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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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In this paper we develop a dynamical model of the propagating nonlinear localized excitations, supersonic kinks, in the cation layer in a silicate mica crystal. We start from purely electrostatic Coulomb interaction and add the Ziegler-Biersack-Littmark short-range repulsive potential and the periodic potential produced by other atoms of the lattice. The proposed approach allows the construction of supersonic kinks which can propagate in the lattice within a large range of energies and velocities. Due to the presence of the short-range repulsive component in the potential, the interparticle distances in the lattice kinks with high energy are limited by physically reasonable values. The introduction of the periodic lattice potential results in the important feature that the kinks propagate with the single velocity and single energy, which are independent on the excitation conditions. The unique average velocity of the supersonic kinks on the periodic substrate potential we relate with the kink amplitude of the relative particle displacements, which is determined by the interatomic distance corresponding to the minimum of the total, interparticle plus substrate, lattice potential. The found kinks are ultradiscrete and can be described with the "magic wave number" q=2π/3a, which was previously revealed in the nonlinear sinusoidal waves and supersonic kinks in the Fermi-Pasta-Ulam lattice. The extreme discreteness of the observed supersonic kinks, with basically two particles moving at the same time, allows the detailed interpretation of their double-kink structure, which is not possible for the multikinks without an account for the lattice discreteness. Analytical calculations of the displacement patterns and energies of the supersonic kinks are confirmed by numerical simulations. The computed energy of the found supersonic kinks in the considered realistic lattice potential is in a good agreement with the experimental evidence for the transport of localized energetic excitations in silicate mica crystals between the points of ^{40}K recoil and subsequent sputtering.

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Reaction rate theory in solids is modified taking into account intrinsic localized modes or discrete breathers (DBs) that can appear in crystals with sufficient anharmonicity, resulting in violation of Arrhenius' law. Large-amplitude oscillations of atoms about their equilibrium positions in the lattice cause local potentials of alternating sign, which are described in terms of time-periodic modulations of the potential barriers for chemical reactions taking place in the vicinity of DBs. The reaction rate averaged over large macroscopic volumes and times including many DBs is increased by a factor that depends on the DB statistics. The breather statistics in thermal equilibrium and in thermal spikes in solids under irradiation with swift particles is considered, and the corresponding reaction rate amplification factors are derived.

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Reconstructive transformations in layered silicates need a high temperature in order to be observed. However, very recently, some systems have been found where transformation can be studied at temperatures 600 degrees C below the lowest experimental results previously reported, including sol-gel methods. We explore the possible relation with the existence of intrinsic localized modes, known as discrete breathers. We construct a model for nonlinear vibrations within the cation layer, obtain their parameters, and calculate them numerically, obtaining their energies. Their statistics show that, although there are far less breathers than phonons, there are much more above the activation energy, making them good candidates to explain the reconstructive transformations at low temperatures.

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We numerically investigate localization properties of electronic states in a static model of poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers with realistic parameters obtained by quantum-chemical calculation. The randomness in the on-site energies caused by the electron-phonon coupling is completely correlated to the off-diagonal parts. In the single electron model, the effect of the hydrogen-bond stretchings, the twist angles between the base pairs and the finite system size effects on the energy dependence of the localization length and on the Lyapunov exponent are given. The localization length is reduced by the influence of the fluctuations in the hydrogen bond stretchings. It is also shown that the helical twist angle affects the localization length in the poly(dG)-poly(dC) DNA polymer more strongly than in the poly(dA)-poly(dT) one. Furthermore, we show resonance structures in the energy dependence of the localization length when the system size is relatively small.

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The formation of bubbles in nucleic acids (NAs) is fundamental in many biological processes such as DNA replication, recombination, telomere formation and nucleotide excision repair, as well as RNA transcription and splicing. These processes are carried out by assembled complexes with enzymes that separate selected regions of NAs. Within the frame of a nonlinear dynamics approach, we model the structure of the DNA duplex by a nonlinear network of coupled oscillators. We show that, in fact, from certain local structural distortions, there originate oscillating localized patterns, that is, radial and torsional breathers, which are associated with localized H-bond deformations, reminiscent of the replication bubble. We further study the temperature dependence of these oscillating bubbles. To this aim, the underlying nonlinear oscillator network of the DNA duplex is brought into contact with a heat bath using the Nosé-Hoover method. Special attention is paid to the stability of the oscillating bubbles under the imposed thermal perturbations. It is demonstrated that the radial and torsional breathers sustain the impact of thermal perturbations even at temperatures as high as room temperature. Generally, for non-zero temperature, the H-bond breathers move coherently along the double chain, whereas at T=0 standing radial and torsional breathers result.

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The DNA molecule is modeled by a parabola embedded chain with long-range interactions between twisted base pair dipoles. A mechanism for bubble generation is presented and investigated in two different configurations. Using random normally distributed initial conditions to simulate thermal fluctuations, a relationship between bubble generation, twist and curvature is established. An analytical approach supports the numerical results.

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A bent chain of coupled Morse oscillators with long-range dispersive interaction is considered. Moving localized excitations may be trapped in the bending region. Thus chain geometry acts like an impurity. An energy funneling effect is observed in the case of random initial conditions.

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We investigate the charge transport in synthetic DNA polymers built up from single type of base pairs. In the context of a polaronlike model, for which an electronic tight-binding system and bond vibrations of the double helix are coupled, we present estimates for the electron-vibration coupling strengths utilizing a quantum-chemical procedure. Subsequent studies concerning the mobility of polaron solutions, representing the state of a localized charge in unison with its associated helix deformation, show that the system for poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers, respectively possess quantitatively distinct transport properties. While the former supports unidirectionally moving electron breathers attributed to highly efficient long-range conductivity, the breather mobility in the latter case is comparatively restrained, inhibiting charge transport. Our results are in agreement with recent experimental results demonstrating that poly(dG)-poly(dC) DNA molecules acts as a semiconducting nanowire and exhibit better conductance than poly(dA)-poly(dT) ones.

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Recent papers that have studied variants of the Peyrard-Bishop model for DNA, have taken into account the long range interaction due to the dipole moments of the hydrogen bonds between base pairs. In these models the helicity of the double strand is not considered. In this paper we have performed an analysis of the influence of the helicity on the properties of static and moving breathers in a Klein-Gordon chain with dipole-dipole interaction. It has been found that the helicity enlarges the range of existence and stability of static breathers, although this effect is small for a typical helical structure of DNA. However, the effect of the orientation of the dipole moments is considerably higher with transcendental consequences for the existence of mobile breathers.

RESUMEN

Most of the studies on mathematical models of DNA are limited to next neighbor interaction. However, the coupling between base pairs is thought to be caused by dipole interaction, and, when the DNA strand is bent, the distances between base pairs become shorter, therefore the interactions with distant base pairs have to be taken into account. In this paper we analyze the existence and stability of breathers, i.e., localized oscillations in a simple model of bent DNA with long-range dipole interaction. Breathers have been suggested as precursors of the denaturation bubble.