41 research outputs found

    Distribution of bubble lengths in DNA

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    Dependence on temperature and GC content of bubble length distributions in DNA

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    We present numerical results on the temperature dependence of the distribution of bubble lengths in DNA segments of various guanine-cytosine (GC) concentrations. Base-pair openings are described by the Peyrard-Bishop-Dauxois model and the corresponding thermal equilibrium distributions of bubbles are obtained through Monte Carlo calculations for bubble sizes up to the order of a hundred base pairs. The dependence of the parameters of bubble length distribution on temperature and the GC content is investigated. We provide simple expressions which approximately describe these relations. The variation of the average bubble length is also presented. We find a temperature dependence of the exponent c that appears in the distribution of bubble lengths. If an analogous dependence exists in the loop entropy exponent of real DNA, it may be relevant to understand overstretching in force-extension experiments.Comment: 8 pages, 6 figures. Published on The Journal of Chemical Physic

    Nonlocal interactions in doped cuprates: correlated motion of Zhang-Rice polarons

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    In-plane, inter-carrier correlations in hole doped cuprates are investigated by ab initio multiconfiguration calculations. The dressed carriers display features that are reminiscent of both Zhang-Rice (ZR) CuO4 singlet states and Jahn-Teller polarons. The interaction between these quasiparticles is repulsive. At doping levels that are high enough, the interplay between long-range unscreened Coulomb interactions and long-range phase coherence among the O-ion half-breathing vibrations on the ZR plaquettes may lead to a strong reduction of the effective adiabatic energy barrier associated to each polaronic state. Tunneling effects cannot be neglected for a relatively flat, multi-well energy landscape. We suggest that the coherent, superconducting quantum state is the result of such coherent quantum lattice fluctuations involving the in-plane O ions. Our findings appear to support models where the superconductivity is related to a lowering of the in-plane kinetic energy

    Bubble propagation in a helicoidal molecular chain

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    We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between complementary bases are disrupted, allowing access to the genetic code. We propose these kind of excitations in alternative to kinks and breathers. The model has been introduced by Barbi et al. [Phys. Lett. A 253, 358 (1999)], and up to now it has been used to study on the one hand low amplitude breather solutions, and on the other hand the DNA melting transition. We extend the model to include the case of heterogeneous chains, in order to get closer to a description of real DNA; in fact, the Morse potential representing the interaction between complementary bases has two possible depths, one for A-T and one for G-C base pairs. We first compute the equilibrium configurations of a chain with a degree of uncoiling, and we find that a static bubble is among them; then we show, by molecular dynamics simulations, that these bubbles, once generated, can move along the chain. We find that also in the most unfavourable case, that of a heterogeneous DNA in the presence of thermal noise, the excitation can travel for well more 1000 base pairs.Comment: 25 pages, 7 figures. Submitted to Phys. Rev.

    Calculation of excited polaron states in the Holstein model

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    An exact diagonalization technique is used to investigate the low-lying excited polaron states in the Holstein model for the infinite one-dimensional lattice. For moderate values of the adiabatic ratio, a new and comprehensive picture, involving three excited (coherent) polaron bands below the phonon threshold, is obtained. The coherent contribution of the excited states to both the single-electron spectral density and the optical conductivity is evaluated and, due to the invariance of the Hamiltonian under the space inversion, the two are shown to contain complementary information about the single-electron system at zero temperature. The chosen method reveals the connection between the excited bands and the renormalized local phonon excitations of the adiabatic theory, as well as the regime of parameters for which the electron self-energy has notable non-local contributions. Finally, it is shown that the hybridization of two polaron states allows a simple description of the ground and first excited state in the crossover regime.Comment: 12 pages, 9 figures, submitted to PR

