780 research outputs found
Unfolding and unzipping of single-stranded DNA by stretching
We present a theoretical study of single-stranded DNA under stretching.
Within the proposed framework, the effects of basepairing on the mechanical
response of the molecule can be studied in combination with an arbitrary
underlying model of chain elasticity. In a generic case, we show that the
stretching curve of ssDNA exhibits two distinct features: the second-order
"unfolding" phase transition, and a sharp crossover, reminiscent of the
first-order "unzipping" transition in dsDNA. We apply the theory to the
particular cases of Worm-like Chain (WLC) and Freely-Joint Chain (FJC) models,
and discuss the universal and model--dependent features of the mechanical
response of ssDNA. In particular, we show that variation of the width of the
unzipping crossover with interaction strength is very sensitive to the
energetics of hairpin loops. This opens a new way of testing the elastic
properties of ssDNA.Comment: 7 pages, 4 figures, substantially revised versio
Global cross-over dynamics of single semiflexible polymers
We present a mean-field dynamical theory for single semiflexible polymers
which can precisely capture, without fitting parameters, recent fluorescence
correlation spectroscopy results on single monomer kinetics of DNA strands in
solution. Our approach works globally, covering three decades of strand length
and five decades of time: it includes the complex cross-overs occurring between
stiffness-dominated and flexible bending modes, along with larger-scale
rotational and center-of-mass motion. The accuracy of the theory stems in part
from long-range hydrodynamic coupling between the monomers, which makes a
mean-field description more realistic. Its validity extends even to short,
stiff fragments, where we also test the theory through Brownian hydrodynamics
simulations.Comment: 6 pages, 5 figures; updated with minor changes to reflect published
versio
Microtubule dynamics depart from wormlike chain model
Thermal shape fluctuations of grafted microtubules were studied using high
resolution particle tracking of attached fluorescent beads. First mode
relaxation times were extracted from the mean square displacement in the
transverse coordinate. For microtubules shorter than 10 um, the relaxation
times were found to follow an L^2 dependence instead of L^4 as expected from
the standard wormlike chain model. This length dependence is shown to result
from a complex length dependence of the bending stiffness which can be
understood as a result of the molecular architecture of microtubules. For
microtubules shorter than 5 um, high drag coefficients indicate contributions
from internal friction to the fluctuation dynamics.Comment: 4 pages, 4 figures. Updated content, added reference, corrected typo
Disordered, stretched, and semiflexible biopolymers in two dimensions
We study the effects of intrinsic sequence-dependent curvature for a two
dimensional semiflexible biopolymer with short-range correlation in intrinsic
curvatures. We show exactly that when not subjected to any external force, such
a system is equivalent to a system with a well-defined intrinsic curvature and
a proper renormalized persistence length. We find the exact expression for the
distribution function of the equivalent system. However, we show that such an
equivalent system does not always exist for the polymer subjected to an
external force. We find that under an external force, the effect of
sequence-disorder depends upon the averaging order, the degree of disorder, and
the experimental conditions, such as the boundary conditions. Furthermore, a
short to moderate length biopolymer may be much softer or has a smaller
apparent persistent length than what would be expected from the "equivalent
system". Moreover, under a strong stretching force and for a long biopolymer,
the sequence-disorder is immaterial for elasticity. Finally, the effect of
sequence-disorder may depend upon the quantity considered
Semiflexible polymers: Dependence on ensemble and boundary orientations
We show that the mechanical properties of a worm-like-chain (WLC) polymer, of
contour length and persistence length \l such that t=L/\l\sim{\cal
O}(1), depend both on the ensemble and the constraint on end-orientations. In
the Helmholtz ensemble, multiple minima in free energy near persists for
all kinds of orientational boundary conditions. The qualitative features of
projected probability distribution of end to end vector depend crucially on the
embedding dimensions. A mapping of the WLC model, to a quantum particle moving
on the surface of an unit sphere, is used to obtain the statistical and
mechanical properties of the polymer under various boundary conditions and
ensembles. The results show excellent agreement with Monte-Carlo simulations.Comment: 15 pages, 15 figures; version accepted for publication in Phys. Rev.
E; one new figure and discussions adde
Getting DNA twist rigidity from single molecule experiments
We use an elastic rod model with contact to study the extension versus
rotation diagrams of single supercoiled DNA molecules. We reproduce
quantitatively the supercoiling response of overtwisted DNA and, using
experimental data, we get an estimation of the effective supercoiling radius
and of the twist rigidity of B-DNA. We find that unlike the bending rigidity,
the twist rigidity of DNA seems to vary widely with the nature and
concentration of the salt buffer in which it is immerged
Thermally induced gluten modification observed with rheology and spectroscopies
The protein vital gluten is mainly used for food while interest for non-food applications, like biodegradable materials, increases. In general, the structure and functionality of proteins is highly dependent on thermal treatments during production or modification. This study presents conformational changes and corresponding rheological effects of vital wheat gluten depending on temperature. Dry samples analyzed by X-ray photoelectron spectroscopy (XPS), Fourier-transform infrared spectroscopy (FTIR) and thermalgravimetric analysis coupled with mass spectrometry (TGA-MS) show surface compositions and conformational changes from 25 to 250 °C. Above 170 °C, XPS reveals a decreased N content at the surface while FTIR band characteristics for β-sheets prove structural changes. At 250 °C, protein denaturation accompanied by a significant mass loss due to dehydration and decarbonylation reactions is observed. Oscillatory measurements of optimally hydrated vital gluten describing network properties of the material show two structural changes along a temperature ramp from 25 to 90 °C: at 56–64 °C, the temperature necessary to trigger structural changes increases with the ratio of gliadin to total protein mass, determined by reversed-phase high performance liquid chromatography (RP-HPLC). At a temperature of 79–81 °C, complete protein denaturation occurs. FTIR confirms the denaturation process by showing band shifts with both temperature steps
Influence of the structural modulations and the Chain-ladder interaction in the compounds
We studied the effects of the incommensurate structural modulations on the
ladder subsystem of the family of compounds
using ab-initio explicitly-correlated calculations. From these calculations we
derived model as a function of the fourth crystallographic coordinate
describing the incommensurate modulations. It was found that in the
highly calcium-doped system, the on-site orbital energies are strongly
modulated along the ladder legs. On the contrary the two sites of the ladder
rungs are iso-energetic and the holes are thus expected to be delocalized on
the rungs. Chain-ladder interactions were also evaluated and found to be very
negligible. The ladder superconductivity model for these systems is discussed
in the light of the present results.Comment: 8 octobre 200
Statistical mechanics of double-stranded semi-flexible polymers
We study the statistical mechanics of double-stranded semi-flexible polymers
using both analytical techniques and simulation. We find a transition at some
finite temperature, from a type of short range order to a fundamentally
different sort of short range order. In the high temperature regime, the
2-point correlation functions of the object are identical to worm-like chains,
while in the low temperature regime they are different due to a twist
structure. In the low temperature phase, the polymers develop a kink-rod
structure which could clarify some recent puzzling experiments on actin.Comment: 4 pages, 3 figures; final version for publication - slight
modifications to text and figure
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