1,668 research outputs found
Partly melted DNA conformations obtained with a probability peak finding method
Peaks in the probabilities of loops or bubbles, helical segments, and
unzipping ends in melting DNA are found in this article using a peak finding
method that maps the hierarchical structure of certain energy landscapes. The
peaks indicate the alternative conformations that coexist in equilibrium and
the range of their fluctuations. This yields a representation of the
conformational ensemble at a given temperature, which is illustrated in a
single diagram called a stitch profile. This article describes the methodology
and discusses stitch profiles vs. the ordinary probability profiles using the
phage lambda genome as an example.Comment: 11 pages, 9 figures; v3: major changes; v4: applications sectio
A simple model for DNA denaturation
Following Poland and Scheraga, we consider a simplified model for the
denaturation transition of DNA. The two strands are modeled as interacting
polymer chains. The attractive interactions, which mimic the pairing between
the four bases, are reduced to a single short range binding term. Furthermore,
base-pair misalignments are forbidden, implying that this binding term exists
only for corresponding (same curvilinear abscissae) monomers of the two chains.
We take into account the excluded volume repulsion between monomers of the two
chains, but neglect intra-chain repulsion. We find that the excluded volume
term generates an effective repulsive interaction between the chains, which
decays as . Due to this long-range repulsion between the chains, the
denaturation transition is first order in any dimension, in agreement with
previous studies.Comment: 10 page
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
Roles of stiffness and excluded volume in DNA denaturation
The nature and the universal properties of DNA thermal denaturation are
investigated by Monte Carlo simulations. For suitable lattice models we
determine the exponent c describing the decay of the probability distribution
of denaturated loops of length l, . If excluded volume effects
are fully taken into account, c= 2.10(4) is consistent with a first order
transition. The stiffness of the double stranded chain has the effect of
sharpening the transition, if it is continuous, but not of changing its order
and the value of the exponent c, which is also robust with respect to inclusion
of specific base-pair sequence heterogeneities.Comment: RevTeX 4 Pages and 4 PostScript figures included. Final version as
publishe
Propfan Test Assessment (PTA)
The objectives of the Propfan Test Assessment (PTA) Program were to validate in flight the structural integrity of large-scale propfan blades and to measure noise characteristics of the propfan in both near and far fields. All program objectives were met or exceeded, on schedule and under budget. A Gulfstream Aerospace Corporation GII aircraft was modified to provide a testbed for the 2.74m (9 ft) diameter Hamilton Standard SR-7 propfan which was driven by a 4475 kw (600 shp) turboshaft engine mounted on the left-hand wing of the aircraft. Flight research tests were performed for 20 combinations of speed and altitude within a flight envelope that extended to Mach numbers of 0.85 and altitudes of 12,192m (40,000 ft). Propfan blade stress, near-field noise on aircraft surfaces, and cabin noise were recorded. Primary variables were propfan power and tip speed, and the nacelle tilt angle. Extensive low altitude far-field noise tests were made to measure flyover and sideline noise and the lateral attenuation of noise. In coopertion with the FAA, tests were also made of flyover noise for the aircraft at 6100m (20,000 ft) and 10,668m (35,000 ft). A final series of tests were flown to evaluate an advanced cabin wall noise treatment that was produced under a separate program by NASA-Langley Research Center
Phase transition in a non-conserving driven diffusive system
An asymmetric exclusion process comprising positive particles, negative
particles and vacancies is introduced. The model is defined on a ring and the
dynamics does not conserve the number of particles. We solve the steady state
exactly and show that it can exhibit a continuous phase transition in which the
density of vacancies decreases to zero. The model has no absorbing state and
furnishes an example of a one-dimensional phase transition in a homogeneous
non-conserving system which does not belong to the absorbing state universality
classes
Finding the optimum activation energy in DNA breathing dynamics: A Simulated Annealing approach
We demonstrate how the stochastic global optimization scheme of Simulated
Annealing can be used to evaluate optimum parameters in the problem of DNA
breathing dynamics. The breathing dynamics is followed in accordance with the
stochastic Gillespie scheme with the denaturation zones in double stranded DNA
studied as a single molecule time series. Simulated Annealing is used to find
the optimum value of the activation energy for which the equilibrium bubble
size distribution matches with a given value. It is demonstrated that the
method overcomes even large noise in the input surrogate data.Comment: 9 pages, 4 figures, iop article package include
Statistical physics of the melting of inhomogeneous DNA
We studied how the inhomogeneity of a sequence affects the phase transition
that takes place at DNA melting. Unlike previous works, which considered
thermodynamic quantities averaged over many different inhomogeneous sequences,
we focused on precise sequences and investigated the succession of local
openings that lead to their dissociation. For this purpose, we performed
Transfer Integral type calculations with two different dynamical models, namely
the heterogeneous Dauxois-Peyrard-Bishop model and the model based on finite
stacking enthalpies we recently proposed. It appears that, for both models, the
essential effect of heterogeneity is to let different portions of the
investigated sequences open at slightly different temperatures. Besides this
macroscopic effect, the local aperture of each portion indeed turns out to be
very similar to that of a homogeneous sequence with the same length. Rounding
of each local opening transition is therefore merely a size effect. For the
Dauxois-Peyrard-Bishop model, sequences with a few thousands base pairs are
still far from the thermodynamic limit, so that it is inappropriate, for this
model, to discuss the order of the transition associated with each local
opening. In contrast, sequences with several hundreds to a few thousands base
pairs are pretty close to the thermodynamic limit for the model we proposed.
The temperature interval where power laws holds is consequently broad enough to
enable the estimation of critical exponents. On the basis of the few examples
we investigated, it seems that, for our model, disorder does not necessarily
induce a decrease of the order of the transition
Numerical study of the disordered Poland-Scheraga model of DNA denaturation
We numerically study the binary disordered Poland-Scheraga model of DNA
denaturation, in the regime where the pure model displays a first order
transition (loop exponent ). We use a Fixman-Freire scheme for the
entropy of loops and consider chain length up to , with
averages over samples. We present in parallel the results of various
observables for two boundary conditions, namely bound-bound (bb) and
bound-unbound (bu), because they present very different finite-size behaviors,
both in the pure case and in the disordered case. Our main conclusion is that
the transition remains first order in the disordered case: in the (bu) case,
the disorder averaged energy and contact densities present crossings for
different values of without rescaling. In addition, we obtain that these
disorder averaged observables do not satisfy finite size scaling, as a
consequence of strong sample to sample fluctuations of the pseudo-critical
temperature. For a given sample, we propose a procedure to identify its
pseudo-critical temperature, and show that this sample then obeys first order
transition finite size scaling behavior. Finally, we obtain that the disorder
averaged critical loop distribution is still governed by in
the regime , as in the pure case.Comment: 12 pages, 13 figures. Revised versio
Why is the DNA Denaturation Transition First Order?
We study a model for the denaturation transition of DNA in which the
molecules are considered as composed of a sequence of alternating bound
segments and denaturated loops. We take into account the excluded-volume
interactions between denaturated loops and the rest of the chain by exploiting
recent results on scaling properties of polymer networks of arbitrary topology.
The phase transition is found to be first order in d=2 dimensions and above, in
agreement with experiments and at variance with previous theoretical results,
in which only excluded-volume interactions within denaturated loops were taken
into account. Our results agree with recent numerical simulations.Comment: Revised version. To appear in Phys. Rev. Let
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