, the same effects appear. These results emphasize the importance of this simple type of local inhomogeneity as it creates a mechanism for the trapping of energy.Finally, the simulations show that, under favorable conditions, several launched moving breathers can be trapped successively at the interface region producing an accumulation of vibrational energy. Moreover, an additional colliding moving breather can produce a saturation of energy and a moving breather with all the accumulated energy is transmitted to the chain.

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“…The interaction of classical anharmonic localized modes with geometry was considered in Refs. [13][14][15][16][17].…”

Section: Introductionmentioning

confidence: 99%

Energy localization and shape transformations in semiflexible polymer rings

et al. 2016

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Shape transformations in driven and damped molecular chains are considered. Closed chains of weakly coupled molecular subunits under the action of spatially homogeneous time-periodic external field are studied. The coupling between the internal excitations and the bending degrees of freedom of the chain modifies the local bending rigidity of the chain. In the absence of driving the array takes a circular shape. When the energy pumped into the system exceeds some critical value the chain undergoes a nonequilibrium phase transition: The circular shape of the aggregate becomes unstable and the chain takes the shape of an ellipse or, in general, of a polygon. The excitation energy distribution becomes spatially nonuniform: It localizes in such places where the chain is more flat. The weak interaction of the chain with a flat surface restricts the dynamics to a flat manifold.

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Bubble generation in a twisted and bent DNA-like model

Cited by 15 publications

References 44 publications

The relevance of nonlinear stacking interactions in simple models of double-stranded DNA

The relevance of nonlinear stacking interactions in simple models of double-stranded DNA

Breather trapping and breather transmission in a DNA model with an interface

Energy localization and shape transformations in semiflexible polymer rings

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