109 research outputs found
Interaction of moving breathers with an impurity
We analyze the influence of an impurity in the evolution of moving discrete
breathers in a Klein--Gordon chain with non-weak nonlinearity. Three different
behaviours can be observed when moving breathers interact with the impurity:
they pass through the impurity continuing their direction of movement; they are
reflected by the impurity; they are trapped by the impurity, giving rise to
chaotic breathers. Resonance with a breather centred at the impurity site is
conjectured to be a necessary condition for the appearance of the trapping
phenomenon.Comment: 4 pages, 2 figures, Proceedings of the Third Conference, San Lorenzo
De El Escorial, Spain 17-21 June 200
Nonlinear charge transport mechanism in periodic and disordered DNA
We study a model for polaron-like charge transport mechanism along DNA
molecules with emphasis on the impact of parametrical and structural disorder.
Our model Hamiltonian takes into account the coupling of the charge carrier to
two different kind of modes representing fluctuating twist motions of the base
pairs and H-bond distortions within the double helix structure of
DNA. Localized stationary states are constructed with the help of a
nonlinear map approach for a periodic double helix and in the presence of
intrinsic static parametrical and/or structural disorder reflecting the impact
of ambient solvent coordinates. It is demonstrated that charge transport is
mediated by moving polarons respectively breather compounds carrying not only
the charge but causing also local temporal deformations of the helix structure
through the traveling torsion and bond breather components illustrating the
interplay of structure and function in biomolecules.Comment: 23 pages, 13 figure
Charge transport in a nonlinear, three--dimensional DNA model with disorder
We study the transport of charge due to polarons in a model of DNA which
takes in account its 3D structure and the coupling of the electron wave
function with the H--bond distortions and the twist motions of the base pairs.
Perturbations of the ground states lead to moving polarons which travel long
distances. The influence of parametric and structural disorder, due to the
impact of the ambient, is considered, showing that the moving polarons survive
to a certain degree of disorder. Comparison of the linear and tail analysis and
the numerical results makes possible to obtain further information on the
moving polaron properties.Comment: 9 pages, 2 figures. Proceedings of the conference on "Localization
and energy transfer in nonlinear systems", June 17-21, 2002, San Lorenzo de
El Escorial, Madrid, Spain. To be publishe
Modeling the thermal evolution of enzyme-created bubbles in DNA
The formation of bubbles in nucleic acids (NAs) are fundamental in many
biological processes such as DNA replication, recombination, telomeres
formation, nucleotide excision repair, as well as RNA transcription and
splicing. These precesses 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,
being 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 in contact with a heat bath
using the Nos-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 nonzero temperature the H-bond breathers move coherently along
the double chain whereas at T=0 standing radial and torsional breathers result.Comment: 19 pages, 7 figure
Charge transport in poly(dG)-poly(dC) and poly(dA)-poly(dT) DNA polymers
We investigate the charge transport in synthetic DNA polymers built up from
single types of base pairs. In the context of a polaron-like 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 exhibits better conductance
than poly(dA)-poly(dT) ones.Comment: 11 pages, 5 figure
Breathers in FPU systems, near and far from the phonon band
There exists a recent mathematical proof on the existence of small amplitude
breathers in FPU systems near the phonon band, which includes a prediction of
their amplitude and width. In this work we obtain numerically these breathers,
and calculate the range of validity of the predictions, which extends
relatively far from the phonon band. There exist also large amplitude breathers
with the same frequency, with the consequence that there is an energy gap for
breather creation in these systems.Comment: 3 pages, 2 figures, proceeding of the conference on Localization and
to and Energy Transfer in Nonlinear Systems, June 17-21, 2002, San Lorenzo de
El Escorial, Madrid, Spain. To be published by World Scientifi
Bright and dark breathers in Fermi-Pasta-Ulam lattices
In this paper we study the existence and linear stability of bright and dark
breathers in one-dimensional FPU lattices. On the one hand, we test the range
of validity of a recent breathers existence proof [G. James, {\em C. R. Acad.
Sci. Paris}, 332, Ser. 1, pp. 581 (2001)] using numerical computations.
Approximate analytical expressions for small amplitude bright and dark
breathers are found to fit very well exact numerical solutions even far from
the top of the phonon band. On the other hand, we study numerically large
amplitude breathers non predicted in the above cited reference. In particular,
for a class of asymmetric FPU potentials we find an energy threshold for the
existence of exact discrete breathers, which is a relatively unexplored
phenomenon in one-dimensional lattices. Bright and dark breathers superposed on
a uniformly stressed static configuration are also investigated.Comment: 11 pages, 16 figure
Influence of moving breathers on vacancies migration
A vacancy defect is described by a Frenkel--Kontorova model with a
discommensuration. This vacancy can migrate when interacts with a moving
breather. We establish that the width of the interaction potential must be
larger than a threshold value in order that the vacancy can move forward. This
value is related to the existence of a breather centred at the particles
adjacent to the vacancy.Comment: 11 pages, 10 figure
Discrete breathers for understanding reconstructive mineral processes at low temperatures
Reconstructive transformations in layered silicates need a high tem- perature
in order to be observed. However, very recently, some systems have been found
where transformation can be studied at temperatures 600 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 shows that although there are far less
breathers than phonons, there are much more above the activation energy, being
therefore a good candidate to explain the reconstructive transformations at low
temperature.Comment: 27 pages, 11 figure
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