755 research outputs found
Adsorption of a semiflexible polymer onto interfaces and surfaces
We consider the adsorption of a semiflexible polymer chain onto interfaces
and surfaces by using the differential equation of the distribution function
of the end-to-end distance , which is associated with the moment
expansion of the latter. We present the results of the approximative treatment
consisting of taking into account the 2nd and 4th moments in the differential
equation for . The essential features of adsorption of the semiflexible
polymer are: {\it i}) the existence of a new local length scale, which results
in two-exponential decay of the monomer density of adsorbed polymer; {\it ii})
the binding of the semiflexible polymer is weaker than that for flexible one
for both interface and wall. The approximative theory presented is restricted
to the regime of weak adsorption, where the effect of the rodlike behavior of
the polymer on small scales is weak.Comment: 9 pages, 2 figure
Sequence-Dependent Effects on the Properties of Semiflexible Biopolymers
Using path integral technique, we show exactly that for a semiflexible
biopolymer in constant extension ensemble, no matter how long the polymer and
how large the external force, the effects of short range correlations in the
sequence-dependent spontaneous curvatures and torsions can be incorporated into
a model with well-defined mean spontaneous curvature and torsion as well as a
renormalized persistence length. Moreover, for a long biopolymer with large
mean persistence length, the sequence-dependent persistence lengths can be
replaced by their mean. However, for a short biopolymer or for a biopolymer
with small persistence lengths, inhomogeneity in persistence lengths tends to
make physical observables very sensitive to details and therefore less
predictable
Three Bead Rotating Chain model shows universality in the stretching of proteins
We introduce a model of proteins in which all of the key atoms in the protein
backbone are accounted for, thus extending the Freely Rotating Chain model. We
use average bond lengths and average angles from the Protein Databank as input
parameters, leaving the number of residues as a single variable. The model is
used to study the stretching of proteins in the entropic regime. The results of
our Monte Carlo simulations are found to agree well with experimental data,
suggesting that the force extension plot is universal and does not depend on
the side chains or primary structure of proteins
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
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
Protein-Mediated DNA Loops: Effects of Protein Bridge Size and Kinks
This paper focuses on the probability that a portion of DNA closes on itself
through thermal fluctuations. We investigate the dependence of this probability
upon the size r of a protein bridge and/or the presence of a kink at half DNA
length. The DNA is modeled by the Worm-Like Chain model, and the probability of
loop formation is calculated in two ways: exact numerical evaluation of the
constrained path integral and the extension of the Shimada and Yamakawa saddle
point approximation. For example, we find that the looping free energy of a 100
base pairs DNA decreases from 24 kT to 13 kT when the loop is closed by a
protein of r = 10 nm length. It further decreases to 5 kT when the loop has a
kink of 120 degrees at half-length.Comment: corrected typos and figures, references updated; 13 pages, 7 figures,
accepted for publication in Phys. Rev.
Radial Distribution Function for Semiflexible Polymers Confined in Microchannels
An analytic expression is derived for the distribution of the
end-to-end distance of semiflexible polymers in external potentials
to elucidate the effect of confinement on the mechanical and statistical
properties of biomolecules. For parabolic confinement the result is exact
whereas for realistic potentials a self-consistent ansatz is developed, so that
is given explicitly even for hard wall confinement. The
theoretical result is in excellent quantitative agreement with fluorescence
microscopy data for actin filaments confined in rectangularly shaped
microchannels. This allows an unambiguous determination of persistence length
and the dependence of statistical properties such as Odijk's deflection
length on the channel width . It is shown that neglecting the
effect of confinement leads to a significant overestimation of bending
rigidities for filaments
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
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
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