286 research outputs found
Experimental and theoretical studies of sequence effects on the fluctuation and melting of short DNA molecules
Understanding the melting of short DNA sequences probes DNA at the scale of
the genetic code and raises questions which are very different from those posed
by very long sequences, which have been extensively studied. We investigate
this problem by combining experiments and theory. A new experimental method
allows us to make a mapping of the opening of the guanines along the sequence
as a function of temperature. The results indicate that non-local effects may
be important in DNA because an AT-rich region is able to influence the opening
of a base pair which is about 10 base pairs away. An earlier mesoscopic model
of DNA is modified to correctly describe the time scales associated to the
opening of individual base pairs well below melting, and to properly take into
account the sequence. Using this model to analyze some characteristic sequences
for which detailed experimental data on the melting is available [Montrichok et
al. 2003 Europhys. Lett. {\bf 62} 452], we show that we have to introduce
non-local effects of AT-rich regions to get acceptable results. This brings a
second indication that the influence of these highly fluctuating regions of DNA
on their neighborhood can extend to some distance.Comment: To be published in J. Phys. Condensed Matte
Dynamics of a bubble formed in double stranded DNA
We study the fluctuational dynamics of a tagged base-pair in double stranded
DNA. We calculate the drift force which acts on the tagged base-pair using a
potential model that describes interactions at base pairs level and use it to
construct a Fokker-Planck equation.The calculated displacement autocorrelation
function is found to be in very good agreement with the experimental result of
Altan-Bonnet {\it et. al.} Phys. Rev. Lett. {\bf 90}, 138101 (2003) over the
entire time range of measurement. We calculate the most probable displacements
which predominately contribute to the autocorrelation function and the
half-time history of these displacements.Comment: 11 pages, 4 figures. submitted to Phys. Rev. Let
Bubbles and denaturation in DNA
The local opening of DNA is an intriguing phenomenon from a statistical
physics point of view, but is also essential for its biological function. For
instance, the transcription and replication of our genetic code can not take
place without the unwinding of the DNA double helix. Although these biological
processes are driven by proteins, there might well be a relation between these
biological openings and the spontaneous bubble formation due to thermal
fluctuations. Mesoscopic models, like the Peyrard-Bishop-Dauxois model, have
fairly accurately reproduced some experimental denaturation curves and the
sharp phase transition in the thermodynamic limit. It is, hence, tempting to
see whether these models could be used to predict the biological activity of
DNA. In a previous study, we introduced a method that allows to obtain very
accurate results on this subject, which showed that some previous claims in
this direction, based on molecular dynamics studies, were premature. This could
either imply that the present PBD should be improved or that biological
activity can only be predicted in a more complex frame work that involves
interactions with proteins and super helical stresses. In this article, we give
detailed description of the statistical method introduced before. Moreover, for
several DNA sequences, we give a thorough analysis of the bubble-statistics as
function of position and bubble size and the so-called -denaturation curves
that can be measured experimentally. These show that some important
experimental observations are missing in the present model. We discuss how the
present model could be improved.Comment: 15 pages, 5 figures, published as Eur. Phys. J. E 20 : 421-434 AUG
200
Mode-locking of incommensurate phase by quantum zero point energy in the Frenkel-Kontorova model
In this paper, it is shown that a configuration modulated system described by
the Frenkel-Kontorova model can be locked at an incommensurate phase when the
quantum zero point energy is taken into account. It is also found that the
specific heat for an incommensurate phase shows different parameter-dependence
in sliding phase and pinning phase. These findings provide a possible way for
experimentalists to verify the phase transition by breaking of analyticity.Comment: 6 pages in Europhys style, 3 eps figure
Lengthscales and Cooperativity in DNA Bubble Formation
It appears that thermally activated DNA bubbles of different sizes play
central roles in important genetic processes. Here we show that the probability
for the formation of such bubbles is regulated by the number of soft AT pairs
in specific regions with lengths which at physiological temperatures are of the
order of (but not equal to) the size of the bubble. The analysis is based on
the Peyrard- Bishop-Dauxois model, whose equilibrium statistical properties
have been accurately calculated here with a transfer integral approach
Effect of defects on thermal denaturation of DNA Oligomers
The effect of defects on the melting profile of short heterogeneous DNA
chains are calculated using the Peyrard-Bishop Hamiltonian. The on-site
potential on a defect site is represented by a potential which has only the
short-range repulsion and the flat part without well of the Morse potential.
The stacking energy between the two neigbouring pairs involving a defect site
is also modified. The results are found to be in good agreement with the
experiments.Comment: 11 pages including 5 postscript figure; To be appear in Phys. Rev.
Controlling the energy flow in nonlinear lattices: a model for a thermal rectifier
We address the problem of heat conduction in 1-D nonlinear chains; we show
that, acting on the parameter which controls the strength of the on site
potential inside a segment of the chain, we induce a transition from conducting
to insulating behavior in the whole system. Quite remarkably, the same
transition can be observed by increasing the temperatures of the thermal baths
at both ends of the chain by the same amount. The control of heat conduction by
nonlinearity opens the possibility to propose new devices such as a thermal
rectifier.Comment: 4 pages with figures included. Phys. Rev. Lett., to be published
(Ref. [10] corrected
Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation
The paper uses mesoscopic, non-linear lattice dynamics based
(Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA
below and near the denaturation temperature. Computationally efficient notation
is introduced for the relevant statistical mechanics. Computed melting profiles
of long and short heterogeneous sequences are presented, using a recently
introduced reparametrization of the PBD model, and critically discussed. The
statistics of extended open bubbles and bound clusters is formulated and
results are presented for selected examples.Comment: to appear in a special issue of the Journal of Nonlinear Mathematical
Physics (ed. G. Gaeta
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