29,360 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
Computing spectral sequences
In this paper, a set of programs enhancing the Kenzo system is presented.
Kenzo is a Common Lisp program designed for computing in Algebraic Topology, in
particular it allows the user to calculate homology and homotopy groups of
complicated spaces. The new programs presented here entirely compute Serre and
Eilenberg-Moore spectral sequences, in particular the groups and differential
maps for arbitrary r. They also determine when the spectral sequence has
converged and describe the filtration of the target homology groups induced by
the spectral sequence
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
Renormalisation group determination of the order of the DNA denaturation transition
We report on the nature of the thermal denaturation transition of homogeneous
DNA as determined from a renormalisation group analysis of the
Peyrard-Bishop-Dauxois model. Our approach is based on an analogy with the
phenomenon of critical wetting that goes further than previous qualitative
comparisons, and shows that the transition is continuous for the average
base-pair separation. However, since the range of universal critical behaviour
appears to be very narrow, numerically observed denaturation transitions may
look first-order, as it has been reported in the literature.Comment: 6 pages; no figures; to appear in Europhysics Letter
Memory effect in triglycine sulfate induced by a transverse electric field: specific heat measurement
The influence of a transverse electric field in the specific heat of
triglycine sulphate (TGS) has been studied. The specific heat of TGS has been
measured heating the sample from ferroelectric to paraelectric phase after
prolonged transverse electric field (i.e. perpendicular to the ferroelectric
axis). It is shown that the specific heat of TGS can remember the temperature
at which the transverse field was previously applied.Comment: ReVTeX4 Twocolumn 4 pages, 4 figure
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