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Evidence for the Universal Scaling Behaviour of a Freely Relaxing DNA Molecule
Relaxation measurements on a fluorescently labelled free DNA molecule after stretching by a Poiseuille flow in a capillary vessel reveal universal scaling features: at intermediate times the scaling exponent of the decay law for the molecule length as a function of time is found to be 0.51 +/- 0.05. This law is in agreement with the prediction of the Brochard-Wyart "stem and flower" model for the relaxation of a stretched polymer chain.Molecular and Cellular BiologyPhysic
Discrete elastic model for stretching-induced flagellar polymorphs
Force-induced reversible transformations between coiled and normal polymorphs
of bacterial flagella have been observed in recent optical-tweezer experiment.
We introduce a discrete elastic rod model with two competing helical states
governed by a fluctuating spin-like variable that represents the underlying
conformational states of flagellin monomers. Using hybrid Brownian dynamics
Monte-Carlo simulations, we show that a helix undergoes shape transitions
dominated by domain wall nucleation and motion in response to externally
applied uniaxial tension. A scaling argument for the critical force is
presented in good agreement with experimental and simulation results.
Stretching rate-dependent elasticity including a buckling instability are
found, also consistent with the experiment
Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems
Biomolecules carry out very specialized tasks inside the cell where energies
involved are few tens of k_BT, small enough for thermal fluctuations to be
relevant in many biomolecular processes. In this paper I discuss a few concepts
and present some experimental results that show how the study of fluctuation
theorems applied to biomolecules contributes to our understanding of the
nonequilibrium thermal behavior of small systems.Comment: Proceedings of the 22nd Statphys Conference 2004 (Bangalore,India).
Invited contributio
Straightening of Thermal Fluctuations in Semi-Flexible Polymers by Applied Tension
We investigate the propagation of a suddenly applied tension along a
thermally excited semi-flexible polymer using analytical approximations,
scaling arguments and numerical simulation. This problem is inherently
non-linear. We find sub-diffusive propagation with a dynamical exponent of 1/4.
By generalizing the internal elasticity, we show that tense strings exhibit
qualitatively different tension profiles and propagation with an exponent of
1/2.Comment: Latex file; with three postscript figures; .ps available at
http://dept.physics.upenn.edu/~nelson/pull.p
Syntectonic mobility of supergene nickel ores of New Caledonia (Southwest Pacific). Evidence from faulted regolith and garnierite veins.
International audienceSupergene nickel deposits of New Caledonia that have been formed in the Neogene by weathering of obducted ultramafic rocks are tightly controlled by fracture development. The relationship of tropical weathering and tectonic structures, faults and tension gashes, have been investigated in order to determine whether fractures have play a passive role only, as previously thought; or alternatively, if brittle tectonics was acting together with alteration. From the observation of time-relationship, textures, and mineralogy of various fracture fills and fault gouges, it may be unambiguously established that active faulting has play a prominent role not only in facilitating drainage and providing room for synkinematic crystallisation of supergene nickel silicate, but also in mobilising already formed sparse nickel ore, giving birth to the very high grade ore nicknamed "green gold"
Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA
By resorting to the thick-chain model we discuss how the stretching response
of a polymer is influenced by the self-avoidance entailed by its finite
thickness. The characterization of the force versus extension curve for a thick
chain is carried out through extensive stochastic simulations. The
computational results are captured by an analytic expression that is used to
fit experimental stretching measurements carried out on DNA and single-stranded
RNA (poly-U) in various solutions. This strategy allows us to infer the
apparent diameter of two biologically-relevant polyelectrolytes, namely DNA and
poly-U, for different ionic strengths. Due to the very different degree of
flexibility of the two molecules, the results provide insight into how the
apparent diameter is influenced by the interplay between the
(solution-dependent) Debye screening length and the polymers' ``bare''
thickness. For DNA, the electrostatic contribution to the effective radius,
, is found to be about 5 times larger than the Debye screening length,
consistently with previous theoretical predictions for highly-charged stiff
rods. For the more flexible poly-U chains the electrostatic contribution to
is found to be significantly smaller than the Debye screening length.Comment: iopart, 14 pages, 13 figures, to appear in J. Phys.: Condens. Matte
Probing complex RNA structures by mechanical force
RNA secondary structures of increasing complexity are probed combining single
molecule stretching experiments and stochastic unfolding/refolding simulations.
