41 research outputs found
Dependence on temperature and GC content of bubble length distributions in DNA
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
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
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
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
We systematically examine all the tight-binding parameters pertinent to
charge transfer along DNA. The 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 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
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
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
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
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 , is the
zone boundary phonon energy and 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 .Comment: To be published in Phys.Rev.B - 3 figure