746 research outputs found
DNA loop statistics and torsional modulus
The modelling of DNA mechanics under external constraints is discussed. Two
analytical models are widely known, but disagree for instance on the value of
the torsional modulus. The origin of this embarassing situation is located in
the concept of writhe. This letter presents a unified model for DNA
establishing a relation between the different approaches. I show that the
writhe created by the loops of DNA is at the origin of the discrepancy. To take
this into account, I propose a new treatment of loop statistics based on
numerical simulations using the most general formula for the writhe, and on
analytic calculations with only one fit parameter. One can then compute the
value of the torsional modulus of DNA without the need of any cut-off.Comment: 8 pages, 1 figure. Accepted by Europhysics Letter
Localization of Denaturation Bubbles in Random DNA Sequences
We study the thermodynamic and dynamic behaviors of twist-induced
denaturation bubbles in a long, stretched random sequence of DNA. The small
bubbles associated with weak twist are delocalized. Above a threshold torque,
the bubbles of several tens of bases or larger become preferentially localized
to \AT-rich segments. In the localized regime, the bubbles exhibit ``aging''
and move around sub-diffusively with continuously varying dynamic exponents.
These properties are derived using results of large-deviation theory together
with scaling arguments, and are verified by Monte-Carlo simulations.Comment: TeX file with postscript figure
Statistical Mechanics of Torque Induced Denaturation of DNA
A unifying theory of the denaturation transition of DNA, driven by
temperature T or induced by an external mechanical torque Gamma is presented.
Our model couples the hydrogen-bond opening and the untwisting of the
helicoidal molecular structure. We show that denaturation corresponds to a
first-order phase transition from B-DNA to d-DNA phases and that the
coexistence region is naturally parametrized by the degree of supercoiling
sigma. The denaturation free energy, the temperature dependence of the twist
angle, the phase diagram in the T,Gamma plane and isotherms in the sigma, Gamma
plane are calculated and show a good agreement with experimental data.Comment: 5 pages, 3 figures, model improve
Layering transitions for adsorbing polymers in poor solvents
An infinite hierarchy of layering transitions exists for model polymers in
solution under poor solvent or low temperatures and near an attractive surface.
A flat histogram stochastic growth algorithm known as FlatPERM has been used on
a self- and surface interacting self-avoiding walk model for lengths up to 256.
The associated phases exist as stable equilibria for large though not infinite
length polymers and break the conjectured Surface Attached Globule phase into a
series of phases where a polymer exists in specified layer close to a surface.
We provide a scaling theory for these phases and the first-order transitions
between them.Comment: 4 pages, 4 figure
Periodically driven stochastic un- and refolding transitions of biopolymers
Mechanical single molecule experiments probe the energy profile of
biomolecules. We show that in the case of a profile with two minima (like
folded/unfolded) periodic driving leads to a stochastic resonance-like
phenomenon. We demonstrate that the analysis of such data can be used to
extract four basic parameters of such a transition and discuss the statistical
requirements of the data acquisition. As advantages of the proposed scheme, a
polymeric linker is explicitly included and thermal fluctuations within each
well need not to be resolved.Comment: 7 pages, 5 figures, submitted to EP
Comment on "Elasticity Model of a Supercoiled DNA Molecule"
We perform simulations to numerically study the writhe distribution of a
stiff polymer. We compare with analytic results of Bouchiat and Mezard (PRL 80
1556- (1998); cond-mat/9706050).Comment: 1 page, 1 figure revtex
Stretching Instability of Helical Spring
We show that when a gradually increasing tensile force is applied to the ends
of a helical spring with sufficiently large ratios of radius to pitch and twist
to bending rigidity, the end-to-end distance undergoes a sequence of
discontinuous stretching transitions. Subsequent decrease of the force leads to
step-like contraction and hysteresis is observed. For finite helices, the
number of these transitions increases with the number of helical turns but only
one stretching and one contraction instability survive in the limit of an
infinite helix. We calculate the critical line that separates the region of
parameters in which the deformation is continuous from that in which stretching
instabilities occur, and propose experimental tests of our predictions.Comment: 5 pages, 4 figure
Real-time detection of cruciform extrusion by single-molecule DNA nanomanipulation
During cruciform extrusion, a DNA inverted repeat unwinds and forms a four-way junction in which two of the branches consist of hairpin structures obtained by self-pairing of the inverted repeats. Here, we use single-molecule DNA nanomanipulation to monitor in real-time cruciform extrusion and rewinding. This allows us to determine the size of the cruciform to nearly base pair accuracy and its kinetics with second-scale time resolution. We present data obtained with two different inverted repeats, one perfect and one imperfect, and extend single-molecule force spectroscopy to measure the torque dependence of cruciform extrusion and rewinding kinetics. Using mutational analysis and a simple two-state model, we find that in the transition state intermediate only the B-DNA located between the inverted repeats (and corresponding to the unpaired apical loop) is unwound, implying that initial stabilization of the four-way (or Holliday) junction is rate-limiting. We thus find that cruciform extrusion is kinetically regulated by features of the hairpin loop, while rewinding is kinetically regulated by features of the stem. These results provide mechanistic insight into cruciform extrusion and help understand the structural features that determine the relative stability of the cruciform and B-form states
Entropic Elasticity of Double-Strand DNA Subject to Simple Spatial Constraints
The aim of the present paper is the study of the entropic elasticity of the
dsDNA molecule, having a cristallographic length L of the order of 10 to 30
persistence lengths A, when it is subject to spatial obstructions. We have not
tried to obtain the single molecule partition function by solving a
Schodringer-like equation. We prefer to stay within a discretized version of
the WLC model with an added one-monomer potential, simulating the spatial
constraints. We derived directly from the discretized Boltzmann formula the
transfer matrix connecting the partition functions relative to adjacent
"effective monomers". We have plugged adequate Dirac delta-functions in the
functional integral to ensure that the monomer coordinate and the tangent
vector are independent variables. The partition function is, then, given by an
iterative process which is both numerically efficient and physically
transparent. As a test of our discretized approach, we have studied two
configurations involving a dsDNA molecule confined between a pair of parallel
plates.Comment: The most formal developments of Section I have been moved into an
appendix and replaced by a direct derivation of the transfer matrix used in
the applications. of Section II. Two paragraphs and two figures have been
added to clarify the physical interpretation of the result
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