We find that force-induced unfolding pathways cannot usually be interpretated
by solely invoking successive openings of native helices. Indeed, typical
force-extension responses of complex RNA molecules are largely shaped by
stretching-induced, long-lived intermediates including non-native helices. This
is first shown for a set of generic structural motifs found in larger RNA
structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA,
which exhibits a surprisingly well-structured and reproducible unfolding
pathway under mechanical stretching. Using out-of-equilibrium stochastic
simulations, we demonstrate that these experimental results reflect the slow
relaxation of RNA structural rearrangements. Hence, micromanipulations of
single RNA molecules probe both their native structures and long-lived
intermediates, so-called "kinetic traps", thereby capturing -at the single
molecular level- the hallmark of RNA folding/unfolding dynamics.Comment: 9 pages, 9 figure
Bending and Base-Stacking Interactions in Double-Stranded Semiflexible Polymer
Simple expressions for the bending and the base-stacking energy of
double-stranded semiflexible biopolymers (such as DNA and actin) are derived.
The distribution of the folding angle between the two strands is obtained by
solving a Schr\"{o}dinger equation variationally. Theoretical results based on
this model on the extension versus force and extension versus degree of
supercoiling relations of DNA chain are in good agreement with the experimental
observations of Cluzel {\it et al.} [Science {\bf 271}, 792 (1996)], Smith {\it
et al.} [{\it ibid.} {\bf 271}, 795 (1996)], and Strick {\it et al.} [{\it
ibid.} {\bf 271}, 1835 (1996)].Comment: 8 pages in Revtex format, with 4 EPS figure
Brane Bremsstrahlung in DBI Inflation
We consider the effect of trapped branes on the evolution of a test brane
whose motion generates DBI inflation along a warped throat. The coupling
between the inflationary brane and a trapped brane leads to the radiation of
non-thermal particles on the trapped brane. We calculate the Gaussian spectrum
of the radiated particles and their backreaction on the DBI motion of the
inflationary brane. Radiation occurs for momenta lower than the speed of the
test brane when crossing the trapped brane. The slowing down effect is either
due to a parametric resonance when the interaction time is small compared to
the Hubble time or a tachyonic resonance when the interaction time is large. In
both cases the motion of the inflationary brane after the interaction is
governed by a chameleonic potential,which tends to slow it down. We find that a
single trapped brane can hardly slow down a DBI inflaton whose fluctuations
lead to the Cosmic Microwave Background spectrum. A more drastic effect is
obtained when the DBI brane encounters a tightly spaced stack of trapped
branes.Comment: 20 pages, 1 figur
Statistical mechanics of triangulated ribbons
We use computer simulations and scaling arguments to investigate statistical
and structural properties of a semiflexible ribbon composed of isosceles
triangles. We study two different models, one where the bending energy is
calculated from the angles between the normal vectors of adjacent triangles,
the second where the edges are viewed as semiflexible polymers so that the
bending energy is related to the angles between the tangent vectors of
next-nearest neighbor triangles. The first model can be solved exactly whereas
the second is more involved. It was recently introduced by Liverpool and
Golestanian Phys.Rev.Lett. 80, 405 (1998), Phys.Rev.E 62, 5488 (2000) as a
model for double-stranded biopolymers such as DNA. Comparing observables such
as the autocorrelation functions of the tangent vectors and the bond-director
field, the probability distribution functions of the end-to-end distance, and
the mean squared twist we confirm the existence of local twist correlation, but
find no indications for other predicted features such as twist-stretch
coupling, kinks, or oscillations in the autocorrelation function of the
bond-director field.Comment: 10 pages, 13 figures. submitted to PRE, revised versio
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