    Tight-binding parameters for charge transfer along DNA

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    We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The π\pi molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination of atomic orbitals method with a recently introduced parametrization. The HOMO and LUMO wavefunctions and energies of DNA bases are discussed and then used for calculating the corresponding wavefunctions of the two B-DNA base-pairs (adenine-thymine and guanine-cytosine). The obtained HOMO and LUMO energies of the bases are in good agreement with available experimental values. Our results are then used for estimating the complete set of charge transfer parameters between neighboring bases and also between successive base-pairs, considering all possible combinations between them, for both electrons and holes. The calculated microscopic quantities can be used in mesoscopic theoretical models of electron or hole transfer along the DNA double helix, as they provide the necessary parameters for a tight-binding phenomenological description based on the π\pi molecular overlap. We find that usually the hopping parameters for holes are higher in magnitude compared to the ones for electrons, which probably indicates that hole transport along DNA is more favorable than electron transport. Our findings are also compared with existing calculations from first principles.Comment: 15 pages, 3 figures, 7 table

    Solitons in Triangular and Honeycomb Dynamical Lattices with the Cubic Nonlinearity

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    We study the existence and stability of localized states in the discrete nonlinear Schr{\"o}dinger equation (DNLS) on two-dimensional non-square lattices. The model includes both the nearest-neighbor and long-range interactions. For the fundamental strongly localized soliton, the results depend on the coordination number, i.e., on the particular type of the lattice. The long-range interactions additionally destabilize the discrete soliton, or make it more stable, if the sign of the interaction is, respectively, the same as or opposite to the sign of the short-range interaction. We also explore more complicated solutions, such as twisted localized modes (TLM's) and solutions carrying multiple topological charge (vortices) that are specific to the triangular and honeycomb lattices. In the cases when such vortices are unstable, direct simulations demonstrate that they turn into zero-vorticity fundamental solitons.Comment: 17 pages, 13 figures, Phys. Rev.

    Variational study of the Holstein polaron

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    The paper deals with the ground and the first excited state of the polaron in the one dimensional Holstein model. Various variational methods are used to investigate both the weak coupling and strong coupling case, as well as the crossover regime between them. Two of the methods, which are presented here for the first time, introduce interesting elements to the understanding of the nature of the polaron. Reliable numerical evidence is found that, in the strong coupling regime, the ground and the first excited state of the self-trapped polaron are well described within the adiabatic limit. The lattice vibration modes associated with the self-trapped polarons are analyzed in detail, and the frequency softening of the vibration mode at the central site of the small polaron is estimated. It is shown that the first excited state of the system in the strong coupling regime corresponds to the excitation of the soft phonon mode within the polaron. In the crossover regime, the ground and the first excited state of the system can be approximated by the anticrossing of the self-trapped and the delocalized polaron state. In this way, the connection between the behavior of the ground and the first excited state is qualitatively explained.Comment: 11 pages, 4 figures, PRB 65, 14430

    Insulator-Superfluid transition of spin-1 bosons in an optical lattice in magnetic field

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    We study the insulator-superfluid transition of spin-1 bosons in an optical lattice in a uniform magnetic field. Based on a mean-field approximation we obtained a zero-temperature phase diagram. We found that depending on the particle number the transition for bosons with antiferromagnetic interaction may occur into different superfluid phases with spins aligned along or opposite to the field direction. This is qualitatively different from the field-free transition for which the mean-field theory predicts a unique (polar) superfluid state for any particle number.Comment: 10 pages, 2 eps figure

    Mass Renormalization in the Su-Schrieffer-Heeger Model

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    This study of the one dimensional Su-Schrieffer-Heeger model in a weak coupling perturbative regime points out the effective mass behavior as a function of the adiabatic parameter ωπ/J\omega_{\pi}/J, ωπ\omega_{\pi} is the zone boundary phonon energy and JJ is the electron band hopping integral. Computation of low order diagrams shows that two phonons scattering processes become appreciable in the intermediate regime in which zone boundary phonons energetically compete with band electrons. Consistently, in the intermediate (and also moderately antiadiabatic) range the relevant mass renormalization signals the onset of a polaronic crossover whereas the electrons are essentially undressed in the fully adiabatic and antiadiabatic systems. The effective mass is roughly twice as much the bare band value in the intermediate regime while an abrupt increase (mainly related to the peculiar 1D dispersion relations) is obtained at ωπ2J\omega_{\pi}\sim \sqrt{2}J.Comment: To be published in Phys.Rev.B - 3 figure
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