51 research outputs found
Coupling of actin hydrolysis and polymerization: Reduced description with two nucleotide states
The polymerization of actin filaments is coupled to the hydrolysis of
adenosine triphosphate (ATP), which involves both the cleavage of ATP and the
release of inorganic phosphate. We describe hydrolysis by a reduced two-state
model with a cooperative cleavage mechanism, where the cleavage rate depends on
the state of the neighboring actin protomer in a filament. We obtain
theoretical predictions of experimentally accessible steady state quantities
such as the size of the ATP-actin cap, the size distribution of ATP-actin
islands, and the cleavage flux for cooperative cleavage mechanisms.Comment: 6 page
Dislocations and the critical endpoint of the melting line of vortex line lattices
We develop a theory for dislocation-mediated structural transitions in the
vortex lattice which allows for a unified description of phase transitions
between the three phases, the elastic vortex glass, the amorphous vortex glass,
and the vortex liquid, in terms of a free energy functional for the dislocation
density. The origin of a critical endpoint of the melting line at high magnetic
fields, which has been recently observed experimentally, is explained.Comment: 4 pages, 1 figur
Large time off-equilibrium dynamics of a manifold in a random potential
We study the out of equilibrium dynamics of an elastic manifold in a random
potential using mean-field theory. We find two asymptotic time regimes: (i)
stationary dynamics, (ii) slow aging dynamics with violation of equilibrium
theorems. We obtain an analytical solution valid for all large times with
universal scalings of two-time quantities with space. A non-analytic scaling
function crosses over to ultrametricity when the correlations become
long-range. We propose procedures to test numerically or experimentally the
extent to which this scenario holds for a given system.Comment: 12 page
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
A Bragg glass phase in the vortex lattice of a type II superconductor
Although crystals are usually quite stable, they are sensitive to a
disordered environment: even an infinitesimal amount of impurities can lead to
the destruction of the crystalline order. The resulting state of matter has
been a longstanding puzzle. Until recently it was believed to be an amorphous
state in which the crystal would break into crystallites. But a different
theory predicts the existence of a novel phase of matter: the so-called Bragg
glass, which is a glass and yet nearly as ordered as a perfect crystal. The
lattice of vortices that can contain magnetic flux in type II superconductors
provide a good system to investigate these ideas. Here we show that neutron
diffraction data of the vortex lattice in type II superconductors provides
unambiguous evidence for a weak, power-law decay of the crystalline order
characteristic of a Bragg glass. The theory also predicts accurately the
electrical transport properties of superconductors; it naturally explains the
observed phase transition and the dramatic jumps in the critical current
associated with the melting of the Bragg glass. Moreover the model explains
experiments as diverse as X-ray scattering in disordered liquid crystals and
conductivity of electronic crystals.Comment: 9 pages, 4 figure
Effects of point defects on the phase diagram of vortex states in high-Tc superconductors in B//c axis
The phase diagram for the vortex states of high- superconductors
with point defects in axis is drawn by large-scale Monte
Carlo simulations. The vortex slush (VS) phase is found between the vortex
glass (VG) and vortex liquid (VL) phases. The first-order transition between
this novel normal phase and the VL phase is characterized by a sharp jump of
the density of dislocations. The first-order transition between the Bragg glass
(BG) and VG or VS phases is also clarified. These two transitions are compared
with the melting transition between the BG and VL phases.Comment: 4 pages, 9 eps figures (included in text), uses revtex.sty, overall
changes with several additional data points, though conclusion is unchange
Effect of electron irradiation on vortex dynamics in YBa_2Cu_3O_{7-x} single crystals
We report on drastic change of vortex dynamics with increase of quenched
disorder: for rather weak disorder we found a single vortex creep regime, which
we attribute to a Bragg-glass phase, while for enhanced disorder we found an
increase of both the depinning current and activation energy with magnetic
field, which we attribute to entangled vortex phase. We also found that
introduction of additional defects always increases the depinning current, but
it increases activation energy only for elastic vortex creep, while it
decreases activation energy for plastic vortex creep.Comment: 4 pages, 3 figures, submited to Phys. Rev.
Disorder Driven Critical Behavior of Periodic Elastic Media in a Crystal Potential
We study a lattice model of a three-dimensional periodic elastic medium at
zero temperature with exact combinatorial optimization methods. A competition
between pinning of the elastic medium, representing magnetic flux lines in the
mixed phase of a superconductor or charge density waves in a crystal, by
randomly distributed impurities and a periodic lattice potential gives rise to
a continuous phase transition from a flat phase to a rough phase. We determine
the critical exponents of this roughening transition via finite size scaling
obtaining , , and find
that they are universal with respect to the periodicity of the lattice
potential. The small order parameter exponent is reminiscent of the random
field Ising critical behavior in 3.Comment: 4 pages, 3 eps-figures include
Instabilities and disorder-driven first-order transition of the vortex lattice
Transport studies in a Corbino disk geometry suggest that the Bragg glass
phase undergoes a first-order transition into a disordered solid. This
transition shows a sharp reentrant behavior at low fields. In contrast, in the
conventional strip configuration, the phase transition is obscured by the
injection of the disordered vortices through the sample edges, which results in
the commonly observed vortex instabilities and smearing of the peak effect in
NbSe2 crystals. These features are found to be absent in the Corbino geometry,
in which the circulating vortices do not cross the sample edges.Comment: 12 pages 3 figures. Accepted for publication in Physical Review
Letter
Mesoscopic models for DNA stretching under force: new results and comparison to experiments
Single molecule experiments on B-DNA stretching have revealed one or two
structural transitions, when increasing the external force. They are
characterized by a sudden increase of DNA contour length and a decrease of the
bending rigidity. It has been proposed that the first transition, at forces of
60--80 pN, is a transition from B to S-DNA, viewed as a stretched duplex DNA,
while the second one, at stronger forces, is a strand peeling resulting in
single stranded DNAs (ssDNA), similar to thermal denaturation. But due to
experimental conditions these two transitions can overlap, for instance for
poly(dA-dT). We derive analytical formula using a coupled discrete worm like
chain-Ising model. Our model takes into account bending rigidity, discreteness
of the chain, linear and non-linear (for ssDNA) bond stretching. In the limit
of zero force, this model simplifies into a coupled model already developed by
us for studying thermal DNA melting, establishing a connexion with previous
fitting parameter values for denaturation profiles. We find that: (i) ssDNA is
fitted, using an analytical formula, over a nanoNewton range with only three
free parameters, the contour length, the bending modulus and the monomer size;
(ii) a surprisingly good fit on this force range is possible only by choosing a
monomer size of 0.2 nm, almost 4 times smaller than the ssDNA nucleobase
length; (iii) mesoscopic models are not able to fit B to ssDNA (or S to ss)
transitions; (iv) an analytical formula for fitting B to S transitions is
derived in the strong force approximation and for long DNAs, which is in
excellent agreement with exact transfer matrix calculations; (v) this formula
fits perfectly well poly(dG-dC) and -DNA force-extension curves with
consistent parameter values; (vi) a coherent picture, where S to ssDNA
transitions are much more sensitive to base-pair sequence than the B to S one,
emerges.Comment: 14 pages, 9 figure
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